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Gentoo's Bugzilla – Attachment 230449 Details for
Bug 318605
sci-chemistry/coot fails tests
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Build log
coot-0.6:20100505-073709.log (text/plain), 929.23 KB, created by
Diego Elio Pettenò (RETIRED)
on 2010-05-05 11:27:27 UTC
(
hide
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2010-05-05 11:27:27 UTC
Size:
929.23 KB
patch
obsolete
> * CPV: sci-chemistry/coot-0.6 > * REPO: gentoo > * USE: elibc_glibc kernel_linux test userland_GNU x86 >>>> Unpacking source... >>>> Unpacking coot-0.6.tar.gz to /var/tmp/portage/sci-chemistry/coot-0.6/work >>>> Unpacking greg-data-0.6.tar.gz to /var/tmp/portage/sci-chemistry/coot-0.6/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/coot-0.6/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6 ... > * Running eautoreconf in '/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' ... > * Running aclocal -I macros ... > [ ok ] > * Running libtoolize --copy --force --install --automake ... > [ ok ] > * Running aclocal -I macros ... > [ ok ] > * Running autoconf ... > [ ok ] > * Running automake --add-missing --copy ... > [ ok ] > * Running elibtoolize in: coot-0.6 > * Applying portage-2.2.patch ... > * Applying sed-1.5.6.patch ... > * Applying as-needed-2.2.6.patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6 ... > * econf: updating coot-0.6/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating coot-0.6/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --includedir=${prefix}/include/coot --with-gtkcanvas-prefix=/usr --with-clipper-prefix=/usr --with-mmdb-prefix=/usr --with-ssmlib-prefix=/usr --with-gtkgl-prefix=/usr --with-guile --with-python=/usr --with-guile-gtk --with-gtk2 --with-pygtk >configure: loading site script /usr/share/config.site >configure: loading site script /usr/share/crossdev/include/site/linux >checking for a BSD-compatible install... /usr/bin/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking for style of include used by make... GNU >checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc >checking whether the C compiler works... yes >checking for C compiler default output file name... a.out >checking for suffix of executables... >checking whether we are cross compiling... no >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether i686-pc-linux-gnu-gcc accepts -g... yes >checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking dependency style of i686-pc-linux-gnu-gcc... gcc3 >checking for library containing strerror... none required >checking for i686-pc-linux-gnu-gcc... (cached) i686-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... (cached) yes >checking whether i686-pc-linux-gnu-gcc accepts -g... (cached) yes >checking for i686-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed >checking dependency style of i686-pc-linux-gnu-gcc... (cached) gcc3 >checking for i686-pc-linux-gnu-gcc... (cached) i686-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... (cached) yes >checking whether i686-pc-linux-gnu-gcc accepts -g... (cached) yes >checking for i686-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed >checking dependency style of i686-pc-linux-gnu-gcc... (cached) gcc3 >checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for ANSI C header files... yes >checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++ >checking whether we are using the GNU C++ compiler... yes >checking whether i686-pc-linux-gnu-g++ accepts -g... yes >checking dependency style of i686-pc-linux-gnu-g++... gcc3 >checking build system type... i686-pc-linux-gnu >checking host system type... i686-pc-linux-gnu >checking for a sed that does not truncate output... /bin/sed >checking for fgrep... /bin/grep -F >checking for ld used by i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld >checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B >checking the name lister (/usr/bin/nm -B) interface... BSD nm >checking whether ln -s works... yes >checking the maximum length of command line arguments... 1572864 >checking whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... yes >checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r >checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar >checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip >checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib >checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for dlfcn.h... yes >checking whether we are using the GNU C++ compiler... (cached) yes >checking whether i686-pc-linux-gnu-g++ accepts -g... (cached) yes >checking dependency style of i686-pc-linux-gnu-g++... (cached) gcc3 >checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E >checking for objdir... .libs >checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if i686-pc-linux-gnu-gcc static flag -static works... yes >checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld >checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes >checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes >checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if i686-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if i686-pc-linux-gnu-g++ static flag -static works... yes >checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if i686-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking for i686-pc-linux-gnu-ranlib... (cached) i686-pc-linux-gnu-ranlib >checking sys/stdtypes.h usability... no >checking sys/stdtypes.h presence... no >checking for sys/stdtypes.h... no >checking if this is MINGW on Windows... no >checking for gsl-config... /usr/bin/gsl-config >checking for GSL - version >= 1.3... yes >checking for i686-pc-linux-gnu-pkg-config... no >checking for pkg-config... /usr/bin/pkg-config >checking pkg-config is at least version 0.9.0... yes >checking for GTK... yes >checking for GNOME_CANVAS... yes >checking for pkg-config... /usr/bin/pkg-config >checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) >checking for GLUT... yes >checking for MMDB... yes >checking for SSMLib... /usr >checking for Clipper... yes >Congratulations, you are using Guile >checking for guile... /usr/bin/guile >checking for guile-config... /usr/bin/guile-config >checking for guile-tools... /usr/bin/guile-tools >checking libguile compile flags... -pthread >checking libguile link flags... -pthread -lguile -lltdl -Wl,-O1 -lgmp -lcrypt -lm -lltdl >checking for net-hhtp... WARNING: (net http client): imported module (net http message) overrides core binding `version' >yes >checking for Guile-Lib... yes >checking for guile-gui... yes >checking GUILE_VERSION: 1.8 >checking for Python... checking Python.h usability... yes >checking Python.h presence... yes >checking for Python.h... yes >Cool, using Python >checking for PYGTK... yes >Good we have pygtk >checking for guile-gtk... >checking libglade... yes >Not using database >checking build type... error: cannot open Name index using db3 - No such file or directory (2) >error: cannot open Name index using db3 - No such file or directory (2) >error: cannot open Name index using db3 - No such file or directory (2) >Linux-AuthenticAMD---python-gtk2 >configure: creating ./config.status >config.status: creating Makefile >config.status: creating macros/Makefile >config.status: creating scheme/Makefile >config.status: creating python/Makefile >config.status: creating compat/Makefile >config.status: creating utils/Makefile >config.status: creating coot-utils/Makefile >config.status: creating ccp4mg-utils/Makefile >config.status: creating coords/Makefile >config.status: creating db-main/Makefile >config.status: creating density-contour/Makefile >config.status: creating surface/Makefile >config.status: creating coot-surface/Makefile >config.status: creating angles/Makefile >config.status: creating mini-mol/Makefile >config.status: creating skeleton/Makefile >config.status: creating ligand/Makefile >config.status: creating geometry/Makefile >config.status: creating ideal/Makefile >config.status: creating build/Makefile >config.status: creating analysis/Makefile >config.status: creating high-res/Makefile >config.status: creating tw/Makefile >config.status: creating cootaneer/Makefile >config.status: creating greg-tests/Makefile >config.status: creating python-tests/Makefile >config.status: creating doc/Makefile >config.status: creating src/Makefile >config.status: creating src/coot >config.status: creating python/coot_load_modules.py >config.status: creating data/Makefile >config.status: creating rama-data/Makefile >config.status: creating auxil/Makefile >config.status: creating auxil/catcheck/Makefile >config.status: creating auxil/rama/Makefile >config.status: creating auxil/sec-str/Makefile >config.status: creating auxil/strand-analysis/Makefile >config.status: creating auxil/vectors/Makefile >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6 ... >make -j14 >Making all in auxil >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >Making all in catcheck >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/catcheck' >make[2]: Nothing to be done for `all'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/catcheck' >Making all in rama >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/rama' >make[2]: Nothing to be done for `all'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/rama' >Making all in sec-str >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/sec-str' >make[2]: Nothing to be done for `all'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/sec-str' >Making all in strand-analysis >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/strand-analysis' >make[2]: Nothing to be done for `all'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/strand-analysis' >Making all in vectors >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/vectors' >make[2]: Nothing to be done for `all'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/vectors' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >make[2]: Nothing to be done for `all-am'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >Making all in scheme >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme' >make[1]: Nothing to be done for `all'. >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme' >Making all in python >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python' >make[1]: Nothing to be done for `all'. >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python' >Making all in macros >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/macros' >make[1]: Nothing to be done for `all'. >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/macros' >Making all in compat >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/compat' >/bin/sh ../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c >/bin/sh ../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c -o getopt1.lo getopt1.c >libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -fPIC -DPIC -o .libs/getopt.o >libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -fPIC -DPIC -o .libs/getopt1.o >libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o >/dev/null 2>&1 >mv -f .deps/getopt.Tpo .deps/getopt.Plo >mv -f .deps/getopt1.Tpo .deps/getopt1.Plo >/bin/sh ../libtool --tag=CC --mode=link i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -o libcoot-compat.la -rpath /usr/lib getopt.lo getopt1.lo >libtool: link: i686-pc-linux-gnu-gcc -shared .libs/getopt.o .libs/getopt1.o -Wl,-O1 -Wl,-soname -Wl,libcoot-compat.so.0 -o .libs/libcoot-compat.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-compat.so.0" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-compat.so" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-compat.a getopt.o getopt1.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-compat.a >libtool: link: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/compat' >Making all in utils >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c -o coot-utils.lo coot-utils.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c -o coot-fasta.lo coot-fasta.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c -o atomic-numbers.lo atomic-numbers.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c -o gdk-keysyms.lo gdk-keysyms.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -fPIC -DPIC -o .libs/coot-utils.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c atomic-numbers.cc -fPIC -DPIC -o .libs/atomic-numbers.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c coot-fasta.cc -fPIC -DPIC -o .libs/coot-fasta.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c gdk-keysyms.cc -fPIC -DPIC -o .libs/gdk-keysyms.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c coot-fasta.cc -o coot-fasta.o >/dev/null 2>&1 >mv -f .deps/coot-fasta.Tpo .deps/coot-fasta.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c atomic-numbers.cc -o atomic-numbers.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -o coot-utils.o >/dev/null 2>&1 >mv -f .deps/atomic-numbers.Tpo .deps/atomic-numbers.Plo >mv -f .deps/coot-utils.Tpo .deps/coot-utils.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c gdk-keysyms.cc -o gdk-keysyms.o >/dev/null 2>&1 >mv -f .deps/gdk-keysyms.Tpo .deps/gdk-keysyms.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-utils.la -rpath /usr/lib coot-utils.lo coot-fasta.lo atomic-numbers.lo gdk-keysyms.lo >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-utils.o .libs/coot-fasta.o .libs/atomic-numbers.o .libs/gdk-keysyms.o -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-utils.so.0 -o .libs/libcoot-utils.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-utils.so.0" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-utils.so" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-utils.a coot-utils.o coot-fasta.o atomic-numbers.o gdk-keysyms.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-utils.a >libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils' >Making all in geometry >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" 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-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -fPIC -DPIC -o .libs/protein-geometry.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -fPIC -DPIC -o .libs/protein-geometry-mmdb.o >mv -f .deps/test-read-components.Tpo .deps/test-read-components.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -o protein-geometry-mmdb.o >/dev/null 2>&1 >mv -f .deps/protein-geometry-mmdb.Tpo .deps/protein-geometry-mmdb.Plo >mv -f .deps/test-geometry.Tpo .deps/test-geometry.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -o protein-geometry.o >/dev/null 2>&1 >mv -f .deps/protein-geometry.Tpo .deps/protein-geometry.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo ../utils/libcoot-utils.la -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../utils/.libs/libcoot-utils.so -L/usr/lib -L/usr /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so.0" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-geometry.a protein-geometry.o protein-geometry-mmdb.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-geometry.a >libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o test-geometry test-geometry.o ./libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o test-read-components test-read-components.o ./libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/test-geometry test-geometry.o ./.libs/libcoot-geometry.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >libtool: link: i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/test-read-components test-read-components.o ./.libs/libcoot-geometry.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry' >Making all in mini-mol >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c -o mini-mol.lo mini-mol.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c -o mini-mol-utils.lo mini-mol-utils.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c -o atom-quads.lo atom-quads.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT testminimol.o -MD -MP -MF .deps/testminimol.Tpo -c -o testminimol.o testminimol.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -fPIC -DPIC -o .libs/mini-mol-utils.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -fPIC -DPIC -o .libs/atom-quads.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -fPIC -DPIC -o .libs/mini-mol.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -o atom-quads.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -o mini-mol-utils.o >/dev/null 2>&1 >mv -f .deps/testminimol.Tpo .deps/testminimol.Po >mv -f .deps/atom-quads.Tpo .deps/atom-quads.Plo >mv -f .deps/mini-mol-utils.Tpo .deps/mini-mol-utils.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -o mini-mol.o >/dev/null 2>&1 >mv -f .deps/mini-mol.Tpo .deps/mini-mol.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-mini-mol.la -rpath /usr/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o -L/usr/lib -L/usr /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so.0" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-mini-mol.a mini-mol.o mini-mol-utils.o atom-quads.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-mini-mol.a >libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o testminimol testminimol.o libcoot-mini-mol.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o .libs/testminimol testminimol.o ./.libs/libcoot-mini-mol.so -L/usr/lib -L/usr /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol' >Making all in coot-utils >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c coot-coord-extras.cc -fPIC -DPIC -o .libs/coot-coord-extras.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c coot-map-heavy.cc -fPIC -DPIC -o .libs/coot-map-heavy.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT xmap-stats.lo -MD -MP -MF .deps/xmap-stats.Tpo -c xmap-stats.cc -fPIC -DPIC -o .libs/xmap-stats.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c coot-tree-extras.cc -fPIC -DPIC -o .libs/coot-tree-extras.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c coot-coord-lsq.cc -fPIC -DPIC -o .libs/coot-coord-lsq.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-utils.lo -MD -MP -MF .deps/coot-map-utils.Tpo -c coot-map-utils.cc -fPIC -DPIC -o .libs/coot-map-utils.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c coot-fffear.cc -fPIC -DPIC -o .libs/coot-fffear.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT trim.lo -MD -MP -MF .deps/trim.Tpo -c trim.cc -fPIC -DPIC -o .libs/trim.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT xmap-stats.lo -MD -MP -MF .deps/xmap-stats.Tpo -c xmap-stats.cc -o xmap-stats.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT trim.lo -MD -MP -MF .deps/trim.Tpo -c trim.cc -o trim.o >/dev/null 2>&1 >mv -f .deps/test-shelx-reader.Tpo .deps/test-shelx-reader.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT test-utils.o -MD -MP -MF .deps/test-utils.Tpo -c -o test-utils.o test-utils.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-rama.lo -MD -MP -MF .deps/coot-rama.Tpo -c coot-rama.cc -o coot-rama.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c coot-map-heavy.cc -o coot-map-heavy.o >/dev/null 2>&1 >mv -f .deps/xmap-stats.Tpo .deps/xmap-stats.Plo >mv -f .deps/trim.Tpo .deps/trim.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c coot-coord-lsq.cc -o coot-coord-lsq.o >/dev/null 2>&1 >mv -f .deps/coot-map-heavy.Tpo .deps/coot-map-heavy.Plo >mv -f .deps/coot-rama.Tpo .deps/coot-rama.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-utils-nucleotides.lo -MD -MP -MF .deps/coot-coord-utils-nucleotides.Tpo -c coot-coord-utils-nucleotides.cc -o coot-coord-utils-nucleotides.o >/dev/null 2>&1 >mv -f .deps/test-utils.Tpo .deps/test-utils.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c coot-coord-extras.cc -o coot-coord-extras.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c coot-fffear.cc -o coot-fffear.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT peak-search.lo -MD -MP -MF .deps/peak-search.Tpo -c peak-search.cc -o peak-search.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c coot-tree-extras.cc -o coot-tree-extras.o >/dev/null 2>&1 >mv -f .deps/coot-coord-lsq.Tpo .deps/coot-coord-lsq.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-utils.lo -MD -MP -MF .deps/coot-map-utils.Tpo -c coot-map-utils.cc -o coot-map-utils.o >/dev/null 2>&1 >mv -f .deps/coot-coord-utils-nucleotides.Tpo .deps/coot-coord-utils-nucleotides.Plo >mv -f .deps/coot-coord-extras.Tpo .deps/coot-coord-extras.Plo >mv -f .deps/coot-fffear.Tpo .deps/coot-fffear.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-shelx-ins.lo -MD -MP -MF .deps/coot-shelx-ins.Tpo -c coot-shelx-ins.cc -o coot-shelx-ins.o >/dev/null 2>&1 >mv -f .deps/peak-search.Tpo .deps/peak-search.Plo >mv -f .deps/coot-tree-extras.Tpo .deps/coot-tree-extras.Plo >mv -f 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--mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-coord-utils.la -rpath /usr/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../utils/.libs/libcoot-utils.so -L/usr/lib /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so 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".libs" && rm -f "libcoot-coord-utils.la" && ln -s "../libcoot-coord-utils.la" "libcoot-coord-utils.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-shelx.la -rpath /usr/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-coord-extras.la -rpath /usr/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol 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-L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ./.libs/libcoot-coord-utils.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0 >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib 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-L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-shelx.so.0" && ln -s "libcoot-shelx.so.0.0.0" "libcoot-shelx.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-shelx.so" && ln -s "libcoot-shelx.so.0.0.0" "libcoot-shelx.so") >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ./.libs/libcoot-coord-utils.so -L/usr/lib -L/usr ../geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-map-utils.so.0" && ln -s "libcoot-map-utils.so.0.0.0" "libcoot-map-utils.so.0") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-shelx.a coot-shelx-ins.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-shelx.a >libtool: link: (cd ".libs" && rm -f "libcoot-map-utils.so" && ln -s "libcoot-map-utils.so.0.0.0" "libcoot-map-utils.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-map-utils.a coot-map-utils.o peak-search.o trim.o xmap-stats.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-map-utils.a >libtool: link: (cd ".libs" && rm -f "libcoot-coord-extras.so.0" && ln -s "libcoot-coord-extras.so.0.0.0" "libcoot-coord-extras.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-coord-extras.so" && ln -s "libcoot-coord-extras.so.0.0.0" "libcoot-coord-extras.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-coord-extras.a coot-coord-extras.o coot-coord-lsq.o coot-tree-extras.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-coord-extras.a >libtool: link: ( cd ".libs" && rm -f "libcoot-shelx.la" && ln -s "../libcoot-shelx.la" "libcoot-shelx.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o testshelxreader test-shelx-reader.o ./libcoot-shelx.la ./libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o testcootutils test-utils.o ./libcoot-shelx.la ./libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: ( cd ".libs" && rm -f "libcoot-map-utils.la" && ln -s "../libcoot-map-utils.la" "libcoot-map-utils.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-map-heavy.la -rpath /usr/lib coot-map-heavy.lo coot-fffear.lo ../mini-mol/libcoot-mini-mol.la libcoot-map-utils.la libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm >libtool: link: ( cd ".libs" && rm -f "libcoot-coord-extras.la" && ln -s "../libcoot-coord-extras.la" "libcoot-coord-extras.la" ) >libtool: link: i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/testshelxreader test-shelx-reader.o ./.libs/libcoot-shelx.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so ./.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >libtool: link: i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/testcootutils test-utils.o ./.libs/libcoot-shelx.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so ./.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-map-heavy.o .libs/coot-fffear.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath 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-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -fPIC -DPIC -o .libs/CXXChargeTable.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereTriangle.lo -MD -MP -MF .deps/CXXSphereTriangle.Tpo -c CXXSphereTriangle.cpp -fPIC -DPIC -o .libs/CXXSphereTriangle.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c CXXSurface.cpp -fPIC -DPIC -o .libs/CXXSurface.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereTriangleEdge.lo -MD -MP -MF .deps/CXXSphereTriangleEdge.Tpo -c CXXSphereTriangleEdge.cpp -fPIC -DPIC -o .libs/CXXSphereTriangleEdge.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXException.lo -MD -MP -MF .deps/CXXException.Tpo -c CXXException.cpp -fPIC -DPIC -o .libs/CXXException.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXCircleNode.lo -MD -MP -MF .deps/CXXCircleNode.Tpo -c CXXCircleNode.cpp -fPIC -DPIC -o .libs/CXXCircleNode.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c CXXTorusElement.cpp -fPIC -DPIC -o .libs/CXXTorusElement.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c CXXFFTSolventMap.cpp -fPIC -DPIC -o .libs/CXXFFTSolventMap.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSurfaceVertex.lo -MD -MP -MF .deps/CXXSurfaceVertex.Tpo -c CXXSurfaceVertex.cpp -fPIC -DPIC -o .libs/CXXSurfaceVertex.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c CXXSphereNode.cpp -fPIC -DPIC -o .libs/CXXSphereNode.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXCoord.lo -MD -MP -MF .deps/CXXCoord.Tpo -c CXXCoord.cpp -o CXXCoord.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXException.lo -MD -MP -MF .deps/CXXException.Tpo -c CXXException.cpp -o CXXException.o >/dev/null 2>&1 >mv -f .deps/CXXCoord.Tpo .deps/CXXCoord.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c -o CXXTorusNode.lo CXXTorusNode.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereTriangle.lo -MD -MP -MF .deps/CXXSphereTriangle.Tpo -c CXXSphereTriangle.cpp -o CXXSphereTriangle.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSurfaceVertex.lo -MD -MP -MF .deps/CXXSurfaceVertex.Tpo -c CXXSurfaceVertex.cpp -o CXXSurfaceVertex.o >/dev/null 2>&1 >mv -f .deps/CXXException.Tpo .deps/CXXException.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c -o CXXFortranFile.lo CXXFortranFile.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c CXXSphereNode.cpp -o CXXSphereNode.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXCircleNode.lo -MD -MP -MF .deps/CXXCircleNode.Tpo -c CXXCircleNode.cpp -o CXXCircleNode.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereTriangleEdge.lo -MD -MP -MF .deps/CXXSphereTriangleEdge.Tpo -c CXXSphereTriangleEdge.cpp -o CXXSphereTriangleEdge.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c CXXTorusNode.cpp -fPIC -DPIC -o .libs/CXXTorusNode.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp -fPIC -DPIC -o .libs/CXXFortranFile.o >mv -f .deps/CXXSphereTriangle.Tpo .deps/CXXSphereTriangle.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c -o CXXNewHood.lo CXXNewHood.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c CXXTorusNode.cpp -o CXXTorusNode.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c CXXCircle.cpp -o CXXCircle.o >/dev/null 2>&1 >mv -f .deps/CXXSphereNode.Tpo .deps/CXXSphereNode.Plo >mv -f .deps/CXXSurfaceVertex.Tpo .deps/CXXSurfaceVertex.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c -o CXXTriangle.lo CXXTriangle.cpp >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c -o CXXNode.lo CXXNode.cpp >mv -f .deps/CXXCircleNode.Tpo .deps/CXXCircleNode.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c -o CXXQADSurface.lo CXXQADSurface.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c CXXFFTSolventMap.cpp -o CXXFFTSolventMap.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c CXXNewHood.cpp -fPIC -DPIC -o .libs/CXXNewHood.o >mv -f .deps/CXXSphereTriangleEdge.Tpo .deps/CXXSphereTriangleEdge.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp >mv -f .deps/CXXTorusNode.Tpo .deps/CXXTorusNode.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c -o CXXSpace.lo CXXSpace.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c CXXTorusElement.cpp -o CXXTorusElement.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp -o CXXFortranFile.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c CXXNode.cpp -fPIC -DPIC -o .libs/CXXNode.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c CXXTriangle.cpp -fPIC -DPIC -o .libs/CXXTriangle.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXCreator.lo -MD -MP -MF .deps/CXXCreator.Tpo -c CXXCreator.cpp -o CXXCreator.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c CXXQADSurface.cpp -fPIC -DPIC -o .libs/CXXQADSurface.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c CXXNode.cpp -o CXXNode.o >/dev/null 2>&1 >mv -f .deps/CXXNode.Tpo .deps/CXXNode.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -fPIC -DPIC -o .libs/CXXSpace.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -o CXXChargeTable.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c CXXTriangle.cpp -o CXXTriangle.o >/dev/null 2>&1 >mv -f .deps/CXXFortranFile.Tpo .deps/CXXFortranFile.Plo >mv -f .deps/CXXTriangle.Tpo .deps/CXXTriangle.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c CXXNewHood.cpp -o CXXNewHood.o >/dev/null 2>&1 >mv -f .deps/CXXFFTSolventMap.Tpo .deps/CXXFFTSolventMap.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -o CXXQADSurfaceStaticData.o >/dev/null 2>&1 >mv -f .deps/CXXCircle.Tpo .deps/CXXCircle.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -o CXXSpace.o >/dev/null 2>&1 >mv -f .deps/CXXTorusElement.Tpo .deps/CXXTorusElement.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSphereElement.lo -MD -MP -MF .deps/CXXSphereElement.Tpo -c CXXSphereElement.cpp -o CXXSphereElement.o >/dev/null 2>&1 >mv -f .deps/CXXQADSurfaceStaticData.Tpo .deps/CXXQADSurfaceStaticData.Plo >mv -f .deps/CXXCreator.Tpo .deps/CXXCreator.Plo >mv -f .deps/CXXNewHood.Tpo .deps/CXXNewHood.Plo >mv -f .deps/CXXChargeTable.Tpo .deps/CXXChargeTable.Plo >mv -f .deps/CXXSpace.Tpo .deps/CXXSpace.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c CXXSurface.cpp -o CXXSurface.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c CXXQADSurface.cpp -o CXXQADSurface.o >/dev/null 2>&1 >mv -f .deps/CXXSphereElement.Tpo .deps/CXXSphereElement.Plo >mv -f .deps/CXXQADSurface.Tpo .deps/CXXQADSurface.Plo >mv -f .deps/CXXSurface.Tpo .deps/CXXSurface.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libccp4mg-surface.la -rpath /usr/lib CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXQADSurfaceStaticData.lo CXXSpace.lo -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o -L/usr/lib /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c -L/usr /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libccp4mg-surface.so.0 -o .libs/libccp4mg-surface.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so.0" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so.0") >libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libccp4mg-surface.a CXXSphereElement.o CXXChargeTable.o CXXSphereNode.o CXXCircle.o CXXSphereTriangle.o CXXCircleNode.o CXXSphereTriangleEdge.o CXXCoord.o CXXSurface.o CXXCreator.o CXXSurfaceVertex.o CXXException.o CXXTorusElement.o CXXFFTSolventMap.o CXXTorusNode.o CXXFortranFile.o CXXNewHood.o CXXTriangle.o CXXNode.o CXXQADSurface.o CXXQADSurfaceStaticData.o CXXSpace.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libccp4mg-surface.a >libtool: link: ( cd ".libs" && rm -f "libccp4mg-surface.la" && ln -s "../libccp4mg-surface.la" "libccp4mg-surface.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface' >Making all in coot-surface >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c -o coot-surface.lo coot-surface.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c -o rgbreps.lo rgbreps.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -fPIC -DPIC -o .libs/rgbreps.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -fPIC -DPIC -o .libs/coot-surface.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -o coot-surface.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -o rgbreps.o >/dev/null 2>&1 >mv -f .deps/coot-surface.Tpo .deps/coot-surface.Plo >mv -f .deps/rgbreps.Tpo .deps/rgbreps.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface/.libs ../surface/.libs/libccp4mg-surface.so -L/usr/lib -L/usr /usr/lib/libglut.so -lGL /usr/lib/libXxf86vm.so /usr/lib/libXi.so /usr/lib/libXmu.so /usr/lib/libXt.so /usr/lib/libSM.so /usr/lib/libICE.so -luuid /usr/lib/libXext.so /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so -lresolv /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libglitz.so /usr/lib/libpng12.so /usr/lib/libxcb-render-util.so /usr/lib/libxcb-render.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so /usr/lib/libfontconfig.so /usr/lib/libfreetype.so /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libglib-2.0.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-surface.so.0" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-surface.so" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-surface.a coot-surface.o rgbreps.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-surface.a >libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface' >Making all in coords >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c -o Bond_lines.lo Bond_lines.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 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-pipe -MT mmdb-crystal.lo -MD -MP -MF .deps/mmdb-crystal.Tpo -c mmdb-crystal.cc -fPIC -DPIC -o .libs/mmdb-crystal.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.cc -o utils.o >/dev/null 2>&1 >mv -f .deps/utils.Tpo .deps/utils.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT cos-sin.lo -MD -MP -MF .deps/cos-sin.Tpo -c cos-sin.cc -o cos-sin.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT coot-close.lo -MD -MP -MF .deps/coot-close.Tpo -c coot-close.cc -o coot-close.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Cartesian.lo -MD -MP -MF .deps/Cartesian.Tpo -c Cartesian.cc -o Cartesian.o >/dev/null 2>&1 >mv -f .deps/cos-sin.Tpo .deps/cos-sin.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Bond_lines_ext.lo -MD -MP -MF .deps/Bond_lines_ext.Tpo -c Bond_lines_ext.cc -o Bond_lines_ext.o >/dev/null 2>&1 >mv -f .deps/coot-close.Tpo .deps/coot-close.Plo >mv -f .deps/Cartesian.Tpo .deps/Cartesian.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb.lo -MD -MP -MF .deps/mmdb.Tpo -c mmdb.cc -o mmdb.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb-extras.lo -MD -MP -MF .deps/mmdb-extras.Tpo -c mmdb-extras.cc -o mmdb-extras.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb-crystal.lo -MD -MP -MF .deps/mmdb-crystal.Tpo -c mmdb-crystal.cc -o mmdb-crystal.o >/dev/null 2>&1 >mv -f .deps/Bond_lines_ext.Tpo .deps/Bond_lines_ext.Plo >mv -f .deps/mmdb.Tpo .deps/mmdb.Plo >mv -f .deps/mmdb-extras.Tpo .deps/mmdb-extras.Plo >mv -f .deps/mmdb-crystal.Tpo .deps/mmdb-crystal.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc -o Bond_lines.o >/dev/null 2>&1 >mv -f .deps/Bond_lines.Tpo .deps/Bond_lines.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -Wl,-O1 -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../geometry/.libs/libcoot-geometry.so -L/usr/lib -L/usr ../coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-coords.so.0" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-coords.so" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-coords.a Bond_lines.o Cartesian.o cos-sin.o mmdb-extras.o utils.o mmdb.o mmdb-crystal.o Bond_lines_ext.o coot-close.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-coords.a >libtool: link: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords' >Making all in angles >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c -o libcoot_AngleInfo_la-AngleInfo.lo `test -f 'AngleInfo.cc' || echo './'`AngleInfo.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo `test -f 'AngleInfo-angle-torsions-autogen.cc' || echo './'`AngleInfo-angle-torsions-autogen.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo `test -f 'AngleInfo-theta_2-autogen.cc' || echo './'`AngleInfo-theta_2-autogen.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c AngleInfo.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o >/dev/null 2>&1 >mv -f .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c AngleInfo.cc -o libcoot_AngleInfo_la-AngleInfo.o >/dev/null 2>&1 >mv -f .deps/libcoot_AngleInfo_la-AngleInfo.Tpo .deps/libcoot_AngleInfo_la-AngleInfo.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o >/dev/null 2>&1 >mv -f .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -g -O1 -O2 -pipe -Wl,-O1 -o libcoot-AngleInfo.la -rpath /usr/lib libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/libcoot_AngleInfo_la-AngleInfo.o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-AngleInfo.so.0 -o .libs/libcoot-AngleInfo.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so.0" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-AngleInfo.a libcoot_AngleInfo_la-AngleInfo.o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-AngleInfo.a >libtool: link: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles' >Making all in skeleton >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT dm-utils.lo -MD -MP -MF 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-DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -fPIC -DPIC -o .libs/dm-utils.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -fPIC -DPIC -o .libs/graphical_skel.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -fPIC -DPIC -o .libs/BuildCas.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -o dm-utils.o >/dev/null 2>&1 >mv -f .deps/dm-utils.Tpo .deps/dm-utils.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -o graphical_skel.o >/dev/null 2>&1 >mv -f .deps/graphical_skel.Tpo .deps/graphical_skel.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -o BuildCas.o >/dev/null 2>&1 >mv -f .deps/BuildCas.Tpo .deps/BuildCas.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs ../angles/.libs/libcoot-AngleInfo.so ../geometry/.libs/libcoot-geometry.so -L/usr/lib -L/usr ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so.0" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-skeleton.a dm-utils.o graphical_skel.o BuildCas.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-skeleton.a >libtool: link: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton' >Making all in ccp4mg-utils >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c -o geomutil.lo geomutil.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c -o mgtree.lo mgtree.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c -o cartesian.lo cartesian.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c -o quat.lo quat.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c -o ppmutil.lo ppmutil.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -fPIC -DPIC -o .libs/cartesian.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -fPIC -DPIC -o .libs/mgtree.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -fPIC -DPIC -o .libs/matrix.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -fPIC -DPIC -o .libs/geomutil.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -fPIC -DPIC -o .libs/quat.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -fPIC -DPIC -o .libs/ppmutil.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -o quat.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -o geomutil.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o >/dev/null 2>&1 >mv -f .deps/quat.Tpo .deps/quat.Plo >mv -f .deps/cartesian.Tpo .deps/cartesian.Plo >mv -f .deps/geomutil.Tpo .deps/geomutil.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -o ppmutil.o >/dev/null 2>&1 >mv -f .deps/matrix.Tpo .deps/matrix.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -o mgtree.o >/dev/null 2>&1 >mv -f .deps/ppmutil.Tpo .deps/ppmutil.Plo >mv -f .deps/mgtree.Tpo .deps/mgtree.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libccp4mg-utils.la -rpath /usr/lib geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/geomutil.o .libs/mgtree.o .libs/cartesian.o .libs/matrix.o .libs/quat.o .libs/ppmutil.o -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libccp4mg-utils.so.0 -o .libs/libccp4mg-utils.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so.0" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so.0") >libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libccp4mg-utils.a geomutil.o mgtree.o cartesian.o matrix.o quat.o ppmutil.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libccp4mg-utils.a >libtool: link: ( cd ".libs" && rm -f "libccp4mg-utils.la" && ln -s "../libccp4mg-utils.la" "libccp4mg-utils.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils' >Making all in density-contour >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c -o Vectors.lo Vectors.cpp >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c -o CIsoSurface.lo CIsoSurface.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c CIsoSurface.cpp -fPIC -DPIC -o .libs/CIsoSurface.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c Vectors.cpp -fPIC -DPIC -o .libs/Vectors.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c Vectors.cpp -o Vectors.o >/dev/null 2>&1 >mv -f .deps/Vectors.Tpo .deps/Vectors.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c CIsoSurface.cpp -o CIsoSurface.o >/dev/null 2>&1 >mv -f .deps/CIsoSurface.Tpo .deps/CIsoSurface.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-isosurface.la -rpath /usr/lib Vectors.lo CIsoSurface.lo ../coords/libcoot-coords.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/Vectors.o .libs/CIsoSurface.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs ../coords/.libs/libcoot-coords.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so.0" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-isosurface.a Vectors.o CIsoSurface.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-isosurface.a >libtool: link: ( cd ".libs" && rm -f "libcoot-isosurface.la" && ln -s "../libcoot-isosurface.la" "libcoot-isosurface.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour' >Making all in db-main >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c -o db-main.lo db-main.cc >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c -o db-strands.lo db-strands.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -MT testdbmain.o -MD -MP -MF .deps/testdbmain.Tpo -c -o testdbmain.o testdbmain.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -MT train-pepflip.o -MD -MP -MF .deps/train-pepflip.Tpo -c -o train-pepflip.o train-pepflip.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -fPIC -DPIC -o .libs/db-main.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -fPIC -DPIC -o .libs/db-strands.o >mv -f .deps/testdbmain.Tpo .deps/testdbmain.Po >mv -f .deps/train-pepflip.Tpo .deps/train-pepflip.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -o db-strands.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -o db-main.o >/dev/null 2>&1 >mv -f .deps/db-strands.Tpo .deps/db-strands.Plo >mv -f .deps/db-main.Tpo .deps/db-main.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -Wl,-O1 -o libcoot-db-main.la -rpath /usr/lib db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/db-main.o .libs/db-strands.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib -L/usr ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so.0" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-db-main.a db-main.o db-strands.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-db-main.a >libtool: link: ( cd ".libs" && rm -f "libcoot-db-main.la" && ln -s "../libcoot-db-main.la" "libcoot-db-main.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -Wl,-O1 -o testdbmain testdbmain.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -Wl,-O1 -o train-pepflip train-pepflip.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -Wl,-O1 -o .libs/testdbmain testdbmain.o ./.libs/libcoot-db-main.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -Wl,-O1 -o .libs/train-pepflip train-pepflip.o ./.libs/libcoot-db-main.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main' >Making all in ideal >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT with-map.o -MD -MP -MF .deps/with-map.Tpo -c -o with-map.o with-map.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT logramatest.o -MD -MP -MF .deps/logramatest.Tpo -c -o logramatest.o logramatest.cpp >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT lograma.lo -MD -MP -MF .deps/lograma.Tpo -c lograma.cpp -fPIC -DPIC -o .libs/lograma.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT pepflip.lo -MD -MP -MF .deps/pepflip.Tpo -c pepflip.cc -fPIC -DPIC -o .libs/pepflip.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c simple-restraint.cc -fPIC -DPIC -o .libs/simple-restraint.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT regularize-minimol.lo -MD -MP -MF .deps/regularize-minimol.Tpo -c regularize-minimol.cc -fPIC -DPIC -o .libs/regularize-minimol.o >mv -f .deps/logramatest.Tpo .deps/logramatest.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT lograma.lo -MD -MP -MF .deps/lograma.Tpo -c lograma.cpp -o lograma.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT pepflip.lo -MD -MP -MF .deps/pepflip.Tpo -c pepflip.cc -o pepflip.o >/dev/null 2>&1 >mv -f .deps/test-indexing.Tpo .deps/test-indexing.Po >mv -f .deps/lograma.Tpo .deps/lograma.Plo >mv -f .deps/pepflip.Tpo .deps/pepflip.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -MT regularize-minimol.lo -MD -MP -MF .deps/regularize-minimol.Tpo -c regularize-minimol.cc -o regularize-minimol.o >/dev/null 2>&1 >mv -f .deps/with-geometry.Tpo .deps/with-geometry.Po >mv -f .deps/regularize-minimol.Tpo .deps/regularize-minimol.Plo >mv -f .deps/with-map.Tpo .deps/with-map.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 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>libtool: link: i686-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -Wl,-O1 -o .libs/with-map with-map.o -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr ./.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-extras.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so 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-I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT chi-angles-autogen.lo -MD -MP -MF .deps/chi-angles-autogen.Tpo -c chi-angles-autogen.cc -fPIC -DPIC -o .libs/chi-angles-autogen.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT monomer-utils.lo -MD -MP -MF .deps/monomer-utils.Tpo -c monomer-utils.cc -fPIC -DPIC -o .libs/monomer-utils.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT dunbrack.lo -MD -MP -MF .deps/dunbrack.Tpo -c dunbrack.cc -fPIC -DPIC -o .libs/dunbrack.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT richardson-rotamers.lo -MD -MP -MF .deps/richardson-rotamers.Tpo -c richardson-rotamers.cc -fPIC -DPIC -o .libs/richardson-rotamers.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT fast-ss-search.lo -MD -MP -MF .deps/fast-ss-search.Tpo -c fast-ss-search.cc -fPIC -DPIC -o .libs/fast-ss-search.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT ideal-rna.lo -MD -MP -MF .deps/ideal-rna.Tpo -c ideal-rna.cc -fPIC -DPIC -o .libs/ideal-rna.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT helix-placement.lo -MD -MP -MF .deps/helix-placement.Tpo -c helix-placement.cc -fPIC -DPIC -o .libs/helix-placement.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT richardson-rotamer.lo -MD -MP -MF .deps/richardson-rotamer.Tpo -c richardson-rotamer.cc -fPIC -DPIC -o .libs/richardson-rotamer.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT richardson-rotamer.lo -MD -MP -MF .deps/richardson-rotamer.Tpo -c richardson-rotamer.cc -o richardson-rotamer.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT ideal-rna.lo -MD -MP -MF .deps/ideal-rna.Tpo -c ideal-rna.cc -o ideal-rna.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT rigid-body.lo -MD -MP -MF .deps/rigid-body.Tpo -c rigid-body.cc -o rigid-body.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT monomer-utils.lo -MD -MP -MF .deps/monomer-utils.Tpo -c monomer-utils.cc -o monomer-utils.o >/dev/null 2>&1 >mv -f .deps/richardson-rotamer.Tpo .deps/richardson-rotamer.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT rotamer.lo -MD -MP -MF .deps/rotamer.Tpo -c -o rotamer.lo rotamer.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT rotamer.lo -MD -MP -MF .deps/rotamer.Tpo -c rotamer.cc -fPIC -DPIC -o .libs/rotamer.o >mv -f .deps/ideal-rna.Tpo .deps/ideal-rna.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT torsion-general.lo -MD -MP -MF .deps/torsion-general.Tpo -c -o torsion-general.lo torsion-general.cc >mv -f .deps/rigid-body.Tpo .deps/rigid-body.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT rotamer-tables.lo -MD -MP -MF .deps/rotamer-tables.Tpo -c -o rotamer-tables.lo rotamer-tables.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT torsion-general.lo -MD -MP -MF .deps/torsion-general.Tpo -c torsion-general.cc -fPIC -DPIC -o .libs/torsion-general.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT rotamer-tables.lo -MD -MP -MF .deps/rotamer-tables.Tpo -c rotamer-tables.cc -fPIC -DPIC -o .libs/rotamer-tables.o >mv -f .deps/monomer-utils.Tpo .deps/monomer-utils.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT primitive-chi-angles.lo -MD -MP -MF .deps/primitive-chi-angles.Tpo -c -o primitive-chi-angles.lo primitive-chi-angles.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT ligand-extras.lo -MD -MP -MF .deps/ligand-extras.Tpo -c ligand-extras.cc -o ligand-extras.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT primitive-chi-angles.lo -MD -MP -MF .deps/primitive-chi-angles.Tpo -c primitive-chi-angles.cc -fPIC -DPIC -o .libs/primitive-chi-angles.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT torsion-general.lo -MD -MP -MF .deps/torsion-general.Tpo -c torsion-general.cc -o torsion-general.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT richardson-rotamers.lo -MD -MP -MF .deps/richardson-rotamers.Tpo -c richardson-rotamers.cc -o richardson-rotamers.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT dunbrack.lo -MD -MP -MF .deps/dunbrack.Tpo -c dunbrack.cc -o dunbrack.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT chi-angles-autogen.lo -MD -MP -MF .deps/chi-angles-autogen.Tpo -c chi-angles-autogen.cc -o chi-angles-autogen.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT residue_by_phi_psi.lo -MD -MP -MF .deps/residue_by_phi_psi.Tpo -c residue_by_phi_psi.cc -o residue_by_phi_psi.o >/dev/null 2>&1 >mv -f .deps/torsion-general.Tpo .deps/torsion-general.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT dipole.lo -MD -MP -MF .deps/dipole.Tpo -c -o dipole.lo dipole.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT dipole.lo -MD -MP -MF .deps/dipole.Tpo -c dipole.cc -fPIC -DPIC -o .libs/dipole.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT helix-placement.lo -MD -MP -MF .deps/helix-placement.Tpo -c helix-placement.cc -o helix-placement.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT chi-angles.lo -MD -MP -MF .deps/chi-angles.Tpo -c chi-angles.cc -o chi-angles.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT fast-ss-search.lo -MD -MP -MF .deps/fast-ss-search.Tpo -c fast-ss-search.cc -o fast-ss-search.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT wiggly-ligand.lo -MD -MP -MF .deps/wiggly-ligand.Tpo -c wiggly-ligand.cc -o wiggly-ligand.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT primitive-chi-angles.lo -MD -MP -MF .deps/primitive-chi-angles.Tpo -c primitive-chi-angles.cc -o primitive-chi-angles.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT rotamer.lo -MD -MP -MF .deps/rotamer.Tpo -c rotamer.cc -o rotamer.o >/dev/null 2>&1 >mv -f .deps/ligand-extras.Tpo .deps/ligand-extras.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT base-pairing.lo -MD -MP -MF .deps/base-pairing.Tpo -c -o base-pairing.lo base-pairing.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT base-pairing.lo -MD -MP -MF .deps/base-pairing.Tpo -c base-pairing.cc -fPIC -DPIC -o .libs/base-pairing.o >mv -f .deps/dunbrack.Tpo .deps/dunbrack.Plo >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT backrub-rotamer.lo -MD -MP -MF .deps/backrub-rotamer.Tpo -c -o backrub-rotamer.lo backrub-rotamer.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT backrub-rotamer.lo -MD -MP -MF .deps/backrub-rotamer.Tpo -c backrub-rotamer.cc -fPIC -DPIC -o .libs/backrub-rotamer.o >mv -f .deps/chi-angles-autogen.Tpo .deps/chi-angles-autogen.Plo >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT find-ligand.o -MD -MP -MF .deps/find-ligand.Tpo -c -o find-ligand.o find-ligand.cc >mv -f .deps/richardson-rotamers.Tpo .deps/richardson-rotamers.Plo >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT find-waters.o -MD -MP -MF .deps/find-waters.Tpo -c -o find-waters.o find-waters.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT base-pairing.lo -MD -MP -MF .deps/base-pairing.Tpo -c base-pairing.cc -o base-pairing.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT rotamer-tables.lo -MD -MP -MF .deps/rotamer-tables.Tpo -c rotamer-tables.cc -o rotamer-tables.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT dipole.lo -MD -MP -MF .deps/dipole.Tpo -c dipole.cc -o dipole.o >/dev/null 2>&1 >mv -f .deps/base-pairing.Tpo .deps/base-pairing.Plo >mv -f .deps/residue_by_phi_psi.Tpo .deps/residue_by_phi_psi.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT ligand.lo -MD -MP -MF .deps/ligand.Tpo -c ligand.cc -o ligand.o >/dev/null 2>&1 >mv -f .deps/find-waters.Tpo .deps/find-waters.Po >mv -f .deps/helix-placement.Tpo .deps/helix-placement.Plo >mv -f .deps/chi-angles.Tpo .deps/chi-angles.Plo >mv -f .deps/primitive-chi-angles.Tpo .deps/primitive-chi-angles.Plo >mv -f .deps/fast-ss-search.Tpo .deps/fast-ss-search.Plo >mv -f .deps/wiggly-ligand.Tpo .deps/wiggly-ligand.Plo >mv -f .deps/rotamer.Tpo .deps/rotamer.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT backrub-rotamer.lo -MD -MP -MF .deps/backrub-rotamer.Tpo -c backrub-rotamer.cc -o backrub-rotamer.o >/dev/null 2>&1 >mv -f .deps/find-ligand.Tpo .deps/find-ligand.Po >mv -f .deps/dipole.Tpo .deps/dipole.Plo >mv -f .deps/rotamer-tables.Tpo .deps/rotamer-tables.Plo >mv -f .deps/backrub-rotamer.Tpo .deps/backrub-rotamer.Plo >mv -f .deps/ligand.Tpo .deps/ligand.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-ligand.la -rpath /usr/lib ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo ../ideal/libcoot-ideal.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../ideal/.libs/libcoot-ideal.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so /usr/lib/libgsl.so -lcblas /usr/lib/libatlas.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-extras.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-ligand.a ligand.o ligand-extras.o residue_by_phi_psi.o wiggly-ligand.o monomer-utils.o dunbrack.o chi-angles-autogen.o chi-angles.o helix-placement.o fast-ss-search.o rigid-body.o ideal-rna.o richardson-rotamers.o richardson-rotamer.o rotamer.o torsion-general.o rotamer-tables.o primitive-chi-angles.o dipole.o base-pairing.o backrub-rotamer.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-ligand.a >libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o findligand-real find-ligand.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o findwaters-real find-waters.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/findwaters-real find-waters.o ./.libs/libcoot-ligand.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs/libccp4mg-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-map-utils.so ../ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so 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/usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz /usr/lib/libmmdb.so /usr/lib/libgsl.so -lcblas /usr/lib/libatlas.so -lpthread -lm >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/findligand-real find-ligand.o ./.libs/libcoot-ligand.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs/libccp4mg-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-map-utils.so ../ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so 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/usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz /usr/lib/libmmdb.so /usr/lib/libgsl.so -lcblas /usr/lib/libatlas.so -lpthread -lm >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand' >Making all in high-res >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../compat -I/usr/include/mmdb 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-I../ligand -I../utils -I../coot-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DHAVE_GSL -I/usr/include -O2 -pipe -MT high-res.lo -MD -MP -MF .deps/high-res.Tpo -c high-res.cc -o high-res.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DHAVE_GSL -I/usr/include -O2 -pipe -MT coot-atom-graph.lo -MD -MP -MF .deps/coot-atom-graph.Tpo -c coot-atom-graph.cc -o coot-atom-graph.o >/dev/null 2>&1 >mv -f .deps/sequence-assignment.Tpo .deps/sequence-assignment.Plo >mv -f .deps/high-res.Tpo .deps/high-res.Plo >mv -f .deps/coot-atom-graph.Tpo .deps/coot-atom-graph.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -O2 -pipe -Wl,-O1 -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib -L/usr ../ligand/.libs/libcoot-ligand.so -L/usr/lib/blas/threaded-atlas /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs/libcoot-ideal.so /usr/lib/libgsl.so -lcblas /usr/lib/libatlas.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs/libccp4mg-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-map-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so.0" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-high-res.a high-res.o coot-atom-graph.o residue-distortions.o sequence-assignment.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-high-res.a >libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" ) >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res' >Making all in build >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/build' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT CalphaBuild.lo -MD -MP -MF .deps/CalphaBuild.Tpo -c -o CalphaBuild.lo CalphaBuild.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT testcabuild.o -MD -MP -MF .deps/testcabuild.Tpo -c -o testcabuild.o testcabuild.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT CalphaBuild.lo -MD -MP -MF .deps/CalphaBuild.Tpo -c CalphaBuild.cc -fPIC -DPIC -o .libs/CalphaBuild.o >mv -f .deps/testcabuild.Tpo .deps/testcabuild.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT CalphaBuild.lo -MD -MP -MF .deps/CalphaBuild.Tpo -c CalphaBuild.cc -o CalphaBuild.o >/dev/null 2>&1 >mv -f .deps/CalphaBuild.Tpo .deps/CalphaBuild.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-cabuild.la -rpath /usr/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib 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/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so.0" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-cabuild.a CalphaBuild.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-cabuild.a >libtool: link: ( cd ".libs" && rm -f "libcoot-cabuild.la" && ln -s "../libcoot-cabuild.la" "libcoot-cabuild.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o testcabuild testcabuild.o ./libcoot-cabuild.la ../angles/libcoot-AngleInfo.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread 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>i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT bfactan.o -MD -MP -MF .deps/bfactan.Tpo -c -o bfactan.o bfactan.cc >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -fPIC -DPIC -o .libs/bfkurt.o >mv -f .deps/bfactan.Tpo .deps/bfactan.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -o bfkurt.o >/dev/null 2>&1 >mv -f .deps/bfkurt.Tpo .deps/bfkurt.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-analysis.la -rpath /usr/lib bfkurt.lo ../coot-utils/libcoot-coord-utils.la -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/bfkurt.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs ../coot-utils/.libs/libcoot-coord-utils.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-analysis.a bfkurt.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-analysis.a >libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o .libs/bfactan bfactan.o ./.libs/libcoot-analysis.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis' >Making all in tw >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/tw' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT tw.lo -MD -MP -MF .deps/tw.Tpo -c -o tw.lo tw.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT tiddly.o -MD -MP -MF .deps/tiddly.Tpo -c -o tiddly.o tiddly.cc >mv -f .deps/tiddly.Tpo .deps/tiddly.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT tw.lo -MD -MP -MF .deps/tw.Tpo -c tw.cc -fPIC -DPIC -o .libs/tw.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT tw.lo -MD -MP -MF .deps/tw.Tpo -c tw.cc -o tw.o >/dev/null 2>&1 >mv -f .deps/tw.Tpo .deps/tw.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o libcoot-tw.la -rpath /usr/lib tw.lo >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/tw.o -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-tw.so.0 -o .libs/libcoot-tw.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcoot-tw.so.0" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so.0") >libtool: link: (cd ".libs" && rm -f "libcoot-tw.so" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-tw.a tw.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-tw.a >libtool: link: ( cd ".libs" && rm -f "libcoot-tw.la" && ln -s "../libcoot-tw.la" "libcoot-tw.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -Wl,-O1 -o coot-tiddly tiddly.o libcoot-tw.la -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o .libs/coot-tiddly tiddly.o ./.libs/libcoot-tw.so /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so -L/usr/lib /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so -lresolv /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libglitz.so /usr/lib/libpng12.so /usr/lib/libxcb-render-util.so /usr/lib/libxcb-render.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so -lm /usr/lib/libfontconfig.so /usr/lib/libfreetype.so -lz /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libglib-2.0.so >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/tw' >Making all in cootaneer >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootaneer' >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c -o buccaneer-lib.lo buccaneer-lib.cpp >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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buccaneer-sequence.cpp >/bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c -o cootaneer-sequence.lo cootaneer-sequence.cpp >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -fPIC -DPIC -o .libs/buccaneer-lib.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -fPIC -DPIC -o .libs/buccaneer-sequence.o >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -fPIC -DPIC -o .libs/cootaneer-sequence.o >mv -f .deps/cootaneer-demo.Tpo .deps/cootaneer-demo.Po >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -o buccaneer-lib.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -o cootaneer-sequence.o >/dev/null 2>&1 >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c buccaneer-prot.cpp -o buccaneer-prot.o >/dev/null 2>&1 >mv -f .deps/buccaneer-lib.Tpo .deps/buccaneer-lib.Plo >libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -o buccaneer-sequence.o >/dev/null 2>&1 >mv -f .deps/cootaneer-sequence.Tpo .deps/cootaneer-sequence.Plo >mv -f .deps/buccaneer-prot.Tpo .deps/buccaneer-prot.Plo >mv -f .deps/buccaneer-sequence.Tpo .deps/buccaneer-sequence.Plo >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcootaneer.la -rpath /usr/lib buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread >libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/buccaneer-lib.o .libs/buccaneer-prot.o .libs/buccaneer-sequence.o .libs/cootaneer-sequence.o -L/usr/lib /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c -L/usr /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcootaneer.so.0 -o .libs/libcootaneer.so.0.0.0 >libtool: link: (cd ".libs" && rm -f "libcootaneer.so.0" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so.0") >libtool: link: (cd ".libs" && rm -f "libcootaneer.so" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so") >libtool: link: i686-pc-linux-gnu-ar cru .libs/libcootaneer.a buccaneer-lib.o buccaneer-prot.o buccaneer-sequence.o cootaneer-sequence.o >libtool: link: i686-pc-linux-gnu-ranlib .libs/libcootaneer.a >libtool: link: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" ) >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o cootaneer-demo cootaneer-demo.o ./libcootaneer.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o .libs/cootaneer-demo cootaneer-demo.o ./.libs/libcootaneer.so -L/usr/lib -L/usr /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootaneer' >Making all in src >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/src' >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT svn-revision.o -MD -MP -MF .deps/svn-revision.Tpo -c -o svn-revision.o svn-revision.cc >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT c-inner-main.o -MD -MP -MF .deps/c-inner-main.Tpo -c -o c-inner-main.o c-inner-main.c >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-build.o -MD -MP -MF .deps/c-interface-build.Tpo -c -o c-interface-build.o c-interface-build.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-build-gui.o -MD -MP -MF .deps/c-interface-build-gui.Tpo -c -o c-interface-build-gui.o c-interface-build-gui.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface 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-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 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.deps/c-interface-pisa.Tpo -c -o c-interface-pisa.o c-interface-pisa.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 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-I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-info.o -MD -MP -MF .deps/c-interface-info.Tpo -c -o c-interface-info.o c-interface-info.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-ligands.o -MD -MP -MF .deps/c-interface-ligands.Tpo -c -o c-interface-ligands.o c-interface-ligands.cc >mv -f .deps/c-interface-database.Tpo .deps/c-interface-database.Po >mv -f .deps/svn-revision.Tpo .deps/svn-revision.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-ligands-gui.o -MD -MP -MF .deps/c-interface-ligands-gui.Tpo -c -o c-interface-ligands-gui.o c-interface-ligands-gui.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-mmdb.o -MD -MP -MF .deps/c-interface-mmdb.Tpo -c -o c-interface-mmdb.o c-interface-mmdb.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-mutate.o -MD -MP -MF .deps/c-interface-mutate.Tpo -c -o c-interface-mutate.o c-interface-mutate.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-ncs.o -MD -MP -MF .deps/c-interface-ncs.Tpo -c -o c-interface-ncs.o c-interface-ncs.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface-python.hh:29, > from c-interface.cc:43: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface-mmdb.hh:42, > from c-interface-mmdb.cc:32: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from c-interface-gtk2.cc:56: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-inner-main.Tpo .deps/c-inner-main.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-nucleotides.o -MD -MP -MF .deps/c-interface-nucleotides.Tpo -c -o c-interface-nucleotides.o c-interface-nucleotides.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-info.cc:65: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-pisa.cc:22: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-ligands.cc:44: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-build.cc:60: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from main.cc:91: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-build-gui.cc:60: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-gui.cc:60: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-ncs.cc:49: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-ligands-gui.cc:44: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-mutate.cc:40: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-nucleotides.cc:30: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-mmdb.Tpo .deps/c-interface-mmdb.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-python.o -MD -MP -MF .deps/c-interface-python.Tpo -c -o c-interface-python.o c-interface-python.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface-python.hh:29, > from c-interface-python.cc:28: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-pisa.Tpo .deps/c-interface-pisa.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-preferences.o -MD -MP -MF .deps/c-interface-preferences.Tpo -c -o c-interface-preferences.o c-interface-preferences.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-preferences.cc:51: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-mutate.Tpo .deps/c-interface-mutate.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-scm.o -MD -MP -MF .deps/c-interface-scm.Tpo -c -o c-interface-scm.o c-interface-scm.cc >mv -f .deps/c-interface-nucleotides.Tpo .deps/c-interface-nucleotides.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-superpose.o -MD -MP -MF .deps/c-interface-superpose.Tpo -c -o c-interface-superpose.o c-interface-superpose.cc >mv -f .deps/c-interface-ligands-gui.Tpo .deps/c-interface-ligands-gui.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-validate.o -MD -MP -MF .deps/c-interface-validate.Tpo -c -o c-interface-validate.o c-interface-validate.cc >mv -f .deps/c-interface-gtk2.Tpo .deps/c-interface-gtk2.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-widgets.o -MD -MP -MF .deps/c-interface-widgets.Tpo -c -o c-interface-widgets.o c-interface-widgets.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-scm.cc:28: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-ncs.Tpo .deps/c-interface-ncs.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT c-interface-waters.o -MD -MP -MF .deps/c-interface-waters.Tpo -c -o c-interface-waters.o c-interface-waters.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-superpose.cc:31: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-validate.cc:48: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-widgets.cc:28: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-python.Tpo .deps/c-interface-python.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT callbacks.o -MD -MP -MF .deps/callbacks.Tpo -c -o callbacks.o callbacks.c >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from c-interface-waters.cc:49: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-build-gui.Tpo .deps/c-interface-build-gui.Po >mv -f .deps/c-interface-ligands.Tpo .deps/c-interface-ligands.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT cmtz-interface.o -MD -MP -MF .deps/cmtz-interface.Tpo -c -o cmtz-interface.o cmtz-interface.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT command-line.o -MD -MP -MF .deps/command-line.Tpo -c -o command-line.o command-line.cc >mv -f .deps/c-interface-scm.Tpo .deps/c-interface-scm.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot-align.o -MD -MP -MF .deps/coot-align.Tpo -c -o coot-align.o coot-align.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from cmtz-interface.cc:53: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from command-line.cc:49: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-widgets.Tpo .deps/c-interface-widgets.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot-nomenclature.o -MD -MP -MF .deps/coot-nomenclature.Tpo -c -o coot-nomenclature.o coot-nomenclature.cc >mv -f .deps/c-interface-gui.Tpo .deps/c-interface-gui.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT coot-glue.o -MD -MP -MF .deps/coot-glue.Tpo -c -o coot-glue.o coot-glue.c >mv -f .deps/main.Tpo .deps/main.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT coot-glue-gtk2.o -MD -MP -MF .deps/coot-glue-gtk2.Tpo -c -o coot-glue-gtk2.o coot-glue-gtk2.c >mv -f .deps/coot-glue.Tpo .deps/coot-glue.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot-glue-gtk2-python.o -MD -MP -MF .deps/coot-glue-gtk2-python.Tpo -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc >mv -f .deps/coot-glue-gtk2-python.Tpo .deps/coot-glue-gtk2-python.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot_pythonmodule.o -MD -MP -MF .deps/coot_pythonmodule.Tpo -c -o coot_pythonmodule.o coot_pythonmodule.cc >mv -f .deps/coot-glue-gtk2.Tpo .deps/coot-glue-gtk2.Po >swig -o coot_wrap_guile_pre_gtk1.cc -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -I../src -guile -c++ ../src/coot.i >mv -f .deps/coot-align.Tpo .deps/coot-align.Po >swig -o coot_wrap_guile_pre_gtk2.cc -DCOOT_USE_GTK2_INTERFACE -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -I../src -guile -c++ ../src/coot.i >In file included from /usr/include/python2.6/Python.h:8:0, > from /usr/include/pygtk-2.0/pygobject.h:5, > from coot_pythonmodule.cc:28: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-superpose.Tpo .deps/c-interface-superpose.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT geometry-graphs.o -MD -MP -MF .deps/geometry-graphs.Tpo -c -o geometry-graphs.o geometry-graphs.cc >mv -f .deps/coot_pythonmodule.Tpo .deps/coot_pythonmodule.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT get-residue.o -MD -MP -MF .deps/get-residue.Tpo -c -o get-residue.o get-residue.cc >mv -f .deps/c-interface-waters.Tpo .deps/c-interface-waters.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT globjects.o -MD -MP -MF .deps/globjects.Tpo -c -o globjects.o globjects.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from geometry-graphs.cc:72: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/callbacks.Tpo .deps/callbacks.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info.o -MD -MP -MF .deps/graphics-info.Tpo -c -o graphics-info.o graphics-info.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from globjects.cc:67: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-defines.o -MD -MP -MF .deps/graphics-info-defines.Tpo -c -o graphics-info-defines.o graphics-info-defines.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from get-residue.cc:3: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-refmac.o -MD -MP -MF .deps/graphics-info-refmac.Tpo -c -o graphics-info-refmac.o graphics-info-refmac.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info.cc:73: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-refmac.cc:81: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-defines.cc:27: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/command-line.Tpo .deps/command-line.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-graphs.o -MD -MP -MF .deps/graphics-info-graphs.Tpo -c -o graphics-info-graphs.o graphics-info-graphs.cc >mv -f .deps/coot-nomenclature.Tpo .deps/coot-nomenclature.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-gui.o -MD -MP -MF .deps/graphics-info-gui.Tpo -c -o graphics-info-gui.o graphics-info-gui.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-graphs.cc:72: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/get-residue.Tpo .deps/get-residue.Po >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-gui.cc:73: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-modelling.o -MD -MP -MF .deps/graphics-info-modelling.Tpo -c -o graphics-info-modelling.o graphics-info-modelling.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-modelling.cc:81: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-validate.Tpo .deps/c-interface-validate.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-navigation.o -MD -MP -MF .deps/graphics-info-navigation.Tpo -c -o graphics-info-navigation.o graphics-info-navigation.cc >mv -f .deps/geometry-graphs.Tpo .deps/geometry-graphs.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-navigation-gtk1.o -MD -MP -MF .deps/graphics-info-navigation-gtk1.Tpo -c -o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk1.cc >mv -f .deps/cmtz-interface.Tpo .deps/cmtz-interface.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-navigation-gtk2.o -MD -MP -MF .deps/graphics-info-navigation-gtk2.Tpo -c -o graphics-info-navigation-gtk2.o graphics-info-navigation-gtk2.cc >mv -f .deps/c-interface-preferences.Tpo .deps/c-interface-preferences.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-preferences.o -MD -MP -MF .deps/graphics-info-preferences.Tpo -c -o graphics-info-preferences.o graphics-info-preferences.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-navigation.cc:52: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-info.Tpo .deps/c-interface-info.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-mutate.o -MD -MP -MF .deps/graphics-info-mutate.Tpo -c -o graphics-info-mutate.o graphics-info-mutate.cc >mv -f .deps/graphics-info-navigation-gtk1.Tpo .deps/graphics-info-navigation-gtk1.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-lsq.o -MD -MP -MF .deps/graphics-info-lsq.Tpo -c -o graphics-info-lsq.o graphics-info-lsq.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-navigation-gtk2.cc:39: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-preferences.cc:28: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-lsq.cc:49: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-mutate.cc:63: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-refmac.Tpo .deps/graphics-info-refmac.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-pick.o -MD -MP -MF .deps/graphics-info-pick.Tpo -c -o graphics-info-pick.o graphics-info-pick.cc >mv -f .deps/c-interface.Tpo .deps/c-interface.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-render.o -MD -MP -MF .deps/graphics-info-render.Tpo -c -o graphics-info-render.o graphics-info-render.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-pick.cc:38: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-render.cc:32: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-defines.Tpo .deps/graphics-info-defines.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-state.o -MD -MP -MF .deps/graphics-info-state.Tpo -c -o graphics-info-state.o graphics-info-state.cc >mv -f .deps/graphics-info-navigation.Tpo .deps/graphics-info-navigation.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT graphics-info-superpose.o -MD -MP -MF .deps/graphics-info-superpose.Tpo -c -o graphics-info-superpose.o graphics-info-superpose.cc >mv -f .deps/globjects.Tpo .deps/globjects.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT gl-matrix.o -MD -MP -MF .deps/gl-matrix.Tpo -c -o gl-matrix.o gl-matrix.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-state.cc:30: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from graphics-info-superpose.cc:26: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-navigation-gtk2.Tpo .deps/graphics-info-navigation-gtk2.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT gtk-manual.o -MD -MP -MF .deps/gtk-manual.Tpo -c -o gtk-manual.o gtk-manual.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from gtk-manual.cc:32: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/c-interface-build.Tpo .deps/c-interface-build.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT gtk2-interface.o -MD -MP -MF .deps/gtk2-interface.Tpo -c -o gtk2-interface.o gtk2-interface.c >mv -f .deps/gl-matrix.Tpo .deps/gl-matrix.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c >mv -f .deps/graphics-info-lsq.Tpo .deps/graphics-info-lsq.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info.o -MD -MP -MF .deps/molecule-class-info.Tpo -c -o molecule-class-info.o molecule-class-info.cc >mv -f .deps/interface.Tpo .deps/interface.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-maps.o -MD -MP -MF .deps/molecule-class-info-maps.Tpo -c -o molecule-class-info-maps.o molecule-class-info-maps.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from molecule-class-info.cc:69: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from molecule-class-info-maps.cc:63: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-mutate.Tpo .deps/graphics-info-mutate.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-other.o -MD -MP -MF .deps/molecule-class-info-other.Tpo -c -o molecule-class-info-other.o molecule-class-info-other.cc >mv -f .deps/gtk-manual.Tpo .deps/gtk-manual.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-mutate.o -MD -MP -MF .deps/molecule-class-info-mutate.Tpo -c -o molecule-class-info-mutate.o molecule-class-info-mutate.cc >mv -f .deps/graphics-info-gui.Tpo .deps/graphics-info-gui.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-residues.o -MD -MP -MF .deps/molecule-class-info-residues.Tpo -c -o molecule-class-info-residues.o molecule-class-info-residues.cc >mv -f .deps/graphics-info-preferences.Tpo .deps/graphics-info-preferences.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-surface.o -MD -MP -MF .deps/molecule-class-info-surface.Tpo -c -o molecule-class-info-surface.o molecule-class-info-surface.cc >mv -f .deps/graphics-info-pick.Tpo .deps/graphics-info-pick.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-ncs.o -MD -MP -MF .deps/molecule-class-info-ncs.Tpo -c -o molecule-class-info-ncs.o molecule-class-info-ncs.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from molecule-class-info-mutate.cc:44: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-graphs.Tpo .deps/graphics-info-graphs.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT molecule-class-info-widget-work.o -MD -MP -MF .deps/molecule-class-info-widget-work.Tpo -c -o molecule-class-info-widget-work.o molecule-class-info-widget-work.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from molecule-class-info-surface.cc:33: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from molecule-class-info-other.cc:64: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-superpose.Tpo .deps/graphics-info-superpose.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT nsv.o -MD -MP -MF .deps/nsv.Tpo -c -o nsv.o nsv.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from molecule-class-info-ncs.cc:42: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from nsv.cc:38: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/graphics-info-modelling.Tpo .deps/graphics-info-modelling.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT pick.o -MD -MP -MF .deps/pick.Tpo -c -o pick.o pick.cc >mv -f .deps/molecule-class-info-residues.Tpo .deps/molecule-class-info-residues.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT read-phs.o -MD -MP -MF .deps/read-phs.Tpo -c -o read-phs.o read-phs.c >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from pick.cc:40: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/molecule-class-info-surface.Tpo .deps/molecule-class-info-surface.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT read-cif.o -MD -MP -MF .deps/read-cif.Tpo -c -o read-cif.o read-cif.c >mv -f .deps/read-phs.Tpo .deps/read-phs.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT rama_mousey.o -MD -MP -MF .deps/rama_mousey.Tpo -c -o rama_mousey.o rama_mousey.cc >mv -f .deps/nsv.Tpo .deps/nsv.Po >mv -f .deps/read-cif.Tpo .deps/read-cif.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT rama_plot.o -MD -MP -MF .deps/rama_plot.Tpo -c -o rama_plot.o rama_plot.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT restraints-editor.o -MD -MP -MF .deps/restraints-editor.Tpo -c -o restraints-editor.o restraints-editor.cc >mv -f .deps/molecule-class-info-widget-work.Tpo .deps/molecule-class-info-widget-work.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT support.o -MD -MP -MF .deps/support.Tpo -c -o support.o support.c >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from rama_plot.cc:79: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from restraints-editor.cc:46: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/rama_mousey.Tpo .deps/rama_mousey.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT support-gtk2-extras.o -MD -MP -MF .deps/support-gtk2-extras.Tpo -c -o support-gtk2-extras.o support-gtk2-extras.c >mv -f .deps/support.Tpo .deps/support.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT testing.o -MD -MP -MF .deps/testing.Tpo -c -o testing.o testing.cc >mv -f .deps/graphics-info-render.Tpo .deps/graphics-info-render.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT trackball.o -MD -MP -MF .deps/trackball.Tpo -c -o trackball.o trackball.c >mv -f .deps/trackball.Tpo .deps/trackball.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT sequence-view.o -MD -MP -MF .deps/sequence-view.Tpo -c -o sequence-view.o sequence-view.cc >mv -f .deps/support-gtk2-extras.Tpo .deps/support-gtk2-extras.Po >i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -MT seq-view-interface.o -MD -MP -MF .deps/seq-view-interface.Tpo -c -o seq-view-interface.o seq-view-interface.c >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from testing.cc:54: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >In file included from /usr/include/python2.6/Python.h:8:0, > from graphics-info.h:88, > from sequence-view.cc:32: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/pick.Tpo .deps/pick.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT user-mods.o -MD -MP -MF .deps/user-mods.Tpo -c -o user-mods.o user-mods.cc >mv -f .deps/seq-view-interface.Tpo .deps/seq-view-interface.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT xmap-utils.o -MD -MP -MF .deps/xmap-utils.Tpo -c -o xmap-utils.o xmap-utils.cc >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface-python.hh:29, > from user-mods.hh:15, > from user-mods.cc:9: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >mv -f .deps/xmap-utils.Tpo .deps/xmap-utils.Po >swig -o coot_wrap_python_pre_gtk2.cc -DCOOT_USE_GTK2_INTERFACE -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -I../src -shadow -python -c++ ../src/coot.i && mv coot.py coot_gtk2.py >mv -f .deps/graphics-info-state.Tpo .deps/graphics-info-state.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT density-score-by-residue.o -MD -MP -MF .deps/density-score-by-residue.Tpo -c -o density-score-by-residue.o density-score-by-residue.cc >mv -f .deps/graphics-info.Tpo .deps/graphics-info.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT fix-nomenclature.o -MD -MP -MF .deps/fix-nomenclature.Tpo -c -o fix-nomenclature.o fix-nomenclature.cc >mv -f .deps/molecule-class-info-mutate.Tpo .deps/molecule-class-info-mutate.Po >/bin/sh ../src/post-process-coot-wrap-guile.sh "/usr/bin/guile-config" gtk1 coot_wrap_guile_pre_gtk1.cc coot_wrap_guile_gtk1.cc >guile_config: /usr/bin/guile-config >guile_version: guile-config - Guile version 1.8.7 >gtk2: gtk1 >sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ -e /.libguile.h./{x;s/.*/#include <cstdio>/;G;} coot_wrap_guile_pre_gtk1.cc ..to.. coot_wrap_guile_gtk1.cc >adding gtk2 and guile ifdefs from coot_wrap_guile_pre_gtk1.cc.tmp coot_wrap_guile_gtk1.cc >/bin/sh ../src/post-process-coot-wrap-guile.sh "/usr/bin/guile-config" gtk2 coot_wrap_guile_pre_gtk2.cc coot_wrap_guile_gtk2.cc >guile_config: /usr/bin/guile-config >guile_version: guile-config - Guile version 1.8.7 >gtk2: gtk2 >sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ -e /.libguile.h./{x;s/.*/#include <cstdio>/;G;} coot_wrap_guile_pre_gtk2.cc ..to.. coot_wrap_guile_gtk2.cc >mv -f .deps/sequence-view.Tpo .deps/sequence-view.Po >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot_wrap_guile_gtk1.o -MD -MP -MF .deps/coot_wrap_guile_gtk1.Tpo -c -o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk1.cc >mv -f .deps/coot_wrap_guile_gtk1.Tpo .deps/coot_wrap_guile_gtk1.Po >adding gtk2 and guile ifdefs from coot_wrap_guile_pre_gtk2.cc.tmp coot_wrap_guile_gtk2.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot_wrap_guile_gtk2.o -MD -MP -MF .deps/coot_wrap_guile_gtk2.Tpo -c -o coot_wrap_guile_gtk2.o coot_wrap_guile_gtk2.cc >mv -f .deps/user-mods.Tpo .deps/user-mods.Po >mv -f .deps/density-score-by-residue.Tpo .deps/density-score-by-residue.Po >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -Wl,-O1 -o density-score-by-residue-real density-score-by-residue.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm >mv -f .deps/rama_plot.Tpo .deps/rama_plot.Po >mv -f .deps/fix-nomenclature.Tpo .deps/fix-nomenclature.Po >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -Wl,-O1 -o fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/libcoot-ligand.la ../db-main/libcoot-db-main.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm >In file included from /usr/include/python2.6/Python.h:8:0, > from c-interface.h:71, > from coot_wrap_guile_gtk2.cc:1324: >/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined >/usr/include/features.h:158:0: note: this is the location of the previous definition >/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined >/usr/include/features.h:160:0: note: this is the location of the previous definition >/bin/sh ../src/post-process-coot-wrap-python.sh gtk2 coot_wrap_python_pre_gtk2.cc coot_wrap_python_gtk2.cc >i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -MT coot_wrap_python_gtk2.o -MD -MP -MF .deps/coot_wrap_python_gtk2.Tpo -c -o coot_wrap_python_gtk2.o coot_wrap_python_gtk2.cc >mv -f .deps/molecule-class-info-maps.Tpo .deps/molecule-class-info-maps.Po >mv -f .deps/molecule-class-info-ncs.Tpo .deps/molecule-class-info-ncs.Po >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-AuthenticAMD---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -Wl,-O1 -o .libs/density-score-by-residue-real density-score-by-residue.o ../geometry/.libs/libcoot-geometry.so -L/usr/lib -L/usr ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz /usr/lib/libmmdb.so /usr/lib/libgsl.so -L/usr/lib/blas/threaded-atlas -lcblas /usr/lib/libatlas.so -lpthread -lm -pthread >mv -f .deps/restraints-editor.Tpo .deps/restraints-editor.Po >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-AuthenticAMD---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -Wl,-O1 -o .libs/fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/.libs/libcoot-ligand.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs/libccp4mg-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-map-utils.so ../db-main/.libs/libcoot-db-main.so ../ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so ../ccp4mg-utils/.libs/libccp4mg-utils.so ../coot-utils/.libs/libcoot-coord-extras.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /usr/lib/libgsl.so -lcblas /usr/lib/libatlas.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm -pthread >mv -f .deps/molecule-class-info.Tpo .deps/molecule-class-info.Po >mv -f .deps/testing.Tpo .deps/testing.Po >mv -f .deps/gtk2-interface.Tpo .deps/gtk2-interface.Po >mv -f .deps/molecule-class-info-other.Tpo .deps/molecule-class-info-other.Po >mv -f .deps/coot_wrap_guile_gtk2.Tpo .deps/coot_wrap_guile_gtk2.Po >mv -f .deps/coot_wrap_python_gtk2.Tpo .deps/coot_wrap_python_gtk2.Po >/bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-AuthenticAMD---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -Wl,-O1 -o coot-real main.o svn-revision.o c-inner-main.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-pisa.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-mmdb.o c-interface-mutate.o c-interface-ncs.o c-interface-nucleotides.o c-interface-python.o c-interface-preferences.o c-interface-scm.o c-interface-superpose.o c-interface-validate.o c-interface-widgets.o c-interface-waters.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o geometry-graphs.o get-residue.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-refmac.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-state.o graphics-info-superpose.o gl-matrix.o gtk-manual.o gtk2-interface.o interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o coot_wrap_python_gtk2.o ../ligand/libcoot-ligand.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../db-main/libcoot-db-main.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libccp4mg-surface.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../analysis/libcoot-analysis.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la -lguilegtk-2.0 -pthread -lguile -lltdl -Wl,-O1 -lgmp -lcrypt -lm -lltdl -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -lssm -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib/python2.6/config -lpython2.6 -lutil -Wl,--export-dynamic -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -lglade-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 >libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-AuthenticAMD---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -Wl,-O1 -o .libs/coot-real main.o svn-revision.o c-inner-main.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-pisa.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-mmdb.o c-interface-mutate.o c-interface-ncs.o c-interface-nucleotides.o c-interface-python.o c-interface-preferences.o c-interface-scm.o c-interface-superpose.o c-interface-validate.o c-interface-widgets.o c-interface-waters.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o geometry-graphs.o get-residue.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-refmac.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-state.o graphics-info-superpose.o gl-matrix.o gtk-manual.o gtk2-interface.o interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o coot_wrap_python_gtk2.o -pthread -Wl,-O1 -Wl,--export-dynamic ../ligand/.libs/libcoot-ligand.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr ../density-contour/.libs/libcoot-isosurface.so ../build/.libs/libcoot-cabuild.so ../skeleton/.libs/libcoot-skeleton.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so ../db-main/.libs/libcoot-db-main.so ../high-res/.libs/libcoot-high-res.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand/.libs/libcoot-ligand.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs/libccp4mg-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs/libcoot-coords.so ../ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so ../coot-surface/.libs/libcoot-surface.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface/.libs/libccp4mg-surface.so ../surface/.libs/libccp4mg-surface.so ../ccp4mg-utils/.libs/libccp4mg-utils.so ../coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../analysis/.libs/libcoot-analysis.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs/libcoot-utils.so ../cootaneer/.libs/libcootaneer.so ../compat/.libs/libcoot-compat.so /usr/lib/libguilegtk-2.0.so /usr/lib/libgthread-2.0.so -lrt /usr/lib/libguile.so /usr/lib/libgmp.so -lcrypt /usr/lib/libltdl.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so /usr/lib/libssm.so -L/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r1/work/ccp4-6.1.3/lib/src /usr/lib/libmmdb.so -L/usr/lib/python2.6/config -lpython2.6 -lutil /usr/lib/libgtkglext-x11-1.0.so /usr/lib/libgdkglext-x11-1.0.so -lGLU /usr/lib/libpangox-1.0.so /usr/lib/libglut.so -lGL /usr/lib/libXxf86vm.so /usr/lib/libXmu.so /usr/lib/libXt.so /usr/lib/libSM.so /usr/lib/libICE.so -luuid /usr/lib/libgnomecanvas-2.so /usr/lib/libgailutil.so /usr/lib/libXi.so /usr/lib/libXrandr.so /usr/lib/libXcursor.so /usr/lib/libXcomposite.so /usr/lib/libXext.so /usr/lib/libXdamage.so /usr/lib/libXfixes.so /usr/lib/libart_lgpl_2.so /usr/lib/libgsl.so -lcblas /usr/lib/libatlas.so -lpthread /usr/lib/libglade-2.0.so /usr/lib/libxml2.so /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so -lresolv /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libglitz.so /usr/lib/libpng12.so /usr/lib/libxcb-render-util.so /usr/lib/libxcb-render.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so -lm /usr/lib/libfontconfig.so /usr/lib/libfreetype.so -lz /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libglib-2.0.so -pthread >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/src' >Making all in data >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/data' >make[1]: Nothing to be done for `all'. >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/data' >Making all in rama-data >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/rama-data' >make[1]: Nothing to be done for `all'. >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/rama-data' >Making all in doc >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/doc' >make[1]: Nothing to be done for `all'. >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/doc' >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' >sed -e 's/#GTK2 //' ./cootrc.template > cootrc >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' >>>> Source compiled. > * Running test with following paths ... > * COOT_STANDARD_RESIDUES /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/standard-residues.pdb > * COOT_SCHEME_DIR /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme/ > * COOT_RESOURCES_FILE /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootrc > * COOT_PIXMAPS_DIR /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/pixmaps > * COOT_DATA_DIR /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6 > * COOT_PYTHON_DIR /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python > * PYTHONPATH /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python:/usr/lib/paraview-3.6 > * PYTHONHOME /usr > * CCP4_SCR /var/tmp/portage/sci-chemistry/coot-0.6/temp/coot_test >INFO:: splash_screen_pixmap_dir /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/pixmaps >WARNING:: Symmetry library not found at /usr/share/coot/syminfo.lib and environment variable SYMINFO is not set. >WARNING:: Symmetry will not be possible >INFO:: Colours file: /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/colours.def loaded >There are 118 data in /usr/share/ccp4//data/monomers/list/mon_lib_list.cif >There are 2 data in /usr/share/ccp4//data/monomers/a/ALA.cif >There are 2 data in /usr/share/ccp4//data/monomers/a/ASP.cif >There are 2 data in /usr/share/ccp4//data/monomers/a/ASN.cif >There are 2 data in /usr/share/ccp4//data/monomers/c/CYS.cif >There are 2 data in /usr/share/ccp4//data/monomers/g/GLN.cif >There are 2 data in /usr/share/ccp4//data/monomers/g/GLY.cif >There are 2 data in /usr/share/ccp4//data/monomers/g/GLU.cif >There are 2 data in /usr/share/ccp4//data/monomers/p/PHE.cif >There are 2 data in /usr/share/ccp4//data/monomers/h/HIS.cif >There are 2 data in /usr/share/ccp4//data/monomers/i/ILE.cif >There are 2 data in /usr/share/ccp4//data/monomers/l/LYS.cif >There are 2 data in /usr/share/ccp4//data/monomers/l/LEU.cif >There are 2 data in /usr/share/ccp4//data/monomers/m/MET.cif >There are 2 data in /usr/share/ccp4//data/monomers/m/MSE.cif >There are 2 data in /usr/share/ccp4//data/monomers/p/PRO.cif >There are 2 data in /usr/share/ccp4//data/monomers/a/ARG.cif >There are 2 data in /usr/share/ccp4//data/monomers/s/SER.cif >There are 2 data in /usr/share/ccp4//data/monomers/t/THR.cif >There are 2 data in /usr/share/ccp4//data/monomers/v/VAL.cif >There are 2 data in /usr/share/ccp4//data/monomers/t/TRP.cif >There are 2 data in /usr/share/ccp4//data/monomers/t/TYR.cif >There are 2 data in /usr/share/ccp4//data/monomers/p/PO4.cif >There are 2 data in /usr/share/ccp4//data/monomers/s/SO4.cif >There are 2 data in /usr/share/ccp4//data/monomers/g/GOL.cif >There are 2 data in /usr/share/ccp4//data/monomers/e/ETH.cif >There are 2 data in /usr/share/ccp4//data/monomers/c/CIT.cif >There are 2 data in /usr/share/ccp4//data/monomers/a/AR.cif >There are 2 data in /usr/share/ccp4//data/monomers/a/AD.cif >There are 2 data in /usr/share/ccp4//data/monomers/c/CR.cif >There are 2 data in /usr/share/ccp4//data/monomers/c/CD.cif >There are 2 data in /usr/share/ccp4//data/monomers/g/GR.cif >There are 2 data in /usr/share/ccp4//data/monomers/g/GD.cif >There are 2 data in /usr/share/ccp4//data/monomers/t/TD.cif >There are 2 data in /usr/share/ccp4//data/monomers/u/UR.cif >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/standard-residues.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/standard-residues.pdb has been read. >Spacegroup: P 1 >Cell: 40.631 109.18 93.243 90 90 90 >initalize graphics molecules...done. >[1m(filter-fileselection-filenames-state)[0m >[1m(get-active-map-drag-flag)[0m >[1m(use-graphics-interface-state)[0m >DEBUG:: stating pydirectory /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python >INFO:: importing coot.py from /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python/coot.py >Importing python module coot using command from coot import * >INFO:: coot.py imported >INFO loading coot python modules >Running python script /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python/coot_load_modules.py >Loading: coot_utils.py >Loading: filter.py >Loading: coot_lsq.py >Loading: shelx.py >Loading: get_ebi.py >Loading: local_code.py >Loading: hello.py >Good Morning None, Welcome to Coot. >[1m(set-display-intro-string "Good Morning None, Welcome to Coot.")[0m >Loading: mutate.py >Loading: refmac.py >Loading: libcheck.py >Loading: gap.py >Loading: fitting.py >Loading: raster3d.py >Loading: povray.py >Loading: remote_control.py >Loading: generic_objects.py >Loading: ncs.py >Loading: parse_pisa_xml.py >Loading: cns2coot.py >Loading: tips.py >Loading: americanisms.py >Loading: group_settings.py >Loading: brute_lsqman.py >INFO:: Creating directory /var/tmp/portage/sci-chemistry/coot-0.6/homedir/.coot-preferences >[1m(filter-fileselection-filenames-state)[0m >[1m(get-active-map-drag-flag)[0m >[1m(use-graphics-interface-state)[0m >Loading scheme files from /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme/ >load "filter.scm" >load "matrices.scm" >load "coot-utils.scm" >load "coot-lsq.scm" >load "shelx.scm" >load "get-ebi.scm" >WARNING: (net http client): imported module (net http message) overrides core binding `version' >load "local-code.scm" >load "hello.scm" >Good morning root. Welcome to Coot. >[1m(set-display-intro-string "Good morning root. Welcome to Coot")[0m >load "mutate.scm" >load "refmac.scm" >load "brute-lsqman.scm" >load "libcheck.scm" >load "gap.scm" >load "fitting.scm" >load "raster3d.scm" >load "povray.scm" >load "remote-control.scm" >load "generic-objects.scm" >load "fascinating-things.scm" >load "ncs.scm" >load "parse-pisa-xml.scm" >load "cns2coot.scm" >load "clear-backup.scm" >load "tips.scm" >load "americanisms.scm" >load "group-settings.scm" >[1m(set-display-lists-for-maps 0)[0m >[1m(filter-fileselection-filenames-state)[0m >[1m(get-active-map-drag-flag)[0m > > === greg-tests tests === > >Loading greg-tests/begin.grg ... >=============================================================== >==================== Testing ================================== >=============================================================== >Loaded greg-tests/begin.grg >Running 01-pdb+mtz.scm ... >Entered testcase - Post Go To Atom no molecules >DEBUG:: post_go_to_atom_window() >[1m(post-go-to-atom-window)[0m >PASS: Post Go To Atom no molecules >Entered testcase - Close bad molecule >[1m(close-molecule -2)[0m >PASS: Close bad molecule >Entered testcase - Read coordinates test >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 0 read successfully >PASS: Read coordinates test >Entered testcase - New molecule from bogus molecule >Molecule number -5 is not a valid model molecule >PASS: New molecule from bogus molecule >Entered testcase - New molecule from bogus atom selection >in new_molecule_by_atom_selection Something bad happened - No atoms selected >[1m(info-dialog "Oops, failed to create fragment. No atoms selected >Incorrect atom specifier? "//A/100"")[0m > INFO:: pre-n-molecules 1 post-n-molecules 1 >PASS: New molecule from bogus atom selection >Entered testcase - ins code change and Goto atom over an ins code break >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/ins-code-fragment-pre.pdb" 0)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/ins-code-fragment-pre.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/ins-code-fragment-pre.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 1 read successfully >[1m(set-go-to-atom-molecule 1)[0m >DEBUG:: Found chain_id A >INFO:: Creating directory coot-backup >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_ins-code-fragment-pre.pdb_Wed_May__5_09:43:26_2010_modification_0.pdb.gz >[1m(change-residue-number 1 "A" 68 "" 68 "A")[0m >DEBUG:: Found chain_id A >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_ins-code-fragment-pre.pdb_Wed_May__5_09:43:26_2010_modification_1.pdb.gz >[1m(change-residue-number 1 "A" 69 "" 68 "B")[0m >DEBUG:: Found chain_id A >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_ins-code-fragment-pre.pdb_Wed_May__5_09:43:26_2010_modification_2.pdb.gz >[1m(change-residue-number 1 "A" 67 "" 68 "")[0m >pre and post ins codes: "" "A" > pass: ("A" 68 "" " CA ") > pass: ("A" 68 "B" " CA ") > pass: ("A" 70 "" " CA ") > pass: ("A" 62 "" " CA ") > pass: ("A" 68 "B" " CA ") > pass: ("A" 68 "A" " CA ") > pass: ("A" 68 "" " CA ") > pass: ("A" 66 "" " CA ") >PASS: ins code change and Goto atom over an ins code break >Entered testcase - Read a bogus map >WARNING:: Error reading bogus.map >Read map bogus.map failed >PASS: Read a bogus map >Entered testcase - Read MTZ test >WARNING:: Can't find file bogus.mtz >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.054 seconds to read MTZ file >INFO:: 0.059 seconds to initialize map >INFO:: 0.075 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.026 seconds for contour map >INFO:: 0.219 seconds in total >PASS: Read MTZ test >Entered testcase - Map Sigma >INFO:: map sigmas 0.311501026153564 #f >PASS: Map Sigma >Entered testcase - Another Level Test >making conventional map from MTZ filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.032 seconds to read MTZ file >INFO:: 0.003 seconds to initialize map >INFO:: 0.074 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.025 seconds for contour map >INFO:: 0.139 seconds in total >[1m(make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00)[0m >[1m(another-level-from-map-molecule-number 2)[0m >PASS: Another Level Test >Entered testcase - Sharpen map from map >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz >Number of OBSERVED reflections: 17920 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 64, 96, 90) >INFO:: 0.045 seconds to read MTZ file >INFO:: 0.035 seconds to initialize map >INFO:: 0.071 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 6.26642e-11 > Map sigma: ....... 0.260405 > Map maximum: ..... 1.71787 > Map minimum: ..... -1.03389 >INFO:: 0.005 seconds for contour map >INFO:: 0.161 seconds in total >INFO:: map file type was determined to be CCP4 type >allocating space in read_ccp4_map >attempting to read CCP4 map: test-3hfl.map >closing CCP4 map: test-3hfl.map >Map statistics: mean: 6.26642e-11 st.d: 0.260405 >Map statistics: min: -1.03389, max: 1.71787 >-0.965098 9 >-0.82751 119 >-0.689922 1019 >-0.552334 4514 >-0.414746 13139 >-0.277158 28550 >-0.13957 59504 >-0.00198239 84317 >0.135606 44993 >0.273194 14815 >0.410781 9178 >0.548369 7021 >0.685957 4753 >0.823545 2717 >0.961133 1265 > 1.09872 403 > 1.23631 108 > 1.3739 34 > 1.51149 18 > 1.64907 3 > 1.78666 1 > Map mean: ........ 6.26642e-11 > Map sigma: ....... 0.260405 > Map maximum: ..... 1.71787 > Map minimum: ..... -1.03389 >PASS: Sharpen map from map >Entered testcase - Set Atom Attribute Test >[1m(set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.50)[0m >PASS: Set Atom Attribute Test >Entered testcase - Add Terminal Residue Test >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 83/90 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 6 read successfully >INFO:: Masking around 41 atoms >fitting terminal residue with rigid body refinement using 100 trials >INFO:: Fitting terminal residue with individual rigid body fitting. >INFO:: found better residue, score: 3.50214 >INFO:: found better residue, score: 3.9272 >INFO:: found better residue, score: 4.379 >INFO:: found better residue, score: 4.61148 > A 0 ALA N :: xyz = ( 49.2, 12.74, 4.454) > A 0 ALA C :: xyz = ( 50.2, 13.69, 2.416) > A 0 ALA CA :: xyz = ( 49.88, 13.9, 3.891) > A 0 ALA O :: xyz = ( 51.28, 14.01, 1.91) >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: mutating residue in add_cb_to_terminal_res >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_May__5_09:43:28_2010_modification_0.pdb.gz >[1m(add-terminal-residue 6 "A" 1 1)[0m >[1m(write-pdb-file 6 "regression-test-terminal-residue.pdb")[0m >In new_molecule_by_atom_selection has contains chain id A >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Wed_May__5_09:43:28_2010_modification_0.pdb.gz >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >PASS: Add Terminal Residue Test >Entered testcase - Select by Sphere >Symmetry available for this molecule >[1m(n-chains 8)[0m >[1m(chain_id 8 0)[0m > Sphere mol: there are 4 residues in chain "B" >[1m(resname-from-serial-number 8 "B" 0)[0m >[1m(setnum-from-serial-number 8 "B" 0)[0m >[1m(insertion-code-from-serial-number 8 "B" 0)[0m >[1m(resname-from-serial-number 8 "B" 1)[0m >[1m(setnum-from-serial-number 8 "B" 1)[0m >[1m(insertion-code-from-serial-number 8 "B" 1)[0m >[1m(resname-from-serial-number 8 "B" 2)[0m >[1m(setnum-from-serial-number 8 "B" 2)[0m >[1m(insertion-code-from-serial-number 8 "B" 2)[0m >[1m(resname-from-serial-number 8 "B" 3)[0m >[1m(setnum-from-serial-number 8 "B" 3)[0m >[1m(insertion-code-from-serial-number 8 "B" 3)[0m > Found 20 sphere atoms >PASS: Select by Sphere >Entered testcase - Test Views >[1m(go-to-view-number 0 1)[0m >PASS: Test Views >Entered testcase - Label Atoms and Delete >In new_molecule_by_atom_selection has contains chain id B >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(set-rotation-centre 31.46 21.41 14.82)[0m > N /10/B is not found in this molecule: (9) atom selection from tutorial-modern.pdb >INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:28_2010_modification_0.pdb.gz >[1m(delete-residue 9 "B" 10 "")[0m >INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:28_2010_modification_1.pdb.gz >[1m(delete-residue 9 "B" 11 "")[0m >INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:28_2010_modification_2.pdb.gz >[1m(delete-residue 9 "B" 12 "")[0m >PASS: Label Atoms and Delete >Entered testcase - Rotamer outliers >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rotamer-test-fragment.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rotamer-test-fragment.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rotamer-test-fragment.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 10 read successfully >INFO:: Reading rotamer probability tables... >primitive chis: Failure to find correct atom quads in residue atoms > quad needed: : N : : CA : : CB : : OG1: >INFO:: un altconfed rotamer with no chis [spec: "A" 16 ""] >PASS: Rotamer outliers >Entered testcase - Alt Conf Occ Sum Reset >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/res098.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/res098.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/res098.pdb has been read. >Spacegroup: P 41 21 2 >Cell: 57.374 57.374 87.384 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 11 read successfully > For atom " CE " "A" returning occ 0.699999988079071 > For atom " CE " "B" returning occ 0.200000002980232 > For atom " NZ " "A" returning occ 0.699999988079071 > For atom " NZ " "B" returning occ 0.200000002980232 >regularize: molecule 11 atom index 4 to 4 >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 3 residues selected for refined and flanking residues >created 6 bond restraints >created 6 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 13 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 15 and 15 of chain X >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >Flanking residue restraints: > 2 bond links > 6 angle links > 4 plane links >INFO:: made 18 non-bonded restraints >initial distortion_score: 8.98705 > Initial Chi Squareds >bonds: 0.149289 >angles: 0.205078 >torsions: N/A >planes: 1.32634 >non-bonded: 0 >chiral vol: 0.0264636 >rama plot: N/A >Minimum found (iteration number 46) at 6.27251 > Final Chi Squareds >bonds: 0.00360071 >angles: 0.29069 >torsions: N/A >planes: 0.653297 >non-bonded: 0 >chiral vol: 0.142241 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73509e+06 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_res098.pdb_Wed_May__5_09:43:31_2010_modification_0.pdb.gz >INFO:: replace_coords: 7 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... > For atom " CE " "A" returning occ 0.699999988079071 > For atom " CE " "B" returning occ 0.200000002980232 > For atom " NZ " "A" returning occ 0.699999988079071 > For atom " NZ " "B" returning occ 0.200000002980232 > test for closeness: 1.79999998211861 1.79999998211861 >PASS: Alt Conf Occ Sum Reset >Entered testcase - Correct occupancies after auto-fit rotamer on alt-confed residue >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 12 read successfully >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.033 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.076 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.023 seconds for contour map >INFO:: 0.139 seconds in total > 0 N :: >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:31_2010_modification_0.pdb.gz >split_residue(int atom_index, int alt_conf_split_type) returns 0 >------------ ERROR! ------------------- > moving_atoms_asc_type not known: 0 >------------ ERROR! ------------------- >INFO:: graphics_info_t::clear_up_moving_atoms... >WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection >Ignoring. >attempting to delete NULL moving_atoms_asc.mol >ignoring >clearing intermediate object... > ==== fitting residue 93 of chain A to map number 13 ====== >DEBUG:: found residue >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:31_2010_modification_1.pdb.gz >INFO:: replace_coords: 8 atoms updated. >Fitting score for best rotamer: 11.6862 >[1m(auto-fit-best-rotamer 93 "A" "" "A" 12 13 1 0.01)[0m >PASS: Correct occupancies after auto-fit rotamer on alt-confed residue >Entered testcase - Pepflip flips the correct alt confed atoms >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-pepflip-test.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-pepflip-test.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-pepflip-test.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 14 read successfully >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_alt-conf-pepflip-test.pdb_Wed_May__5_09:43:31_2010_modification_0.pdb.gz >flipped 65 A >PASS: Pepflip flips the correct alt confed atoms >Entered testcase - Correction of CISPEP test >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 15 read successfully >[1m(go-to-view-number 1 1)[0m >omega: 1 12.7704 degrees >INFO This is a CIS peptide - making it TRANS >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_0.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_1.pdb.gz >INFO:: Removing CIS peptide from PDB header: A 11 A 12 >flipped 11 A >INFO:: mutate 11 A to a GLY >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_2.pdb.gz >[1m(mutate 11 "A" 15 "GLY")[0m >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 4 residues selected for refined and flanking residues >created 10 bond restraints >created 10 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 21 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A >Link restraints: > 1 bond links > 3 angle links > 2 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >Flanking residue restraints: > 2 bond links > 6 angle links > 4 plane links >INFO:: made 62 non-bonded restraints >initial distortion_score: 565.206 > Initial Chi Squareds >bonds: 237.864 >angles: 54.5685 >torsions: N/A >planes: 7.86923 >non-bonded: 1.84407 >chiral vol: 9.26976 >rama plot: N/A >Minimum found (iteration number 5) at -4818.58 > Final Chi Squareds >bonds: 1.04813 >angles: 0.764662 >torsions: N/A >planes: 5.75558 >non-bonded: 0 >chiral vol: 0.00532023 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73509e+06 >Refinement elapsed time: 0.039 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_3.pdb.gz >INFO:: replace_coords: 11 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >INFO:: mutate 11 A to a LEU >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_4.pdb.gz >[1m(mutate 11 "A" 15 "LEU")[0m > ==== fitting residue 11 of chain A to map number 2 ====== >DEBUG:: found residue >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_5.pdb.gz >INFO:: replace_coords: 8 atoms updated. >Fitting score for best rotamer: 8.41927 >[1m(auto-fit-best-rotamer 11 "" "" "A" 15 2 1 1.00)[0m >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 4 residues selected for refined and flanking residues >created 14 bond restraints >created 16 angle restraints >created 0 plane restraints >created 2 chiral vol restraints >created 32 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A >Link restraints: > 1 bond links > 3 angle links > 2 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >Flanking residue restraints: > 2 bond links > 6 angle links > 4 plane links >INFO:: made 142 non-bonded restraints >initial distortion_score: -6001 > Initial Chi Squareds >bonds: 1.01582 >angles: 1.1948 >torsions: N/A >planes: 9.04355 >non-bonded: 0 >chiral vol: 0.00821338 >rama plot: N/A >Minimum found (iteration number 41) at -6078.09 > Final Chi Squareds >bonds: 1.16144 >angles: 0.603897 >torsions: N/A >planes: 5.9383 >non-bonded: 0 >chiral vol: 0.296976 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73509e+06 >Refinement elapsed time: 0.04 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Wed_May__5_09:43:31_2010_modification_6.pdb.gz >INFO:: replace_coords: 15 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >------------ ERROR! ------------------- > moving_atoms_asc_type not known: 0 >------------ ERROR! ------------------- >INFO:: graphics_info_t::clear_up_moving_atoms... >WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection >Ignoring. >attempting to delete NULL moving_atoms_asc.mol >ignoring >clearing intermediate object... >[1m(write-pdb-file 15 "tmp-fixed-cis.pdb")[0m >/bin/grep >CISPEPs: "3" >PASS: Correction of CISPEP test >Entered testcase - Refine Zone with Alt conf >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 16 read successfully >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.033 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.077 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.026 seconds for contour map >INFO:: 0.143 seconds in total >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 3 residues selected for refined and flanking residues >created 5 bond restraints >created 4 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 10 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 72 and 72 of chain B >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) >Flanking residue restraints: > 2 bond links > 6 angle links > 4 plane links >INFO:: made 12 non-bonded restraints >initial distortion_score: -2784.62 > Initial Chi Squareds >bonds: 1.62991 >angles: 1.14414 >torsions: N/A >planes: 0.831346 >non-bonded: 0 >chiral vol: 2.13751 >rama plot: N/A >Minimum found (iteration number 9) at -3085.72 > Final Chi Squareds >bonds: 2.46216 >angles: 3.87868 >torsions: N/A >planes: 3.80214 >non-bonded: 0.00908405 >chiral vol: 4.58486 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73509e+06 >Refinement elapsed time: 0.017 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:32_2010_modification_0.pdb.gz >INFO:: replace_coords: 6 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... > refined moved: d=0.595366857982687 >PASS: Refine Zone with Alt conf >Entered testcase - Sphere Refine >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 83/90 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 18 read successfully > 0 N :: >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-add-terminal-1-test.pdb_Wed_May__5_09:43:32_2010_modification_0.pdb.gz >split_residue(int atom_index, int alt_conf_split_type) returns 0 >[1m(set-go-to-atom-molecule 18)[0m >imol: 18 residues: (("A" 93 "") ("A" 5 "") ("A" 3 "") ("A" 92 "")) > DEUBG:: There are 56 atoms total (including flankers) >created 20 bond restraints >created 23 angle restraints >created 0 plane restraints >created 4 chiral vol restraints >created 47 restraints > >Link restraints: > 0 bond links > 0 angle links > 0 plane links >Flanking residue restraints: > 5 bond links > 15 angle links > 10 plane links >INFO:: made 364 non-bonded restraints >initial distortion_score: -10877.8 > Initial Chi Squareds >bonds: 1.73263 >angles: 0.794308 >torsions: N/A >planes: 1.15557 >non-bonded: 0 >chiral vol: 0.447536 >rama plot: N/A >Minimum found (iteration number 23) at -11061.5 > Final Chi Squareds >bonds: 1.38576 >angles: 0.419266 >torsions: N/A >planes: 0.934936 >non-bonded: 0 >chiral vol: 0.12692 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73509e+06 >PASS: Sphere Refine >Entered testcase - Rigid Body Refine Alt Conf Waters >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-waters.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-waters.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-waters.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 19 read successfully >masking....masking done >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_alt-conf-waters.pdb_Wed_May__5_09:43:33_2010_modification_0.pdb.gz >INFO:: replace_coords: 1 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >WARNING:: refine_zone: Can't get index for resno1: 2 >------------ ERROR! ------------------- > moving_atoms_asc_type not known: 0 >------------ ERROR! ------------------- >INFO:: graphics_info_t::clear_up_moving_atoms... >WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection >Ignoring. >attempting to delete NULL moving_atoms_asc.mol >ignoring >clearing intermediate object... >PASS: Rigid Body Refine Alt Conf Waters >Entered testcase - Setting multiple atom attributes >PASS: Setting multiple atom attributes >Entered testcase - Tweak Alt Confs on Active Residue >[1m(update-go-to-atom-window-on-other-molecule-chosen)[0m >[1m(set-go-to-atom-molecule 0)[0m >[1m(set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B")[0m >PASS: Tweak Alt Confs on Active Residue >Entered testcase - Backrub rotamer >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb" 0)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 20 read successfully >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 20)[0m >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_backrub-fragment.pdb_Wed_May__5_09:43:33_2010_modification_0.pdb.gz >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_backrub-fragment.pdb_Wed_May__5_09:43:33_2010_modification_1.pdb.gz >INFO:: replace_coords: 14 atoms updated. >PASS: Backrub rotamer >Entered testcase - Libcif horne >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/coords-B3A.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/coords-B3A.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/coords-B3A.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 22 read successfully >regularize: molecule 22 atom index 0 to 0 >DEUBG:: check_dictionary_for_residues - problem... >WARNING:: Failed to find restraints for :B3A: >INFO:: 1 residues selected for refined and flanking residues >created 0 bond restraints >created 0 angle restraints >created 0 plane restraints >created 0 chiral vol restraints >created 0 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >No restraints: regularize() >------------ ERROR! ------------------- > moving_atoms_asc_type not known: 0 >------------ ERROR! ------------------- >INFO:: graphics_info_t::clear_up_moving_atoms... >WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection >Ignoring. >attempting to delete NULL moving_atoms_asc.mol >ignoring >clearing intermediate object... >WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/lib-B3A.cif not found. >init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/lib-B3A.cif had no bond restraints >regularize: molecule 22 atom index 0 to 0 >DEUBG:: check_dictionary_for_residues - problem... >WARNING:: Failed to find restraints for :B3A: >INFO:: 1 residues selected for refined and flanking residues >created 0 bond restraints >created 0 angle restraints >created 0 plane restraints >created 0 chiral vol restraints >created 0 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >No restraints: regularize() >------------ ERROR! ------------------- > moving_atoms_asc_type not known: 0 >------------ ERROR! ------------------- >INFO:: graphics_info_t::clear_up_moving_atoms... >WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection >Ignoring. >attempting to delete NULL moving_atoms_asc.mol >ignoring >clearing intermediate object... > > > > >There are 3 data in /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/lib-both.cif >Read 28 atoms/links in restraints from /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/lib-both.cif >regularize: molecule 22 atom index 0 to 0 >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >created 5 bond restraints >created 5 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 11 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 10 non-bonded restraints >initial distortion_score: 0.00371314 > Initial Chi Squareds >bonds: 0.00061433 >angles: 0.000126593 >torsions: N/A >planes: N/A >non-bonded: 0 >chiral vol: 8.51661e-06 >rama plot: N/A >Minimum found (iteration number 6) at 3.86343e-05 > Final Chi Squareds >bonds: 1.20485e-07 >angles: 7.25441e-06 >torsions: N/A >planes: N/A >non-bonded: 0 >chiral vol: 1.75988e-06 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73509e+06 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_coords-B3A.pdb_Wed_May__5_09:43:33_2010_modification_0.pdb.gz >INFO:: replace_coords: 6 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >PASS: Libcif horne >Entered testcase - Refmac Parameters Storage >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.033 seconds to read MTZ file >INFO:: 0.003 seconds to initialize map >INFO:: 0.074 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.023 seconds for contour map >INFO:: 0.138 seconds in total >INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. >PASS: Refmac Parameters Storage >Entered testcase - OXT is added before TER record - add only one >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/test-TER-OXT.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/test-TER-OXT.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/test-TER-OXT.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 24 read successfully >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_test-TER-OXT.pdb_Wed_May__5_09:43:34_2010_modification_0.pdb.gz >Added OXT at 1/A/14/ASP/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45 >[1m(add-OXT-to-residue 24 14 "" "A")[0m >WARNING:: This residue already has an OXT - aborting >[1m(add-OXT-to-residue 24 14 "" "A")[0m >[1m(write-pdb-file 24 "test-TER-OXT-added.pdb")[0m >found TER "TER 25 ASP A 14 " >PASS: OXT is added before TER record - add only one >Entered testcase - The position of the oxygen after a mutation >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/val.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/val.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/val.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 25 read successfully >INFO:: mutate 3 C to a HIS >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_val.pdb_Wed_May__5_09:43:34_2010_modification_0.pdb.gz >[1m(mutate 3 "C" 25 "HIS")[0m >[1m(write-pdb-file 25 "his.pdb")[0m >PASS: The position of the oxygen after a mutation >Entered testcase - Deleting (non-existing) Alt conf and Go To Atom [JED] >failed to delete residue atoms A 88 :A: >[1m(delete-residue-with-altconf 0 "A" 88 "" "A")[0m >PASS: Deleting (non-existing) Alt conf and Go To Atom [JED] >Entered testcase - Mask and difference map >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.033 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.075 seconds for FFT >INFO:: 0.006 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.025 seconds for contour map >INFO:: 0.141 seconds in total >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 2.2 >INFO grid sampling...Nuvw = ( 160, 192, 96) >INFO:: 0.032 seconds to read MTZ file >INFO:: 0.187 seconds to initialize map >INFO:: 0.176 seconds for FFT >INFO:: 0.011 seconds for statistics > Map mean: ........ 1.19275e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 3.05176 > Map minimum: ..... -0.921659 >INFO:: 0.062 seconds for contour map >INFO:: 0.468 seconds in total >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 0)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 28 read successfully >INFO:: Masking around 64 atoms >Map statistics: mean: -0.00140323 st.d: 0.305597 >Map statistics: min: -0.875045, max: 2.97757 >-0.77873 55 >-0.586099 2468 >-0.393468 24912 >-0.200837 59810 >-0.00820671 81565 >0.184424 31729 >0.377055 10140 >0.569685 6763 >0.762316 4842 >0.954947 3073 > 1.14758 1603 > 1.34021 726 > 1.53284 283 > 1.72547 93 > 1.9181 24 > 2.11073 3 > 2.30336 5 > 2.49599 1 > 2.68862 0 > 2.88125 1 > 3.07389 0 >[1m(atom-info-string 28 "A" 20 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 21 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 22 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 23 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 24 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 25 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 26 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 27 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 28 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 29 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 30 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 1 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 2 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 3 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 4 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 5 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 6 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 7 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 8 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 9 "" " CA " "")[0m >[1m(atom-info-string 28 "A" 10 "" " CA " "")[0m >high-values: (0.923012852668762 0.928160607814789 0.963148534297943 0.588746070861816 0.692066550254822 0.7519770860672 0.68085777759552 0.954908907413483 1.00084161758423 0.981854677200317 0.726146519184113) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) >Map statistics: mean: -0.00140318 st.d: 0.0601239 >Map statistics: min: -2.78832, max: 0.730463 >-2.70035 2 >-2.52441 2 >-2.34847 2 >-2.17253 1 >-1.99659 3 >-1.82065 2 >-1.64471 8 >-1.46877 10 >-1.29283 37 > -1.1169 76 >-0.940957 122 >-0.765018 193 >-0.589079 261 >-0.41314 329 >-0.237201 473 >-0.0612622 224025 >0.114677 1297 >0.290616 919 >0.466554 308 >0.642493 26 >0.818432 0 >diff-high-values: (0.00255923601798713 0.00100333080627024 0.00106658169534057 -0.00237780530005693 0.00169643643312156 7.11918575689197e-4 0.00212939316406846 0.00194922112859786 0.00229494529776275 6.56027521472424e-4 0.00835369620472193) diff-low-values: (-0.887997150421143 -0.79390150308609 -1.18933141231537 -1.06666219234467 -0.988452911376953 -0.759092688560486 -0.748683929443359 -0.650666296482086 -0.90451967716217 -0.545242130756378) >PASS: Mask and difference map >Entered testcase - Simple Averaged maps >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.033 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.074 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.026 seconds for contour map >INFO:: 0.14 seconds in total >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 2.5 >INFO grid sampling...Nuvw = ( 180, 216, 108) >INFO:: 0.034 seconds to read MTZ file >INFO:: 0.264 seconds to initialize map >INFO:: 0.252 seconds for FFT >INFO:: 0.014 seconds for statistics > Map mean: ........ 1.23372e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 3.07133 > Map minimum: ..... -0.877519 >INFO:: 0.081 seconds for contour map >INFO:: 0.645 seconds in total >Map statistics: mean: -4.27604e-07 st.d: 0.311072 >Map statistics: min: -0.873369, max: 2.97503 >-0.777159 58 >-0.584739 2569 >-0.392319 25676 > -0.1999 61199 >-0.00747969 77803 > 0.18494 32128 > 0.37736 10498 > 0.56978 7060 > 0.7622 5057 >0.954619 3192 > 1.14704 1668 > 1.33946 756 > 1.53188 288 > 1.7243 102 > 1.91672 25 > 2.10914 4 > 2.30156 7 > 2.49398 3 > 2.6864 1 > 2.87882 1 > 3.07124 1 >Map statistics: mean: 4.28809e-07 st.d: 0.00106883 >Map statistics: min: -0.00685637, max: 0.0119245 >-0.00638685 26 >-0.0054478 84 >-0.00450876 335 >-0.00356971 1277 >-0.00263067 4286 >-0.00169163 14039 >-0.000752584 59649 >0.00018646 105525 >0.0011255 30403 >0.00206455 7562 >0.00300359 2850 >0.00394263 1180 >0.00488168 486 >0.00582072 253 >0.00675977 93 >0.00769881 28 >0.00863785 13 >0.0095769 4 >0.0105159 2 >0.011455 1 >0.012394 0 > INFO:: map sigmas: normal 0.311072051525116 and diff-map: 0.00106883200351149 >PASS: Simple Averaged maps >Entered testcase - Make a glycosidic linkage >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/multi-carbo-coot-2.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/multi-carbo-coot-2.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/multi-carbo-coot-2.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 35 read successfully >bond-length: 2.97694066606539: >regularize: molecule 35 atom index 0 to 20 >There are 2 data in /usr/share/ccp4//data/monomers/f/FUC-A-L.cif >There are 2 data in /usr/share/ccp4//data/monomers/n/NAG-B-D.cif >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 2 residues selected for refined and flanking residues >created 46 bond restraints >created 71 angle restraints >created 1 plane restraints >created 8 chiral vol restraints >created 126 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A >INFO:: glycosidic_linkage type :BETA1-4: >INFO:: No chem link for groups L-pyranose D-pyranose and comp_ids FUC NAG >Link restraints: > 1 bond links > 3 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 1560 non-bonded restraints >initial distortion_score: 6392.77 > Initial Chi Squareds >bonds: 127.526 >angles: 4.95566 >torsions: N/A >planes: 0.00816956 >non-bonded: 0.0150013 >chiral vol: 1.112 >rama plot: N/A >Minimum found (iteration number 201) at 245.949 > Final Chi Squareds >bonds: 1.72287 >angles: 1.79444 >torsions: N/A >planes: 0.000635488 >non-bonded: 0.0149043 >chiral vol: 1.11671 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_multi-carbo-coot-2.pdb_Wed_May__5_09:43:45_2010_modification_0.pdb.gz >INFO:: replace_coords: 46 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >bond-length: 1.44007558894186: >PASS: Make a glycosidic linkage >Entered testcase - Test for flying hydrogens on undo >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-VAL.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-VAL.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-VAL.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 36 read successfully >regularize: molecule 36 atom index 0 to 0 >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >created 14 bond restraints >created 25 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 40 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 132 non-bonded restraints >initial distortion_score: 35.0317 > Initial Chi Squareds >bonds: 0.268606 >angles: 0.0269163 >torsions: N/A >planes: N/A >non-bonded: 0.230261 >chiral vol: 0.20393 >rama plot: N/A >Minimum found (iteration number 2) at 0.24709 > Final Chi Squareds >bonds: 0.00015685 >angles: 0.00898205 >torsions: N/A >planes: N/A >non-bonded: 0 >chiral vol: 0.0203434 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_monomer-VAL.pdb_Wed_May__5_09:43:45_2010_modification_0.pdb.gz >INFO:: replace_coords: 15 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >INFO:: undo molecule number set to: 36 >[1m(set-undo-molecule 36)[0m >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_monomer-VAL.pdb_Wed_May__5_09:43:45_2010_modification_1.pdb.gz >restoring from backup 2 2 >Reading coordinate file: coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_monomer-VAL.pdb_Wed_May__5_09:43:45_2010_modification_0.pdb.gz > PDB file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_monomer-VAL.pdb_Wed_May__5_09:43:45_2010_modification_0.pdb.gz has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 >[1m(apply-undo)[0m >regularize: molecule 36 atom index 0 to 0 >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >created 14 bond restraints >created 25 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 40 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 132 non-bonded restraints >initial distortion_score: 35.0317 > Initial Chi Squareds >bonds: 0.268606 >angles: 0.0269163 >torsions: N/A >planes: N/A >non-bonded: 0.230261 >chiral vol: 0.20393 >rama plot: N/A >Minimum found (iteration number 2) at 0.24709 > Final Chi Squareds >bonds: 0.00015685 >angles: 0.00898205 >torsions: N/A >planes: N/A >non-bonded: 0 >chiral vol: 0.0203434 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_monomer-VAL.pdb_Wed_May__5_09:43:45_2010_modification_0.pdb.gz >INFO:: replace_coords: 15 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >PASS: Test for flying hydrogens on undo >Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3ins-6B-3.0.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3ins-6B-3.0.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3ins-6B-3.0.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 37 read successfully >regularize: molecule 37 atom index 0 to 0 >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >Unknown element : D: >created 16 bond restraints >created 28 angle restraints >created 0 plane restraints >created 1 chiral vol restraints >created 45 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 6 and 6 of chain B >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 254 non-bonded restraints >initial distortion_score: 20907.8 > Initial Chi Squareds >bonds: 31.4514 >angles: 12.6131 >torsions: N/A >planes: N/A >non-bonded: 78.9403 >chiral vol: 0.567548 >rama plot: N/A >Minimum found (iteration number 2) at 0.252135 > Final Chi Squareds >bonds: 0.000109444 >angles: 0.00824919 >torsions: N/A >planes: N/A >non-bonded: 5.49746e-08 >chiral vol: 0.0193928 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_3ins-6B-3.0.pdb_Wed_May__5_09:43:46_2010_modification_0.pdb.gz >INFO:: replace_coords: 19 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >PASS: Test for mangling of hydrogen names from a PDB v 3.0 >Entered testcase - update monomer restraints >In new_molecule_by_atom_selection has contains chain id A >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >created 11 bond restraints >created 15 angle restraints >created 1 plane restraints >created 1 chiral vol restraints >created 28 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 78 non-bonded restraints >initial distortion_score: -1120.52 > Initial Chi Squareds >bonds: 1.16837 >angles: 0.718389 >torsions: N/A >planes: 9.33775 >non-bonded: 40.0438 >chiral vol: 0.995302 >rama plot: N/A >Minimum found (iteration number 42) at -4202.57 > Final Chi Squareds >bonds: 5.00836 >angles: 0.722753 >torsions: N/A >planes: 0.917354 >non-bonded: 0.0787007 >chiral vol: 0.995449 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >Refinement elapsed time: 0.025 >INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:46_2010_modification_0.pdb.gz >INFO:: replace_coords: 12 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... > Bond-length: 2.26496023826543: >pass intermediate 2.8 tolerance test >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >created 12 bond restraints >created 15 angle restraints >created 1 plane restraints >created 1 chiral vol restraints >created 29 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 74 non-bonded restraints >initial distortion_score: -3037.33 > Initial Chi Squareds >bonds: 102.206 >angles: 0.722753 >torsions: N/A >planes: 0.917354 >non-bonded: 0 >chiral vol: 0.995449 >rama plot: N/A >Minimum found (iteration number 55) at -4306.6 > Final Chi Squareds >bonds: 1.22289 >angles: 0.808266 >torsions: N/A >planes: 2.56059 >non-bonded: 0 >chiral vol: 0.99558 >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >Refinement elapsed time: 0.025 >INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:46_2010_modification_1.pdb.gz >INFO:: replace_coords: 12 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... > OK plane atom " CB " > Bond-length: 1.53219260748336: >PASS: update monomer restraints >Entered testcase - Refinement OK with zero bond esd >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 39 read successfully >There are 2 data in /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_ACT.cif >Read 7 atoms/links in restraints from /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_ACT.cif >DEBUG:: check_dictionary_for_residues returns OK! >INFO:: 1 residues selected for refined and flanking residues >created 6 bond restraints >created 9 angle restraints >created 1 plane restraints >created 0 chiral vol restraints >created 15 restraints > >INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A >Link restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) >INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) >Flanking residue restraints: > 0 bond links > 0 angle links > 0 plane links >INFO:: made 0 non-bonded restraints >initial distortion_score: 108.409 > Initial Chi Squareds >bonds: 0.00014374 >angles: 4.27673e-05 >torsions: N/A >planes: 0 >non-bonded: N/A >chiral vol: N/A >rama plot: N/A >Minimum found (iteration number 64) at -1093.91 > Final Chi Squareds >bonds: 0.236262 >angles: 0.647995 >torsions: N/A >planes: 0.000251282 >non-bonded: N/A >chiral vol: N/A >rama plot: N/A > SUCCESS > TIME:: (dragged refinement): 1.73511e+06 >Refinement elapsed time: 0.08 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_monomer-ACT.pdb_Wed_May__5_09:43:46_2010_modification_0.pdb.gz >INFO:: replace_coords: 7 atoms updated. >INFO:: graphics_info_t::clear_up_moving_atoms... >clearing intermediate object... >PASS: Refinement OK with zero bond esd >Entered testcase - Change Chain IDs and Chain Sorting >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 40 read successfully >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_0.pdb.gz >istat: ; 1 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_1.pdb.gz >INFO:: Removing CIS peptide from PDB header: A 26 A 27 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_2.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_3.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_4.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_5.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_6.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_7.pdb.gz >[1m(n-chains 40)[0m >[1m(chain_id 40 0)[0m >[1m(chain_id 40 1)[0m >[1m(chain_id 40 2)[0m >[1m(chain_id 40 3)[0m >[1m(chain_id 40 4)[0m >[1m(chain_id 40 5)[0m >[1m(chain_id 40 6)[0m >[1m(chain_id 40 7)[0m >[1m(chain_id 40 8)[0m >PASS: Change Chain IDs and Chain Sorting >Entered testcase - Replace Fragment >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 0)[0m >In new_molecule_by_atom_selection has contains chain id A >In new_molecule_by_atom_selection has contains chain id B >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_0.pdb.gz >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:47_2010_modification_0.pdb.gz >INFO:: replace_coords: 1465 atoms updated. >[1m(replace-fragement 41 "//A70-80")[0m >distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) >PASS: Replace Fragment >Entered testcase - Residues in Region of Residue >found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) >found 0 neighbours () >PASS: Residues in Region of Residue >Entered testcase - Residues in region of a point >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 43 read successfully >PASS: Residues in region of a point >Entered testcase - Empty molecule on type selection >in new_molecule_by_residue_type_selection Something bad happened - No residues selected >[1m(info-dialog "Oops, failed to select residue type. No residues selected >Residue "TRP" does not exist in molecule 0!?")[0m >in new_molecule_by_residue_type_selection Something bad happened - No residues selected >[1m(info-dialog "Oops, failed to select residue type. No residues selected >Residue "TRP" does not exist in molecule 0!?")[0m >PASS: Empty molecule on type selection >Entered testcase - Set Rotamer >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:48_2010_modification_0.pdb.gz >oops! in rotamer::GetResidue() No tree in restraint >oops! in rotamer::GetResidue() No tree in restraint >PASS: Set Rotamer >Entered testcase - Rotamer names and scores are correct >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 44 read successfully >[1m(backup-state 44)[0m >[1m(turn-off-backup 44)[0m >[1m(rotamer-score 44 "A" 28 "")[0m > Rotamer 0 : "m-85" 100.0 >[1m(rotamer-score 44 "A" 28 "")[0m > Rotamer 1 : "t80" 90.1668395996094 >[1m(rotamer-score 44 "A" 28 "")[0m > Rotamer 2 : "p90" 50.7077865600586 >[1m(rotamer-score 44 "A" 28 "")[0m > Rotamer 3 : "m -30 " 21.4231548309326 >[1m(rotamer-score 44 "A" 28 "")[0m > Rotamer 4 : "m -30 " 21.4231548309326 >[1m(turn-on-backup 44)[0m >PASS: Rotamer names and scores are correct >Entered testcase - Align and mutate a model with deletions >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnase-A-needs-an-insertion.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnase-A-needs-an-insertion.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 50/87 >Molecule 45 read successfully >INFO:: aligning to mol number 45chain: A > > >------------------------------------------------- > chain A >------------------------------------------------- > > >INFO:: input model sequence:GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID >INFO:: input target sequence:DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID >INFO:: align with gap penalty: -3 and extension penalty: -0.4 >> /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnase-A-needs-an-insertion.pdb >---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID >> target seq: >DVSGTVCLSALPPEATDTLNLIAS-DGPFPYSQ-DGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID >INFO:: alignment score 151 >There are 8 single_insertions >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_rnase-A-needs-an-insertion.pdb_Wed_May__5_09:43:49_2010_modification_0.pdb.gz >INFO:: Removing CIS peptide from PDB header: A 26 A 27 >The alignment resulted in the following > Insertions (coalesced): > from 1 to 4 ASP VAL SER > from 11 to 14 LEU PRO PRO > from 62 to 64 PRO GLY > Insertions (singles): > [spec: "A" 1 ""] -> ASP > [spec: "A" 2 ""] -> VAL > [spec: "A" 3 ""] -> SER > [spec: "A" 11 ""] -> LEU > [spec: "A" 12 ""] -> PRO > [spec: "A" 13 ""] -> PRO > [spec: "A" 62 ""] -> PRO > [spec: "A" 63 ""] -> GLY > Deletions: > [spec: "A" 25 ""] > [spec: "A" 34 ""] > Mutations: > [spec: "A" 24 ""] -> SER > [spec: "A" 33 ""] -> GLN >INFO:: mutate 24 A to a SER >INFO:: mutate 33 A to a GLN >apply resno updates... >Applied 3 insertions >Applied 2 mutations >Applied 2 deletions >[1m(write-pdb-file 45 "mutated.pdb")[0m >::::: (45 "A" 1 "") #f #f >::::: (45 "A" 4 "") #t #t >::::: (45 "A" 59 "") #t #t >::::: (45 "A" 60 "") #f #f >::::: (45 "A" 61 "") #f #f >::::: (45 "A" 92 "") #t #t >::::: (45 "A" 94 "") #f #f >PASS: Align and mutate a model with deletions >Entered testcase - Autofit Rotamer on Residues with Insertion codes >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb3hfl.ent" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb3hfl.ent > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb3hfl.ent has been read. >No Spacegroup found for this PDB file >Cell: 54.79 74.82 78.95 90 101.82 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: NCS chain comparison 15/212 >INFO:: NCS chain comparison 7/212 >INFO:: NCS chain comparison 10/215 >Molecule 46 read successfully >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz >Number of OBSERVED reflections: 17920 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 64, 96, 90) >INFO:: 0.031 seconds to read MTZ file >INFO:: 0.003 seconds to initialize map >INFO:: 0.062 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 6.26642e-11 > Map sigma: ....... 0.260405 > Map maximum: ..... 1.71787 > Map minimum: ..... -1.03389 >INFO:: 0.011 seconds for contour map >INFO:: 0.112 seconds in total > ==== fitting residue 52A of chain H to map number 47 ====== >DEBUG:: found residue >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb3hfl.ent_Wed_May__5_09:43:50_2010_modification_0.pdb.gz >INFO:: replace_coords: 7 atoms updated. >Fitting score for best rotamer: 5.82781 >[1m(auto-fit-best-rotamer 52 "" "A" "H" 46 47 0 0.00)[0m >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb3hfl.ent_Wed_May__5_09:43:50_2010_modification_1.pdb.gz >PASS: Autofit Rotamer on Residues with Insertion codes >Entered testcase - RNA base has correct residue type after mutation >INFO:: 5 matched atoms had: > mean devi: 0 > rms devi: 0 > max devi: 0 > min devi: 0 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.0120681 > rms devi: 0.0134464 > max devi: 0.0214179 > min devi: 0.00385596 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.270216 > rms devi: 0.335002 > max devi: 0.536002 > min devi: 0.08463 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >INFO:: 5 matched atoms had: > mean devi: 0.26738 > rms devi: 0.322791 > max devi: 0.495136 > min devi: 0.112289 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 0.270247 > rms devi: 0.335033 > max devi: 0.536044 > min devi: 0.0847029 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >INFO:: 5 matched atoms had: > mean devi: 0.267411 > rms devi: 0.322823 > max devi: 0.495177 > min devi: 0.112221 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 0.011982 > rms devi: 0.013349 > max devi: 0.0212578 > min devi: 0.0038732 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.000242576 > rms devi: 0.000242751 > max devi: 0.000256671 > min devi: 0.000231275 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.270185 > rms devi: 0.334971 > max devi: 0.535961 > min devi: 0.0845571 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >INFO:: 5 matched atoms had: > mean devi: 0.267349 > rms devi: 0.322759 > max devi: 0.495094 > min devi: 0.112357 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 6.9313e-05 > rms devi: 6.93629e-05 > max devi: 7.33402e-05 > min devi: 6.60841e-05 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.0120334 > rms devi: 0.0134072 > max devi: 0.0213538 > min devi: 0.00386188 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.000138622 > rms devi: 0.000138721 > max devi: 0.000146676 > min devi: 0.000132164 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.011999 > rms devi: 0.0133684 > max devi: 0.0212898 > min devi: 0.0038691 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.267426 > rms devi: 0.322839 > max devi: 0.495197 > min devi: 0.112187 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 0.270294 > rms devi: 0.335079 > max devi: 0.536106 > min devi: 0.0848122 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_May__5_09:43:50_2010_modification_0.pdb.gz >[1m(ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")[0m >INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_May__5_09:43:50_2010_modification_1.pdb.gz >INFO:: 5 matched atoms had: > mean devi: 0.269035 > rms devi: 0.337196 > max devi: 0.547544 > min devi: 0.0817551 > mutated base to type "Cr" >PASS: RNA base has correct residue type after mutation >Entered testcase - DNA bases are the correct residue type after mutation >INFO:: 5 matched atoms had: > mean devi: 0.00589883 > rms devi: 0.00670957 > max devi: 0.0101325 > min devi: 0.00258111 >request std_res of type Gd and got Gd >coot::util::mutate_base Gd with std Gd >INFO:: 5 matched atoms had: > mean devi: 0.00725623 > rms devi: 0.00778801 > max devi: 0.0125644 > min devi: 0.00456024 >request std_res of type Ad and got Ad >coot::util::mutate_base Ad with std Ad >INFO:: 5 matched atoms had: > mean devi: 0.271793 > rms devi: 0.336384 > max devi: 0.533839 > min devi: 0.0878288 >request std_res of type Cd and got Cd >coot::util::mutate_base Cd with std Cd >INFO:: 5 matched atoms had: > mean devi: 0.26776 > rms devi: 0.326512 > max devi: 0.505569 > min devi: 0.10459 >request std_res of type Td and got Td >coot::util::mutate_base Td with std Td >INFO:: 5 matched atoms had: > mean devi: 0.271823 > rms devi: 0.336416 > max devi: 0.53388 > min devi: 0.0879009 >request std_res of type Cd and got Cd >coot::util::mutate_base Cd with std Cd >INFO:: 5 matched atoms had: > mean devi: 0.267791 > rms devi: 0.326544 > max devi: 0.505617 > min devi: 0.104522 >request std_res of type Td and got Td >coot::util::mutate_base Td with std Td >INFO:: 5 matched atoms had: > mean devi: 0.00717866 > rms devi: 0.00770023 > max devi: 0.0124098 > min devi: 0.00457508 >request std_res of type Ad and got Ad >coot::util::mutate_base Ad with std Ad >INFO:: 5 matched atoms had: > mean devi: 0.00574436 > rms devi: 0.00657052 > max devi: 0.0099594 > min devi: 0.0024248 >request std_res of type Gd and got Gd >coot::util::mutate_base Gd with std Gd >INFO:: 5 matched atoms had: > mean devi: 0.271762 > rms devi: 0.336353 > max devi: 0.533797 > min devi: 0.0877567 >request std_res of type Cd and got Cd >coot::util::mutate_base Cd with std Cd >INFO:: 5 matched atoms had: > mean devi: 0.267729 > rms devi: 0.326479 > max devi: 0.505521 > min devi: 0.104657 >request std_res of type Td and got Td >coot::util::mutate_base Td with std Td >INFO:: 5 matched atoms had: > mean devi: 0.00585391 > rms devi: 0.00666923 > max devi: 0.0100827 > min devi: 0.00253528 >request std_res of type Gd and got Gd >coot::util::mutate_base Gd with std Gd >INFO:: 5 matched atoms had: > mean devi: 0.00722485 > rms devi: 0.00775255 > max devi: 0.0125025 > min devi: 0.00456535 >request std_res of type Ad and got Ad >coot::util::mutate_base Ad with std Ad >INFO:: 5 matched atoms had: > mean devi: 0.00580961 > rms devi: 0.00662938 > max devi: 0.0100332 > min devi: 0.00249036 >request std_res of type Gd and got Gd >coot::util::mutate_base Gd with std Gd >INFO:: 5 matched atoms had: > mean devi: 0.00719394 > rms devi: 0.00771755 > max devi: 0.0124407 > min devi: 0.00457156 >request std_res of type Ad and got Ad >coot::util::mutate_base Ad with std Ad >INFO:: 5 matched atoms had: > mean devi: 0.267807 > rms devi: 0.326561 > max devi: 0.505641 > min devi: 0.104488 >request std_res of type Td and got Td >coot::util::mutate_base Td with std Td >INFO:: 5 matched atoms had: > mean devi: 0.27187 > rms devi: 0.336463 > max devi: 0.533942 > min devi: 0.088009 >request std_res of type Cd and got Cd >coot::util::mutate_base Cd with std Cd >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_May__5_09:43:50_2010_modification_0.pdb.gz >[1m(ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG")[0m >INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_May__5_09:43:50_2010_modification_1.pdb.gz >INFO:: 5 matched atoms had: > mean devi: 0.270191 > rms devi: 0.336363 > max devi: 0.538427 > min devi: 0.0854029 > mutated base to type "Cd" >INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_May__5_09:43:50_2010_modification_2.pdb.gz >INFO:: 5 matched atoms had: > mean devi: 0.271895 > rms devi: 0.336278 > max devi: 0.534478 > min devi: 0.0923473 > mutated base to type "Gd" >INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_May__5_09:43:50_2010_modification_3.pdb.gz >INFO:: 5 matched atoms had: > mean devi: 0.0043292 > rms devi: 0.00481764 > max devi: 0.00738267 > min devi: 0.00186162 > mutated base to type "Ad" >INFO:: backup file coot-backup/Ideal-A-form-DNA_Wed_May__5_09:43:50_2010_modification_4.pdb.gz >INFO:: 5 matched atoms had: > mean devi: 0.265718 > rms devi: 0.326008 > max devi: 0.501859 > min devi: 0.0926641 > mutated base to type "Td" >PASS: DNA bases are the correct residue type after mutation >Entered testcase - SegIDs are correct after mutate >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 0)[0m >INFO:: mutate 32 A to a LYS >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:50_2010_modification_0.pdb.gz >[1m(mutate 32 "A" 50 "LYS")[0m >PASS: SegIDs are correct after mutate >Entered testcase - TER on water chain is removed on adding a water by hand >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/some-waters-with-ter.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/some-waters-with-ter.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/some-waters-with-ter.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 51 read successfully >[1m(set-rotation-centre 3.00 4.00 5.00)[0m >INFO:: adding atom of type Water at (3,4,5) >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_some-waters-with-ter.pdb_Wed_May__5_09:43:51_2010_modification_0.pdb.gz >1/D/79/HOH/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(write-pdb-file 51 "tmp-with-new-water.pdb")[0m >PASS: TER on water chain is removed on adding a water by hand >Entered testcase - TER on water chain is removed on adding waters automatically >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tm+some-waters.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tm+some-waters.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tm+some-waters.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 52 read successfully >Protein centre at: xyz = ( 41.57, 8.745, 12.89) >using sigma cut off 2 >Calling lig.water_fit() >INFO:: find_clusters map_rms is 0.311501 >INFO:: Using density cut-off: 0.623002 (2 sigma) (mean -0.0337018 stdev: 0.146071) >INFO:: Using water to protein distance limits: 2.2 3.4 >Finding clusters...done >------------------------------------------------------------- >INFO:: cluster at xyz = ( 59.91, 3.027, -4.296) is too big to be water >INFO:: cluster at xyz = ( 70.01, 19.05, 18.63) is too big to be water >INFO:: found 48 waters in water fitting >Done - back from lig.water_fit() >DEBUG:: new_waters_mol_flag: 0 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tm+some-waters.pdb_Wed_May__5_09:43:51_2010_modification_0.pdb.gz >INFO:: Adding to solvent chain: D >[1m(write-pdb-file 52 "auto-waters.pdb")[0m >[1m(write-pdb-file 52 "tmp-with-new-water.pdb")[0m >PASS: TER on water chain is removed on adding waters automatically >Entered testcase - Arrange waters round protein >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/water-test-no-cell.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/water-test-no-cell.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/water-test-no-cell.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 53 read successfully >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_water-test-no-cell.pdb_Wed_May__5_09:43:52_2010_modification_0.pdb.gz >No symmetry available >INFO:: moved 0 water molecules >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pathological-water-test.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pathological-water-test.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pathological-water-test.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 54 read successfully >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pathological-water-test.pdb_Wed_May__5_09:43:52_2010_modification_0.pdb.gz >INFO:: moved 181 water molecules >[1m(write-pdb-file 54 "waters-moved-failure.pdb")[0m >PASS: Arrange waters round protein >Entered testcase - Correct Segid After Add Terminal Residue >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 0)[0m >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.035 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.081 seconds for FFT >INFO:: 0.006 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.024 seconds for contour map >INFO:: 0.148 seconds in total >INFO:: Masking around 58 atoms >fitting terminal residue with rigid body refinement using 100 trials >INFO:: Fitting terminal residue with individual rigid body fitting. >INFO:: found better residue, score: 5.5329 >INFO:: found better residue, score: 7.65684 >INFO:: found better residue, score: 10.2175 > A 94 ALA N :: xyz = ( 58.94, 2.905, -1.681) > A 94 ALA C :: xyz = ( 60.31, 1.87, -3.439) > A 94 ALA CA :: xyz = ( 59.96, 1.903, -1.956) > A 94 ALA O :: xyz = ( 61.48, 1.739, -3.805) >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: mutating residue in add_cb_to_terminal_res >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:53_2010_modification_0.pdb.gz >DEBUG:: insert_coords_internal() add residue >0 of 8 1/A/93/ASP/ N altLoc :: segid :A: pos: (57.032,5.59,-0.723) B-factor: 10.7 >1 of 8 1/A/93/ASP/ CA altLoc :: segid :A: pos: (56.859,4.651,-1.821) B-factor: 9.77 >2 of 8 1/A/93/ASP/ CB altLoc :: segid :A: pos: (56.223,5.398,-3.023) B-factor: 7.83 >3 of 8 1/A/93/ASP/ CG altLoc :: segid :A: pos: (56.097,4.54,-4.207) B-factor: 10.96 >4 of 8 1/A/93/ASP/ OD1 altLoc :: segid :A: pos: (55.497,4.981,-5.242) B-factor: 10.83 >5 of 8 1/A/93/ASP/ OD2 altLoc :: segid :A: pos: (56.623,3.401,-4.248) B-factor: 12.14 >6 of 8 1/A/93/ASP/ C altLoc :: segid :A: pos: (58.283,4.084,-2.167) B-factor: 10.98 >7 of 8 1/A/93/ASP/ O altLoc :: segid :A: pos: (59.091,4.976,-2.587) B-factor: 10.33 >[1m(add-terminal-residue 55 "A" 93 1)[0m >PASS: Correct Segid After Add Terminal Residue >Entered testcase - Correct Segid after NCS residue range copy >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 0)[0m >PASS: Correct Segid after NCS residue range copy >Entered testcase - Merge Water Chains >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 58 read successfully >[1m(backup-state 58)[0m >[1m(turn-off-backup 58)[0m >INFO:: adding atom of type Water at (41.5953,8.68654,12.9093) >0//-32767/HOH/ O altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain) >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 43.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (43.5953,8.68654,12.9093) >1/C/2/HOH/ O altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 45.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (45.5953,8.68654,12.9093) >1/C/3/HOH/ O altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 47.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (47.5953,8.68654,12.9093) >1/C/4/HOH/ O altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 49.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (49.5953,8.68654,12.9093) >1/C/5/HOH/ O altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 51.60 8.69 12.91)[0m >[1m(renumber-residue-range 58 "D" 1 5 10)[0m >INFO:: adding atom of type Water at (51.5953,8.68654,12.9093) >1/D/16/HOH/ O altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 53.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (53.5953,8.68654,12.9093) >1/D/17/HOH/ O altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 55.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (55.5953,8.68654,12.9093) >1/D/18/HOH/ O altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 57.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (57.5953,8.68654,12.9093) >1/D/19/HOH/ O altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 59.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (59.5953,8.68654,12.9093) >1/D/20/HOH/ O altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 61.60 8.69 12.91)[0m >[1m(renumber-residue-range 58 "E" 11 15 5)[0m >INFO:: adding atom of type Water at (61.5953,8.68654,12.9093) >1/D/21/HOH/ O altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 63.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (63.5953,8.68654,12.9093) >1/D/22/HOH/ O altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 65.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (65.5953,8.68654,12.9093) >1/D/23/HOH/ O altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 67.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (67.5953,8.68654,12.9093) >1/D/24/HOH/ O altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 69.60 8.69 12.91)[0m >INFO:: adding atom of type Water at (69.5953,8.68654,12.9093) >1/D/25/HOH/ O altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 71.60 8.69 12.91)[0m >[1m(renumber-residue-range 58 "F" 16 20 2)[0m >[1m(n-chains 58)[0m >[1m(chain_id 58 0)[0m >[1m(chain_id 58 1)[0m >[1m(chain_id 58 2)[0m >[1m(chain_id 58 3)[0m >[1m(chain_id 58 4)[0m >[1m(is-solvent-chain-p 58 "A")[0m >[1m(is-solvent-chain-p 58 "B")[0m >[1m(is-solvent-chain-p 58 "D")[0m >[1m(is-solvent-chain-p 58 "E")[0m >[1m(is-solvent-chain-p 58 "F")[0m >[1m(setnum-from-serial-number 58 "D" 4)[0m >[1m(renumber-residue-range 58 "E" 1 5 5)[0m >[1m(setnum-from-serial-number 58 "D" 9)[0m >[1m(renumber-residue-range 58 "F" 1 10 10)[0m >[1m(turn-on-backup 58)[0m >[1m(n-chains 58)[0m >[1m(chain_id 58 2)[0m >[1m(setnum-from-serial-number 58 "D" 0)[0m >[1m(setnum-from-serial-number 58 "D" 14)[0m >PASS: Merge Water Chains >Entered testcase - LSQ by atom >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 0)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 0)[0m >INFO:: Matching/moving molecule number 60 to 59 >INFO:: LSQ matched 4 atoms >INFO:: 4 matched atoms had: > mean devi: 0.0353197 > rms devi: 0.0377881 > max devi: 0.0545286 > min devi: 0.016676 >INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076) >INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313) >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:54_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| 0.9737, 0.007115, -0.2278| >| 0.2062, 0.3981, 0.8939| >| 0.09703, -0.9173, 0.3861| >( 37.45, -16.6, 12.88) >INFO:: fractional coordinates matrix: >| 0.9737, 0.008587, -0.1361| >| 0.1708, 0.3981, 0.4427| >| 0.1623, -1.852, 0.3861| >( 0.577, -0.2119, 0.3319) >successfully set cell and symmetry >PASS: LSQ by atom >Entered testcase - LSQing changes the space-group and cell to that of the reference molecule >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 61 read successfully >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1py3.ent" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1py3.ent > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1py3.ent has been read. >Spacegroup: C 1 2 1 >Cell: 102.29 68.7 57.51 90 100.4 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 91/204 >INFO:: NCS chain comparison 90/204 >INFO:: NCS chain comparison 175/179 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain C onto Chain B" >Molecule 62 read successfully >INFO:: spacegroup: P 21 21 21 >INFO:: spacegroup: C 1 2 1 >INFO:: Matching/moving molecule number 61 to 62 >INFO:: LSQ matched 164 atoms >INFO:: 164 matched atoms had: > mean devi: 0.502333 > rms devi: 0.593803 > max devi: 1.67852 > min devi: 0.0431788 >INFO:: Axis orientation: ( 0.567, -0.7175, 0.4046) >INFO:: Rotation in CCP4 Polar Angles: Polar = (113.863,128.32,41.8019) >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:43:55_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| 0.8273, 0.1661, 0.5366| >| -0.3732, 0.8765, 0.3041| >| -0.4199, -0.4519, 0.7871| >( 33.77, -3.902, -16.53) >INFO:: fractional coordinates matrix: >| 0.8273, 0.2005, 0.3208| >| -0.3092, 0.8765, 0.1506| >| -0.7024, -0.9123, 0.7871| >( 0.5204, -0.04982, -0.426) >successfully set cell and symmetry >INFO:: spacegroup: C 1 2 1 >PASS: LSQing changes the space-group and cell to that of the reference molecule >Entered testcase - Phosphate distance in pucker analysis is sane >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2goz-manip.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2goz-manip.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2goz-manip.pdb has been read. >Spacegroup: C 1 2 1 >Cell: 49.886 69.21 60.076 90 111.83 90 >INFO:: Found 1 models > Model 1 had 7 links >Symmetry available for this molecule >INFO:: NCS chain comparison 10/85 >Molecule 63 read successfully >PASS: Phosphate distance in pucker analysis is sane >Ended 01-pdb+mtz.scm >Running 02-shelx.scm ... >Entered testcase - Read small molecule .res file >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/HOF.RES" 1)[0m >SFAC LINE: SFAC C H N O S >INFO:: CELL set to 5.9028 13.6977 9.2374 90 98.211 90 >INFO:: set space group to :P 1 21/c 1: >READ-INS:: Spacegroup: P 1 21/c 1 >INFO:: chain has 1 residues >Symmetry available for this molecule >Molecule 64 read successfully >[1m(read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/HOF.RES")[0m >PASS: Read small molecule .res file >Entered testcase - Read hollander small molecule .res file >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/hollander.ins" 1)[0m >LATT LINE: LATT -2 >SFAC LINE: SFAC C H N O CO >INFO:: CELL set to 34.3243 34.3243 11.0887 90 90 90 >INFO:: set space group to :I 41 2 2: >READ-INS:: Spacegroup: I 41 2 2 >INFO:: chain has 1 residues >Symmetry available for this molecule >Molecule 65 read successfully >[1m(read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/hollander.ins")[0m >INFO:: spacegroup: I 41 2 2 >PASS: Read hollander small molecule .res file >Entered testcase - read shelx insulin with fcf >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res" 1)[0m >LATT LINE: LATT -2 >SFAC LINE: SFAC C H N O S >INFO:: CELL set to 77.726 77.726 77.726 90 90 90 >INFO:: set space group to :I 21 3: >READ-INS:: Spacegroup: I 21 3 >INFO:: chain has 120 residues >Symmetry available for this molecule >Molecule 66 read successfully >[1m(read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res")[0m >/usr/bin/awk >exit status: 0 >got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) >Found symmetry equivalents..... >INFO:: Found cif symmetry operator x, y, z >INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 >INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 >INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z >INFO:: Found cif symmetry operator z, x, y >INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y >INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 >INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 >INFO:: Found cif symmetry operator y, z, x >INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 >INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x >INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 >INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 >INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 >INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 >INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 >INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 >INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 >INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 >INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 >INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 >INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 >INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 >INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 >INFO:: space_group from symm ops in cif: I 21 3 >got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) >Found symmetry equivalents..... >INFO:: Found cif symmetry operator x, y, z >INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 >INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 >INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z >INFO:: Found cif symmetry operator z, x, y >INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y >INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 >INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 >INFO:: Found cif symmetry operator y, z, x >INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 >INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x >INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 >INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 >INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 >INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 >INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 >INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 >INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 >INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 >INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 >INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 >INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 >INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 >INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 >INFO:: space_group from symm ops in cif: I 21 3 >import_hkl_info read 16736 hkls >16736 calculated data read on close_read() >Read 16735 from CIF file (sigmaa). >sigmaa and scaling... >initializing map...done. >doing fft...done. >Mean and sigma of map from CIF file (make_map_from_cif): -5.04464e-05 and 0.305067 >Reading cif file (with phases - diff) : /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.fcf.cif >got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) >Found symmetry equivalents..... >INFO:: Found cif symmetry operator x, y, z >INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 >INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 >INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z >INFO:: Found cif symmetry operator z, x, y >INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y >INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 >INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 >INFO:: Found cif symmetry operator y, z, x >INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 >INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x >INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 >INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 >INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 >INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 >INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 >INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 >INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 >INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 >INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 >INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 >INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 >INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 >INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 >INFO:: space_group from symm ops in cif: I 21 3 >got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) >Found symmetry equivalents..... >INFO:: Found cif symmetry operator x, y, z >INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 >INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 >INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z >INFO:: Found cif symmetry operator z, x, y >INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y >INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 >INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 >INFO:: Found cif symmetry operator y, z, x >INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 >INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x >INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 >INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 >INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 >INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 >INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 >INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 >INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 >INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 >INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 >INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 >INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 >INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 >INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 >INFO:: space_group from symm ops in cif: I 21 3 >import_hkl_info read 16736 hkls >16736 calculated data read on close_read() >Read 16735 from CIF file (sigmaa). >sigmaa and scaling... >initializing map...done. >doing fft...done. >Mean and sigma of map from CIF file (make_map_from_cif): -1.00621e-05 and 0.046808 >INFO:: spacegroup: I 21 3 >INFO:: spacegroup: I 21 3 >INFO:: spacegroup: I 21 3 >PASS: read shelx insulin with fcf >Entered testcase - Write an INS from PDB test >WARNING:: invalid molecule (204050) for write_shelx_ins_file >ERROR transfering afix back >WARNING:: failed to get AFIX handle for ASP N , >WARNING:: failed to get AFIX handle for ASP CA , >WARNING:: failed to get AFIX handle for ASP CB , >WARNING:: failed to get AFIX handle for ASP CG , >WARNING:: failed to get AFIX handle for ASP OD1 , >WARNING:: failed to get AFIX handle for ASP OD2 , >WARNING:: failed to get AFIX handle for ASP C , >WARNING:: failed to get AFIX handle for ASP O , >WARNING:: failed to get AFIX handle for VAL N , >WARNING:: failed to get AFIX handle for VAL CA , >INFO:: SHELXL file rnase.ins written. >PASS: Write an INS from PDB test >Entered testcase - new molecule by atom selection inherits shelx molecule flag >In new_molecule_by_atom_selection has contains chain id B >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >PASS: new molecule by atom selection inherits shelx molecule flag >Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy >In new_molecule_by_atom_selection has contains chain id B >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >INFO:: Masking around 32 atoms >fitting terminal residue with rigid body refinement using 100 trials >INFO:: Fitting terminal residue with individual rigid body fitting. >INFO:: found better residue, score: 1.66482 >INFO:: found better residue, score: 2.99274 >INFO:: found better residue, score: 4.17734 >INFO:: found better residue, score: 5.3028 >INFO:: found better residue, score: 5.32311 >INFO:: found better residue, score: 6.70159 > B 2021 ALA N :: xyz = ( -10.65, 18.09, 60.91) > B 2021 ALA C :: xyz = ( -8.829, 18.52, 62.51) > B 2021 ALA CA :: xyz = ( -10.33, 18.6, 62.24) > B 2021 ALA O :: xyz = ( -8.235, 19.47, 63.03) >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: mutating residue in add_cb_to_terminal_res >INFO:: backup file coot-backup/atom_selection_from_insulin.res_Wed_May__5_09:44:01_2010_modification_0.res >ERROR transfering afix back >WARNING:: failed to get AFIX handle for Ú HIS N , >WARNING:: failed to get AFIX handle for Ú HIS CA , >WARNING:: failed to get AFIX handle for Ú HIS C , >WARNING:: failed to get AFIX handle for Ú HIS O , >WARNING:: failed to get AFIX handle for Ú HIS CB , >WARNING:: failed to get AFIX handle for Ú HIS CG , >WARNING:: failed to get AFIX handle for Ú HIS ND1 , >WARNING:: failed to get AFIX handle for Ú HIS CE1 , >WARNING:: failed to get AFIX handle for Ú HIS NE2 , >WARNING:: failed to get AFIX handle for Ú HIS CD2 , >DEBUG:: insert_coords_internal() add residue >0 of 4 1/B/2020/GLY/ N altLoc :: segid :: pos: (-9.63515,16.2417,57.4359) B-factor: 16.1806 >1 of 4 1/B/2020/GLY/ CA altLoc :: segid :: pos: (-10.681,17.2571,57.2255) B-factor: 20.069 >2 of 4 1/B/2020/GLY/ C altLoc :: segid :: pos: (-10.6427,18.37,58.2259) B-factor: 21.6855 >3 of 4 1/B/2020/GLY/ O altLoc :: segid :: pos: (-9.56854,18.8859,58.5732) B-factor: 20.832 >[1m(add-terminal-residue 70 "B" 2020 1)[0m >PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy >Entered testcase - Add water to SHELX molecule >[1m(set-rotation-centre 3.00 -1.00 60.00)[0m >INFO:: adding atom of type Water at (3,-1,60) >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_insulin.res_Wed_May__5_09:44:01_2010_modification_0.res >INFO :: padding UNIT card from size 5 to 5 >1/D/3069/HOH/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule >[1m(place-typed-atom-at-pointer "Water")[0m >[1m(resname-from-serial-number 66 "D" 68)[0m >[1m(setnum-from-serial-number 66 "D" 68)[0m >[1m(insertion-code-from-serial-number 66 "D" 68)[0m >PASS: Add water to SHELX molecule >Entered testcase - Find Waters for a SHELXL molecule >[1m(n-chains 66)[0m >Protein centre at: xyz = ( -0.2998, 10.6, 57.56) >using sigma cut off 0.6 >Calling lig.water_fit() >INFO:: find_clusters map_rms is 0.305067 >INFO:: Using density cut-off: 0.18304 (0.6 sigma) (mean -0.0203646 stdev: 0.112003) >INFO:: Using water to protein distance limits: 2.2 3.4 >Finding clusters...done >------------------------------------------------------------- >INFO:: cluster at xyz = ( -4.85, 20.81, 69.67) is too big to be water >INFO:: cluster at xyz = ( 0.0273, 16.3, 69.67) is too big to be water >INFO:: cluster at xyz = ( -4.576, 10.3, 69.42) is too big to be water >INFO:: cluster at xyz = ( 15.6, 8.133, 53.54) is too big to be water >INFO:: cluster at xyz = ( 20.54, 4.889, 65.84) is too big to be water >WARNING:: refinement failure > start pos: xyz = ( 7.187, 17.29, 73.17) > final pos: xyz = ( 7.957, 17.95, 73.23) > >WARNING:: refinement failure > start pos: xyz = ( 7.187, 17.29, 73.17) > final pos: xyz = ( 7.957, 17.95, 73.23) > >WARNING:: refinement failure > start pos: xyz = ( 7.187, 17.29, 73.17) > final pos: xyz = ( 7.957, 17.95, 73.23) > >INFO:: found 58 waters in water fitting >Done - back from lig.water_fit() >DEBUG:: new_waters_mol_flag: 0 >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_insulin.res_Wed_May__5_09:44:01_2010_modification_1.res >ERROR transfering afix back >INFO :: padding UNIT card from size 5 to 5 >WARNING:: failed to get AFIX handle for ý HOH O , >INFO:: Adding to solvent chain: D >[1m(n-chains 66)[0m >[1m(resname-from-serial-number 66 "D" 126)[0m >[1m(setnum-from-serial-number 66 "D" 126)[0m >[1m(insertion-code-from-serial-number 66 "D" 126)[0m >PASS: Find Waters for a SHELXL molecule >Entered testcase - NPD Anisotropic Atom [Mitch Miller] >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/miller/shelx-test4-NPD-mini.res" 1)[0m >LATT LINE: LATT -1 >SFAC LINE: SFAC C H N O S SE CL >WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: >INFO:: CELL set to 42.14 83.03 89.79 90 90 90 >INFO:: set space group to :P 21 21 21: >READ-INS:: Spacegroup: P 21 21 21 >INFO:: chain has 4 residues >Symmetry available for this molecule >Molecule 71 read successfully >[1m(read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/miller/shelx-test4-NPD-mini.res")[0m >[1m(close-molecule 71)[0m >PASS: NPD Anisotropic Atom [Mitch Miller] >Entered testcase - close shelx molecules >[1m(close-molecule 67)[0m >[1m(close-molecule 66)[0m >PASS: close shelx molecules >Entered testcase - Aniso Bs in P21 >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/horma-p21.res" 1)[0m >LATT LINE: LATT -1 >SFAC LINE: SFAC C H N O MG CL >INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 >INFO:: set space group to :P 1 21 1: >READ-INS:: Spacegroup: P 1 21 1 >INFO:: chain has 22 residues >Symmetry available for this molecule >Molecule 72 read successfully >[1m(read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/horma-p21.res")[0m >INFO :: padding UNIT card from size 6 to 6 >INFO:: SHELXL file new-horma.ins written. >[1m(handle-read-draw-molecule-with-recentre "new-horma.ins" 1)[0m >LATT LINE: LATT -1 >SFAC LINE: SFAC C H N O MG CL >INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 >INFO:: set space group to :P 1 21 1: >READ-INS:: Spacegroup: P 1 21 1 >INFO:: chain has 22 residues >Symmetry available for this molecule >Molecule 73 read successfully >[1m(read-shelx-ins-file "new-horma.ins")[0m >b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) >b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) >PASS: Aniso Bs in P21 >Ended 02-shelx.scm >Running 03-ligand.scm ... >Entered testcase - Get monomer test >No CCP4 - Copying in test files >INFO:: Creating directory coot-ccp4 > copy-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-3GP.pdb" "coot-ccp4/monomer-3GP.pdb" >Ooops file not found "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif" >/usr/bin/libcheck >================= debug: libcheck-monomer-gui: dir-prefix: "coot-ccp4/" code-str: "3GP" cif-file-name: "coot-ccp4/libcheck_3GP.cif" pdb-file-name: "coot-ccp4/libcheck_3GP.pdb" post-refmac-pdb-file-name: "coot-ccp4/monomer-3GP.pdb" >passing libcheck these data lines: ("N" "MON 3GP" "") >/usr/bin/libcheck >: >: --- LIBCHECK --- /Vers 4.2.8 ; 02.06.2009/ >: >: >: Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A : >: N - means without DOC-file >: Y - with new contents >: A - means to keep old contents and add new information >: with DOC-file program creates batch file: libcheck.bat >: _DOC: >: >: # >: # Keywords: >: # >: #FILE_L: < > - additional library, " " means without this file >: #MON: < > - give info about this monomer >: # if = * , give list all monomers in the library >: #FILE_PDB: < > - input PDB_file ," " means without this file >: #FILE_SMILE: < > - input SMILE_file ," " means without this fil e >: #FILE_SDF: < > - input SDF file, " " means without this file >: #FILE_MOL: < > - input MOL file, " " means without this file >: # use keyword MON as compound_id >: #FILE_CIF: < > - input CIFile ," " means without this file >: #FILE_CSD: < > - input CSD CIFile," " means without this file >: #HFLAG: <Y>/A/N - Y - hydrogen atoms where they are >: # A - with all hydrogen atoms >: # N - without hydrogen atoms >: #IND: <N>/Y - Y - create index of mon_lib.cif >: # output file: "new_mon_lib_ind.cif" >: #FILE_O: <libcheck > - output files /library,coords,ps/, name without >: # extention >: #FILE_L2: < > - additional library (FILE_L) will be added to this library >: # in this case program performs only adding >: #ANGLE: <0.0> - rotation angle for picture ( around X ) >: #LIST: <M>/S/L - S short output, L - long, M - medium >: #REF: <Y>/S,N,0 - 0 no refinement of new monomer >: # N only crd->ang and ang->crd >: # S plus torsion ref, Y plus restr.ref >: # >: #TEST: <0> - for program testing only >: #COOR: <N>/Y - use Vobs from coords instead Videal >: #LCOOR: <Y>/N - Y use coords from lib description >: #NODIST: <N>/Y - Y not read the distributed library >: # (only with FILE_L) >: #SRCH: <N>/Y/0 - Y - global search, 0 - for MON from PDB_file >: # (only with NODIST = N) >: >: #--- type "keyword parameters" and/or --- >: #--- press key "CR" to run program --- >: --> --> MON : 3GP >: ------------- >: ------------- >: Keywords: >: HFLAG : Y >: COOR : N >: LCOOR : Y >: SRCH : N >: REF : Y >: NODIST: N >: ERROR: can"t open (lib) list/mon_lib_list >exit status: 0 >INFO:: libcheck status: 0 >libcheck failed to write the output cif file. > No ligand molecule - monomer test >UNTESTED: Get monomer test >Entered testcase - Set Bond thickness > No ligand molecule - Skipping bond thickness test >UNTESTED: Set Bond thickness >Entered testcase - Move and Refine Ligand test >UNTESTED: Move and Refine Ligand test >Entered testcase - Many Molecules - Ligand Fitting >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" 0)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 74 read successfully >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 74)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 74)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 74)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 74)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 74)[0m >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. >Spacegroup: C 2 2 21 >Cell: 106.25 110.86 244.42 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 10/113 >INFO:: NCS chain comparison 107/113 >INFO:: NCS chain comparison 10/113 >INFO:: NCS chain comparison 107/113 >INFO:: NCS chain comparison 10/113 >INFO:: NCS chain comparison 107/113 >INFO:: NCS chain comparison 10/113 >INFO:: NCS chain comparison 0/113 >INFO:: NCS chain comparison 10/117 >INFO:: NCS chain comparison 112/117 >INFO:: NCS chain comparison 10/117 >INFO:: NCS chain comparison 112/117 >INFO:: NCS chain comparison 10/117 >INFO:: NCS chain comparison 112/117 >INFO:: NCS chain comparison 0/117 > INFO:: fill_ghost_info Constructed 6 ghosts > Ghost 0 name: "NCS found from matching Chain C onto Chain A" > Ghost 1 name: "NCS found from matching Chain E onto Chain A" > Ghost 2 name: "NCS found from matching Chain G onto Chain A" > Ghost 3 name: "NCS found from matching Chain D onto Chain B" > Ghost 4 name: "NCS found from matching Chain F onto Chain B" > Ghost 5 name: "NCS found from matching Chain H onto Chain B" >Molecule 80 read successfully >making conventional map from MTZ filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT >Number of OBSERVED reflections: 54440 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 160, 160, 336) >INFO:: 0.303 seconds to read MTZ file >INFO:: 0.57 seconds to initialize map >INFO:: 0.341 seconds for FFT >INFO:: 0.031 seconds for statistics > Map mean: ........ -8.79078e-07 > Map sigma: ....... 0.171188 > Map maximum: ..... 1.34304 > Map minimum: ..... -0.695441 >INFO:: 0.013 seconds for contour map >INFO:: 1.258 seconds in total >[1m(make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00)[0m >making difference map from MTZ filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT >Number of OBSERVED reflections: 54440 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 160, 160, 336) >INFO:: 0.125 seconds to read MTZ file >INFO:: 0.009 seconds to initialize map >INFO:: 0.342 seconds for FFT >INFO:: 0.031 seconds for statistics > Map mean: ........ 2.0939e-06 > Map sigma: ....... 0.0333923 > Map maximum: ..... 0.366077 > Map minimum: ..... -0.191665 >INFO:: 0.006 seconds for contour map >INFO:: 0.513 seconds in total >[1m(make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "DELFWT" "PHDELWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00)[0m >Executing ligand search... >INFO:: ligand number 0 is molecule number 74 with wiggly flag: 0 >Protein centre at: xyz = ( 58.29, 34.65, 30.63) >Map statistics: mean: -0.0216745 st.d: 0.0886263 >Map statistics: min: -0.695441, max: 0.754209 > -0.6592 14 >-0.586717 143 >-0.514235 1331 >-0.441752 5299 >-0.36927 11732 >-0.296787 16725 >-0.224305 21484 >-0.151822 46755 >-0.0793395 161103 >-0.006857 614774 >0.0656255 162933 >0.138108 28508 >0.210591 3055 >0.283073 813 >0.355556 334 >0.428038 197 >0.500521 78 >0.573003 48 >0.645486 25 >0.717968 9 >0.790451 0 >INFO:: find_clusters map_rms is 0.171188 >INFO:: Using density cut-off: 0.171188 (1 sigma) (mean -0.0216776 stdev: 0.0886191) >INFO:: Using water to protein distance limits: 2.4 3.2 >Finding clusters...done >WARNING: many badly fitting atoms for best ligand in cluster 4. > Coordinates not written. >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule >Symmetry available for this molecule > Fitting NPO gave these results: (84 85 86 87 88 89 90 91 92 93) >PASS: Many Molecules - Ligand Fitting >Entered testcase - flip residue (around eigen vectors) >[1m(handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 1)[0m >Reading coordinate file: coot-ccp4/monomer-3GP.pdb > PDB file coot-ccp4/monomer-3GP.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 94 read successfully >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 94)[0m >INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_May__5_09:44:12_2010_modification_0.pdb.gz >INFO:: replace_coords: 36 atoms updated. >distance: 4.79714893189444 >INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_May__5_09:44:12_2010_modification_1.pdb.gz >INFO:: replace_coords: 36 atoms updated. >INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_May__5_09:44:12_2010_modification_2.pdb.gz >INFO:: replace_coords: 36 atoms updated. >INFO:: backup file coot-backup/Copy_of_coot-ccp4_monomer-3GP.pdb_Wed_May__5_09:44:12_2010_modification_3.pdb.gz >INFO:: replace_coords: 36 atoms updated. >distance d2: 2.66560074985002e-7 >PASS: flip residue (around eigen vectors) >Entered testcase - Test dipole >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/dipole-residues.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/dipole-residues.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/dipole-residues.pdb has been read. >No Spacegroup found for this PDB file >Cell: 1 1 1 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >Molecule 96 read successfully >info:: dipole components (-2.21999993920326 3.6949610038306e-16 -4.61870125478825e-17) >PASS: Test dipole >Entered testcase - Reading new dictionary restraints replaces >WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif not found. >init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif had no bond restraints >WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif not found. >init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif had no bond restraints >WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif not found. >init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/libcheck_3GP.cif had no bond restraints >Exception: (wrong-type-arg assoc Wrong type argument in position ~A (expecting ~A): ~S (2 association list #f) (#f)) >UNRESOLVED: Reading new dictionary restraints replaces >Ended 03-ligand.scm >Running 04-cootaneer.scm ... >Entered testcase - Assignment of new PIR sequence overwrites old assignment >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 97 read successfully >in assign_pir_sequence >storing sequence: ACDEFGHIKLMNPQ for chain id: A >[1m(assign-pir-sequence 97 "A" ">test > >ACDEFGHIKLMNPQ*")[0m >debug seq: ("A" . "ACDEFGHIKLMNPQ") >in assign_pir_sequence >storing sequence: ACDEFGHIKLMNPQRST for chain id: A >[1m(assign-pir-sequence 97 "A" ">test > >ACDEFGHIKLMNPQRST*")[0m >PASS: Assignment of new PIR sequence overwrites old assignment >Entered testcase - Cootaneer Beta Strand >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/crashes_on_cootaneering.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/crashes_on_cootaneering.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/crashes_on_cootaneering.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 2/2 >INFO:: NCS chain comparison 0/2 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain A onto Chain " >Molecule 98 read successfully >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.032 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.074 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.024 seconds for contour map >INFO:: 0.137 seconds in total >in assign_pir_sequence >storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A >[1m(assign-pir-sequence 98 "A" "> tutorial-modern chain A >RNASE >DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG >YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * > >")[0m >[1m(set-rotation-centre 64.27 7.04 14.42)[0m > Cootaneering: imol 98 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" >Ooops! Can't find cootaneer likelihood data! - failure >PASS: Cootaneer Beta Strand >Ended 04-cootaneer.scm >Running 05-rna-ghosts.scm ... >Entered testcase - RNA NCS Ghosts >INFO:: 5 matched atoms had: > mean devi: 0 > rms devi: 0 > max devi: 0 > min devi: 0 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.0120681 > rms devi: 0.0134464 > max devi: 0.0214179 > min devi: 0.00385596 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.270216 > rms devi: 0.335002 > max devi: 0.536002 > min devi: 0.08463 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >INFO:: 5 matched atoms had: > mean devi: 0.26738 > rms devi: 0.322791 > max devi: 0.495136 > min devi: 0.112289 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 0.270247 > rms devi: 0.335033 > max devi: 0.536044 > min devi: 0.0847029 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >INFO:: 5 matched atoms had: > mean devi: 0.267411 > rms devi: 0.322823 > max devi: 0.495177 > min devi: 0.112221 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 0.011982 > rms devi: 0.013349 > max devi: 0.0212578 > min devi: 0.0038732 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.000242576 > rms devi: 0.000242751 > max devi: 0.000256671 > min devi: 0.000231275 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.270185 > rms devi: 0.334971 > max devi: 0.535961 > min devi: 0.0845571 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >INFO:: 5 matched atoms had: > mean devi: 0.267349 > rms devi: 0.322759 > max devi: 0.495094 > min devi: 0.112357 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 6.9313e-05 > rms devi: 6.93629e-05 > max devi: 7.33402e-05 > min devi: 6.60841e-05 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.0120334 > rms devi: 0.0134072 > max devi: 0.0213538 > min devi: 0.00386188 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.000138622 > rms devi: 0.000138721 > max devi: 0.000146676 > min devi: 0.000132164 >request std_res of type Gr and got Gr >coot::util::mutate_base Gr with std Gr >INFO:: 5 matched atoms had: > mean devi: 0.011999 > rms devi: 0.0133684 > max devi: 0.0212898 > min devi: 0.0038691 >request std_res of type Ar and got Ar >coot::util::mutate_base Ar with std Ar >INFO:: 5 matched atoms had: > mean devi: 0.267426 > rms devi: 0.322839 > max devi: 0.495197 > min devi: 0.112187 >request std_res of type Ur and got Ur >coot::util::mutate_base Ur with std Ur >INFO:: 5 matched atoms had: > mean devi: 0.270294 > rms devi: 0.335079 > max devi: 0.536106 > min devi: 0.0848122 >request std_res of type Cr and got Cr >coot::util::mutate_base Cr with std Cr >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >INFO:: backup file coot-backup/Ideal-A-form-RNA_Wed_May__5_09:44:14_2010_modification_0.pdb.gz >[1m(ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG")[0m >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 100)[0m >[1m(rotation-centre-position 0)[0m >[1m(rotation-centre-position 1)[0m >[1m(rotation-centre-position 2)[0m >[1m(set-rotation-centre 76.27 10.04 14.42)[0m >[1m(go-to-view-number 2 1)[0m >[1m(n-chains 101)[0m >[1m(chain_id 101 0)[0m >[1m(chain_id 101 1)[0m >[1m(is-solvent-chain-p 101 "A")[0m > There are 8 residues in chain "A" >[1m(resname-from-serial-number 101 "A" 0)[0m >[1m(setnum-from-serial-number 101 "A" 0)[0m >[1m(insertion-code-from-serial-number 101 "A" 0)[0m >[1m(resname-from-serial-number 101 "A" 1)[0m >[1m(setnum-from-serial-number 101 "A" 1)[0m >[1m(insertion-code-from-serial-number 101 "A" 1)[0m >[1m(resname-from-serial-number 101 "A" 2)[0m >[1m(setnum-from-serial-number 101 "A" 2)[0m >[1m(insertion-code-from-serial-number 101 "A" 2)[0m >[1m(resname-from-serial-number 101 "A" 3)[0m >[1m(setnum-from-serial-number 101 "A" 3)[0m >[1m(insertion-code-from-serial-number 101 "A" 3)[0m >[1m(resname-from-serial-number 101 "A" 4)[0m >[1m(setnum-from-serial-number 101 "A" 4)[0m >[1m(insertion-code-from-serial-number 101 "A" 4)[0m >[1m(resname-from-serial-number 101 "A" 5)[0m >[1m(setnum-from-serial-number 101 "A" 5)[0m >[1m(insertion-code-from-serial-number 101 "A" 5)[0m >[1m(resname-from-serial-number 101 "A" 6)[0m >[1m(setnum-from-serial-number 101 "A" 6)[0m >[1m(insertion-code-from-serial-number 101 "A" 6)[0m >[1m(resname-from-serial-number 101 "A" 7)[0m >[1m(setnum-from-serial-number 101 "A" 7)[0m >[1m(insertion-code-from-serial-number 101 "A" 7)[0m >[1m(is-solvent-chain-p 101 "B")[0m > There are 8 residues in chain "B" >[1m(resname-from-serial-number 101 "B" 0)[0m >[1m(setnum-from-serial-number 101 "B" 0)[0m >[1m(insertion-code-from-serial-number 101 "B" 0)[0m >[1m(resname-from-serial-number 101 "B" 1)[0m >[1m(setnum-from-serial-number 101 "B" 1)[0m >[1m(insertion-code-from-serial-number 101 "B" 1)[0m >[1m(resname-from-serial-number 101 "B" 2)[0m >[1m(setnum-from-serial-number 101 "B" 2)[0m >[1m(insertion-code-from-serial-number 101 "B" 2)[0m >[1m(resname-from-serial-number 101 "B" 3)[0m >[1m(setnum-from-serial-number 101 "B" 3)[0m >[1m(insertion-code-from-serial-number 101 "B" 3)[0m >[1m(resname-from-serial-number 101 "B" 4)[0m >[1m(setnum-from-serial-number 101 "B" 4)[0m >[1m(insertion-code-from-serial-number 101 "B" 4)[0m >[1m(resname-from-serial-number 101 "B" 5)[0m >[1m(setnum-from-serial-number 101 "B" 5)[0m >[1m(insertion-code-from-serial-number 101 "B" 5)[0m >[1m(resname-from-serial-number 101 "B" 6)[0m >[1m(setnum-from-serial-number 101 "B" 6)[0m >[1m(insertion-code-from-serial-number 101 "B" 6)[0m >[1m(resname-from-serial-number 101 "B" 7)[0m >[1m(setnum-from-serial-number 101 "B" 7)[0m >[1m(insertion-code-from-serial-number 101 "B" 7)[0m >finding new chain id for chain id :A: 0/2 >finding new chain id for chain id :B: 1/2 >INFO:: Merge From chains: > :A: :B: >INFO:: Merge To chains: > :C: :D: >!! Warning:: No symmetry available for this molecule >No Symmetry for this model >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 100)[0m >INFO:: Matching/moving molecule number 102 to 102 >ERROR:: No symmetry available >INFO:: LSQ matched 125 atoms >INFO:: 125 matched atoms had: > mean devi: 0.141862 > rms devi: 0.1486 > max devi: 0.243102 > min devi: 0.0283184 >INFO:: Axis orientation: ( 0.3864, -0.6781, -0.6252) >INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3226,0.295211) >INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Wed_May__5_09:44:15_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| 1, 0.003218, -0.003497| >| -0.003225, 1, -0.001985| >| 0.003491, 0.001997, 1| >( -24.02, -23.69, -24.44) >No unit cell for this molecule, hence no fractional matrix. >[1m(close-molecule 102)[0m >[1m(close-molecule 101)[0m >[1m(go-to-view-number 3 1)[0m >PASS: RNA NCS Ghosts >Ended 05-rna-ghosts.scm >Running 06-ssm.scm ... >Entered testcase - SSM - Frank von Delft's Example >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1wly.pdb" 0)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1wly.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1wly.pdb has been read. >Spacegroup: C 1 2 1 >Cell: 140.797 49.176 59.053 90 100.97 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 103 read successfully >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1yb5.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1yb5.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1yb5.pdb has been read. >Spacegroup: P 21 21 2 >Cell: 99.484 110.239 77.253 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 324/324 >INFO:: NCS chain comparison 0/324 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 104 read successfully >do_Ca_plus_ligands_bonds with atom_colour_type 0 >[1m(graphics-to-ca-plus-ligands-representation 103)[0m >do_Ca_plus_ligands_bonds with atom_colour_type 0 >[1m(graphics-to-ca-plus-ligands-representation 104)[0m >INFO:: reference 103 has 750 atoms selected >INFO:: moving 104 has 842 atoms selected >superposing... >number of Ca atoms in selections: 110 (moving) and 100 (reference) >Another Go... > > Moving Reference Distance > A 6 > A 7 > A 8 <---> A 2 : 0.751 A > A 9 <---> A 3 : 0.942174 A > A 10 <---> A 4 : 0.629981 A > A 11 <---> A 5 : 0.711865 A > A 12 <---> A 6 : 0.631005 A > A 13 <---> A 7 : 0.467533 A > A 14 <---> A 8 : 0.426381 A > A 15 <---> A 9 : 0.97919 A > A 16 <---> A 10 : 0.754876 A > A 17 <---> A 11 : 0.488388 A > A 18 <---> A 12 : 0.745058 A > A 19 <---> A 13 : 0.460612 A > A 20 <---> A 14 : 1.2809 A > A 21 <---> A 15 : 1.24119 A > A 22 <---> A 16 : 1.07334 A > A 23 <---> A 17 : 0.973042 A > A 24 <---> A 18 : 0.470509 A > A 25 <---> A 19 : 0.355977 A > A 26 <---> A 20 : 3.11453 A > A 27 > A 28 <---> A 21 : 1.57537 A > A 29 <---> A 22 : 1.63223 A > A 30 > A 31 <---> A 23 : 1.9973 A > A 32 <---> A 25 : 1.83236 A > A 33 <---> A 26 : 0.930954 A > A 34 <---> A 27 : 0.680752 A > A 35 <---> A 28 : 0.267434 A > A 36 <---> A 29 : 0.599491 A > A 37 <---> A 30 : 0.699234 A > A 38 <---> A 31 : 0.862022 A > A 39 <---> A 32 : 0.842095 A > A 40 <---> A 33 : 0.720834 A > A 41 <---> A 34 : 0.86807 A > A 42 <---> A 35 : 0.778132 A > A 43 <---> A 36 : 0.621112 A > A 44 <---> A 37 : 0.465701 A > A 45 <---> A 38 : 0.747499 A > A 46 <---> A 39 : 0.517002 A > A 47 <---> A 40 : 0.505788 A > A 48 <---> A 41 : 0.889736 A > A 49 <---> A 42 : 0.583476 A > A 50 <---> A 43 : 0.434661 A > A 51 <---> A 44 : 0.619207 A > A 52 <---> A 45 : 0.215003 A > A 53 <---> A 46 : 0.747368 A > A 54 <---> A 47 : 1.02135 A > A 55 <---> A 48 : 0.920754 A > A 56 <---> A 49 : 0.939245 A > A 57 > A 58 > A 59 > A 60 > A 61 > A 62 > A 63 > A 64 > A 65 <---> A 60 : 0.466577 A > A 66 <---> A 61 : 0.0522595 A > A 67 <---> A 62 : 1.07191 A > A 68 <---> A 63 : 0.793315 A > A 69 <---> A 64 : 0.891607 A > A 70 <---> A 65 : 1.25797 A > A 71 <---> A 66 : 0.693217 A > A 72 <---> A 67 : 1.03452 A > A 73 <---> A 68 : 1.44168 A > A 74 <---> A 69 : 0.909171 A > A 75 <---> A 70 : 1.61656 A > A 76 <---> A 71 : 0.87415 A > A 77 <---> A 72 : 0.238771 A > A 78 <---> A 73 : 0.311753 A > A 79 <---> A 74 : 0.388701 A > A 80 <---> A 75 : 0.761327 A > A 81 <---> A 76 : 0.904406 A > A 82 <---> A 77 : 0.609012 A > A 83 <---> A 78 : 1.79778 A > A 84 <---> A 79 : 1.92564 A > A 85 <---> A 80 : 1.34157 A > A 86 <---> A 81 : 0.565753 A > A 87 <---> A 82 : 0.448017 A > A 88 <---> A 83 : 0.90782 A > A 89 <---> A 84 : 0.362515 A > A 90 <---> A 85 : 0.404031 A > A 91 <---> A 86 : 0.458593 A > A 92 <---> A 87 : 0.434035 A > A 93 <---> A 88 : 0.366361 A > A 94 <---> A 89 : 0.492061 A > A 95 <---> A 90 : 0.649822 A > A 96 <---> A 91 : 1.58048 A > A 97 <---> A 92 : 2.88385 A > A 98 > A 99 > A 100 > > Moving: KLMRAVRVFEFGGPEVLKLRSDIAVP.IPKDHQVLIKVHACGVNPVETYIRSGTYSRKPLLPYTPGSDVA > Target: --VMAAVIHKKGGPDNFVWEE-VK-VGSPGPGQVRLRNTAIGVNFLDTYHRA--------PPIVVGFEAA > > Moving: GVIEAVGDNASAFKKGDRVFTSSTIS.GGYAEYALAADHTVY > Target: AVVEEVGPGVTDFTVGERVCTCL---PGAYSQERLYPAEKLI > >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_1yb5.pdb_Wed_May__5_09:44:15_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| -0.9117, -0.3803, 0.1557| >| -0.3625, 0.9227, 0.131| >| -0.1935, 0.06299, -0.9791| >( 70.65, 7.793, 21.29) > Rotation - polar (omega,phi,kappa) 87.1413 101.022 169.739 > Rotation - euler (alpha,beta,gamma) 40.0716 168.257 18.0277 > Translation - Angstroms 70.6538 7.793 21.2852 >do_Ca_plus_ligands_bonds with atom_colour_type 0 >INFO: core rmsd achieved: 1.01989 Angstroems > number of residues in reference structure: 322 > number of residues in moving structure: 324 > number of residues in aligned sections (reference): 100 > number of residues in aligned sections (moving): 110 > number of aligned residues: 95 > number of gaps: 4 > number of misdirections: 0 > number of SSE combinations: 4 > sequence identity: 30.5263% >[1m(set-rotation-centre 65.65 -3.00 -4.00)[0m >[1m(go-to-view-number 4 1)[0m >PASS: SSM - Frank von Delft's Example >Entered testcase - SSM - Alice Dawson's Example >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1pyd.pdb" 0)[0m >Error reading /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1pyd.pdb >[1m(graphics-to-ca-plus-ligands-representation -1)[0m >[1m(set-graphics-window-size 687 452)[0m >[1m(molecule-name 0)[0m > 0 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 1)[0m > 1 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/ins-code-fragment-pre.pdb" > 2 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" > 3 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" > 4 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" > 5 "test-3hfl.map" >[1m(molecule-name 6)[0m > 6 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb" >[1m(molecule-name 7)[0m > 7 "atom selection from tutorial-add-terminal-1-test.pdb" >[1m(molecule-name 8)[0m > 8 "sphere selection from tutorial-modern.pdb" >[1m(molecule-name 10)[0m > 10 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rotamer-test-fragment.pdb" >[1m(molecule-name 11)[0m > 11 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/res098.pdb" >[1m(molecule-name 12)[0m > 12 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" > 13 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" >[1m(molecule-name 14)[0m > 14 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-pepflip-test.pdb" >[1m(molecule-name 15)[0m > 15 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" >[1m(molecule-name 16)[0m > 16 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" > 17 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" >[1m(molecule-name 18)[0m > 18 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb" >[1m(molecule-name 19)[0m > 19 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-waters.pdb" >[1m(molecule-name 20)[0m > 20 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb" >[1m(molecule-name 21)[0m > 21 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb" >[1m(molecule-name 22)[0m > 22 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/coords-B3A.pdb" > 23 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" >[1m(molecule-name 24)[0m > 24 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/test-TER-OXT.pdb" >[1m(molecule-name 25)[0m > 25 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/val.pdb" > 26 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" > 27 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" >[1m(molecule-name 28)[0m > 28 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" > 29 "Generic Masked Map" > 30 "difference-map" > 31 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" > 32 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" > 33 "averaged-map" > 34 "difference-map" >[1m(molecule-name 35)[0m > 35 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/multi-carbo-coot-2.pdb" >[1m(molecule-name 36)[0m > 36 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-VAL.pdb" >[1m(molecule-name 37)[0m > 37 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3ins-6B-3.0.pdb" >[1m(molecule-name 38)[0m > 38 "atom selection from tutorial-modern.pdb" >[1m(molecule-name 39)[0m > 39 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb" >[1m(molecule-name 40)[0m > 40 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 41)[0m > 41 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 42)[0m > 42 "atom selection from tutorial-modern.pdb" >[1m(molecule-name 43)[0m > 43 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 44)[0m > 44 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 45)[0m > 45 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnase-A-needs-an-insertion.pdb" >[1m(molecule-name 46)[0m > 46 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb3hfl.ent" > 47 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" >[1m(molecule-name 48)[0m > 48 "Ideal-A-form-RNA" >[1m(molecule-name 49)[0m > 49 "Ideal-A-form-DNA" >[1m(molecule-name 50)[0m > 50 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 51)[0m > 51 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/some-waters-with-ter.pdb" >[1m(molecule-name 52)[0m > 52 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tm+some-waters.pdb" >[1m(molecule-name 53)[0m > 53 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/water-test-no-cell.pdb" >[1m(molecule-name 54)[0m > 54 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pathological-water-test.pdb" >[1m(molecule-name 55)[0m > 55 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" > 56 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" >[1m(molecule-name 57)[0m > 57 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 58)[0m > 58 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 59)[0m > 59 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 60)[0m > 60 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 61)[0m > 61 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 62)[0m > 62 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1py3.ent" >[1m(molecule-name 63)[0m > 63 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2goz-manip.pdb" >[1m(molecule-name 64)[0m > 64 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/HOF.RES" >[1m(molecule-name 65)[0m > 65 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/hollander.ins" > 68 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.fcf.cif Difference SigmaA" >[1m(molecule-name 69)[0m > 69 "atom selection from insulin.res" >[1m(molecule-name 70)[0m > 70 "atom selection from insulin.res" >[1m(molecule-name 72)[0m > 72 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/horma-p21.res" >[1m(molecule-name 73)[0m > 73 "new-horma.ins" >[1m(molecule-name 74)[0m > 74 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" >[1m(molecule-name 75)[0m > 75 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" >[1m(molecule-name 76)[0m > 76 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" >[1m(molecule-name 77)[0m > 77 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" >[1m(molecule-name 78)[0m > 78 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" >[1m(molecule-name 79)[0m > 79 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" >[1m(molecule-name 80)[0m > 80 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" > 81 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" > 82 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" > 83 "Masked (by protein)" >[1m(molecule-name 84)[0m > 84 "Fitted ligand #0" >[1m(molecule-name 85)[0m > 85 "Fitted ligand #1" >[1m(molecule-name 86)[0m > 86 "Fitted ligand #2" >[1m(molecule-name 87)[0m > 87 "Fitted ligand #3" >[1m(molecule-name 88)[0m > 88 "Fitted ligand #4" >[1m(molecule-name 89)[0m > 89 "Fitted ligand #5" >[1m(molecule-name 90)[0m > 90 "Fitted ligand #6" >[1m(molecule-name 91)[0m > 91 "Fitted ligand #7" >[1m(molecule-name 92)[0m > 92 "Fitted ligand #8" >[1m(molecule-name 93)[0m > 93 "Fitted ligand #9" >[1m(molecule-name 94)[0m > 94 "coot-ccp4/monomer-3GP.pdb" >[1m(molecule-name 95)[0m > 95 "Copy of coot-ccp4/monomer-3GP.pdb" >[1m(molecule-name 96)[0m > 96 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/dipole-residues.pdb" >[1m(molecule-name 97)[0m > 97 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" >[1m(molecule-name 98)[0m > 98 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/crashes_on_cootaneering.pdb" > 99 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" >[1m(molecule-name 100)[0m > 100 "Ideal-A-form-RNA" >[1m(molecule-name 103)[0m > 103 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1wly.pdb" >[1m(molecule-name 104)[0m > 104 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1yb5.pdb" >do_Ca_plus_ligands_bonds with atom_colour_type 0 >[1m(graphics-to-ca-plus-ligands-representation 104)[0m >PASS: SSM - Alice Dawson's Example >Entered testcase - SSM by atom selection [JED Example] >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2qd9.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2qd9.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2qd9.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 65.65 74.36 78.98 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 105 read successfully >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2gtn.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2gtn.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2gtn.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.986 74.554 78.029 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 0/337 >Molecule 106 read successfully >INFO:: reference 105 has 169 atoms selected >INFO:: moving 106 has 169 atoms selected >superposing... >number of Ca atoms in selections: 21 (moving) and 21 (reference) >Another Go... > > Moving Reference Distance > A 140 <---> A 140 : 0.180421 A > A 141 <---> A 141 : 0.0760176 A > A 142 <---> A 142 : 0.105242 A > A 143 <---> A 143 : 0.124554 A > A 144 <---> A 144 : 0.136965 A > A 145 <---> A 145 : 0.138022 A > A 146 <---> A 146 : 0.166154 A > A 147 <---> A 147 : 0.274391 A > A 148 <---> A 148 : 0.272752 A > A 149 <---> A 149 : 0.117299 A > A 150 <---> A 150 : 0.168421 A > A 151 <---> A 151 : 0.0928138 A > A 152 <---> A 152 : 0.120023 A > A 153 <---> A 153 : 0.128061 A > A 154 <---> A 154 : 0.253908 A > A 155 <---> A 155 : 0.635071 A > A 156 <---> A 156 : 0.130036 A > A 157 <---> A 157 : 0.147806 A > A 158 <---> A 158 : 0.223824 A > A 159 <---> A 159 : 0.227128 A > A 160 <---> A 160 : 0.23718 A > > Moving: YIHSADIIHRDLKPSNLAVNE > Target: YIHSADIIHRDLKPSNLAVNE > >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_2gtn.pdb_Wed_May__5_09:44:17_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| 0.9998, 0.009845, -0.01938| >| -0.009814, 1, 0.001689| >| 0.0194, -0.001498, 0.9998| >( 0.3207, 0.6598, 0.8819) > Rotation - polar (omega,phi,kappa) 116.804 -94.6984 1.24908 > Rotation - euler (alpha,beta,gamma) 175.02 1.11487 -175.583 > Translation - Angstroms 0.320703 0.659802 0.881869 >INFO: core rmsd achieved: 0.221041 Angstroems > number of residues in reference structure: 330 > number of residues in moving structure: 337 > number of residues in aligned sections (reference): 21 > number of residues in aligned sections (moving): 21 > number of aligned residues: 21 > number of gaps: 0 > number of misdirections: 0 > number of SSE combinations: 1 > sequence identity: 100% >PASS: SSM by atom selection [JED Example] >Ended 06-ssm.scm >Running 07-ncs.scm ... >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res" 1)[0m >LATT LINE: LATT -2 >SFAC LINE: SFAC C H N O S >INFO:: CELL set to 77.726 77.726 77.726 90 90 90 >INFO:: set space group to :I 21 3: >READ-INS:: Spacegroup: I 21 3 >INFO:: chain has 120 residues >Symmetry available for this molecule >Molecule 107 read successfully >[1m(read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res")[0m >Entered testcase - NCS maps test >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnasa-1.8-all_refmac1.mtz >Number of OBSERVED reflections: 17939 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 108, 132, 64) >INFO:: 0.033 seconds to read MTZ file >INFO:: 0.002 seconds to initialize map >INFO:: 0.075 seconds for FFT >INFO:: 0.005 seconds for statistics > Map mean: ........ 1.20509e-09 > Map sigma: ....... 0.311501 > Map maximum: ..... 2.97757 > Map minimum: ..... -0.875045 >INFO:: 0.023 seconds for contour map >INFO:: 0.138 seconds in total >INFO:: NCS chain comparison 93/93 >First atom of 720 in first selection 1/A/1/ASP/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 >First atom of 745 in second selection 1/B/1/ASP/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 >INFO:: LSQ matched 93 atoms >INFO:: 93 matched atoms had: > mean devi: 1.17877 > rms devi: 4.85919 > max devi: 46.259 > min devi: 0.125386 > find_ncs_matrix returns (LSQ) >| 0.9637, -0.07462, -0.2563| >| 0.2651, 0.3804, 0.886| >| 0.0314, -0.9218, 0.3864| >( 38.09, -17.87, 14.32) > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A >Done install_ghost_map >Reference matcher: 0 and 0 >| 0.9637, -0.07462, -0.2563| >| 0.2651, 0.3804, 0.886| >| 0.0314, -0.9218, 0.3864| >( 38.09, -17.87, 14.32) >inverse of reference matcher transformation: >| 0.9637, 0.2651, 0.0314| >| -0.07462, 0.3804, -0.9218| >| -0.2563, 0.886, 0.3864| >( -32.42, 22.84, 20.06) >boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) >INFO:: There were 2 maps contributing to the average >INFO:: rescaling by 0.5 >INFO:: 228096 out of 228096 (100%) map points were masked out of NCS average target volume, chain A >INFO:: made 1 averaged map(s) >Map statistics: mean: 0.000355334 st.d: 0.323619 >Map statistics: min: -1.44957, max: 2.34115 > -1.3548 4 >-1.16527 12 >-0.975731 37 >-0.786195 453 >-0.596659 4596 >-0.407123 26403 >-0.217587 59478 >-0.0280513 58289 >0.161485 36006 >0.351021 20752 >0.540556 11414 >0.730092 5769 >0.919628 2875 > 1.10916 1265 > 1.2987 484 > 1.48824 176 > 1.67777 54 > 1.86731 20 > 2.05684 7 > 2.24638 2 > 2.43592 0 >INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A >Done install_ghost_map >Reference matcher: 0 and 0 >| 0.9637, -0.07462, -0.2563| >| 0.2651, 0.3804, 0.886| >| 0.0314, -0.9218, 0.3864| >( 38.09, -17.87, 14.32) >inverse of reference matcher transformation: >| 0.9637, 0.2651, 0.0314| >| -0.07462, 0.3804, -0.9218| >| -0.2563, 0.886, 0.3864| >( -32.42, 22.84, 20.06) >boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) >INFO:: There were 2 maps contributing to the average >INFO:: rescaling by 0.5 >INFO:: 228096 out of 228096 (100%) map points were masked out of NCS average target volume, chain A >INFO:: made 1 averaged map(s) >Map statistics: mean: 0.000355334 st.d: 0.323619 >Map statistics: min: -1.44957, max: 2.34115 > -1.3548 4 >-1.16527 12 >-0.975731 37 >-0.786195 453 >-0.596659 4596 >-0.407123 26403 >-0.217587 59478 >-0.0280513 58289 >0.161485 36006 >0.351021 20752 >0.540556 11414 >0.730092 5769 >0.919628 2875 > 1.10916 1265 > 1.2987 484 > 1.48824 176 > 1.67777 54 > 1.86731 20 > 2.05684 7 > 2.24638 2 > 2.43592 0 >PASS: NCS maps test >Entered testcase - NCS chains info > NCS info: (("A" "B")) >PASS: NCS chains info >Entered testcase - NCS deviation info >no diffs >NCS target chain has 93 peers. >resinfo: 93 92 to 93 92 diff: 0.82761 >resinfo: 92 91 to 92 91 diff: 0.799087 >resinfo: 91 90 to 91 90 diff: 1.30941 >resinfo: 90 89 to 90 89 diff: 0.848865 >resinfo: 89 88 to 89 88 diff: 3.47756 >resinfo: 88 87 to 88 87 diff: 1.00522 >resinfo: 87 86 to 87 86 diff: 0.793719 >resinfo: 86 85 to 86 85 diff: 0.753689 >resinfo: 85 84 to 85 84 diff: 0.809313 >resinfo: 84 83 to 84 83 diff: 0.846976 >resinfo: 83 82 to 83 82 diff: 0.88646 >resinfo: 82 81 to 82 81 diff: 0.761955 >resinfo: 81 80 to 81 80 diff: 0.804923 >resinfo: 80 79 to 80 79 diff: 0.777717 >resinfo: 79 78 to 79 78 diff: 0.606336 >resinfo: 78 77 to 78 77 diff: 0.586572 >resinfo: 77 76 to 77 76 diff: 0.605209 >resinfo: 76 75 to 76 75 diff: 0.809205 >resinfo: 75 74 to 75 74 diff: 0.473272 >resinfo: 74 73 to 74 73 diff: 0.975401 >resinfo: 73 72 to 73 72 diff: 0.597465 >resinfo: 72 71 to 72 71 diff: 0.58493 >resinfo: 71 70 to 71 70 diff: 0.606996 >resinfo: 70 69 to 70 69 diff: 0.585566 >resinfo: 69 68 to 69 68 diff: 0.64561 >resinfo: 68 67 to 68 67 diff: 0.875328 >resinfo: 67 66 to 67 66 diff: 0.864427 >resinfo: 66 65 to 66 65 diff: 0.732479 >resinfo: 65 64 to 65 64 diff: 0.401137 >resinfo: 64 63 to 64 63 diff: 1.05664 >resinfo: 63 62 to 63 62 diff: 2.85913 >resinfo: 62 61 to 62 61 diff: 1.77684 >resinfo: 61 60 to 61 60 diff: 1.97246 >resinfo: 60 59 to 60 59 diff: 0.721019 >resinfo: 59 58 to 59 58 diff: 0.873866 >resinfo: 58 57 to 58 57 diff: 0.614926 >resinfo: 57 56 to 57 56 diff: 0.604415 >resinfo: 56 55 to 56 55 diff: 0.445784 >resinfo: 55 54 to 55 54 diff: 0.356409 >resinfo: 54 53 to 54 53 diff: 1.29157 >resinfo: 53 52 to 53 52 diff: 0.456392 >resinfo: 52 51 to 52 51 diff: 0.640025 >resinfo: 51 50 to 51 50 diff: 0.545634 >resinfo: 50 49 to 50 49 diff: 0.574687 >resinfo: 49 48 to 49 48 diff: 0.512681 >resinfo: 48 47 to 48 47 diff: 1.2413 >resinfo: 47 46 to 47 46 diff: 0.96611 >resinfo: 46 45 to 46 45 diff: 1.01008 >resinfo: 45 44 to 45 44 diff: 0.968595 >resinfo: 44 43 to 44 43 diff: 0.655634 >resinfo: 43 42 to 43 42 diff: 0.705425 >resinfo: 42 41 to 42 41 diff: 1.02306 >resinfo: 41 40 to 41 40 diff: 1.80032 >resinfo: 40 39 to 40 39 diff: 2.08207 >resinfo: 39 38 to 39 38 diff: 0.401147 >resinfo: 38 37 to 38 37 diff: 0.775939 >resinfo: 37 36 to 37 36 diff: 0.613512 >resinfo: 36 35 to 36 35 diff: 0.401273 >resinfo: 35 34 to 35 34 diff: 0.26647 >resinfo: 34 33 to 34 33 diff: 0.168051 >resinfo: 33 32 to 33 32 diff: 0.246069 >resinfo: 32 31 to 32 31 diff: 1.32047 >resinfo: 31 30 to 31 30 diff: 1.15952 >resinfo: 30 29 to 30 29 diff: 0.319934 >resinfo: 29 28 to 29 28 diff: 0.527386 >resinfo: 28 27 to 28 27 diff: 0.345661 >resinfo: 27 26 to 27 26 diff: 0.55164 >resinfo: 26 25 to 26 25 diff: 0.337172 >resinfo: 25 24 to 25 24 diff: 0.745821 >resinfo: 24 23 to 24 23 diff: 0.596737 >resinfo: 23 22 to 23 22 diff: 0.492913 >resinfo: 22 21 to 22 21 diff: 0.462489 >resinfo: 21 20 to 21 20 diff: 0.507017 >resinfo: 20 19 to 20 19 diff: 0.513467 >resinfo: 19 18 to 19 18 diff: 0.435725 >resinfo: 18 17 to 18 17 diff: 0.406794 >resinfo: 17 16 to 17 16 diff: 0.391245 >resinfo: 16 15 to 16 15 diff: 0.43917 >resinfo: 15 14 to 15 14 diff: 0.503078 >resinfo: 14 13 to 14 13 diff: 0.49505 >resinfo: 13 12 to 13 12 diff: 0.580727 >resinfo: 12 11 to 12 11 diff: 0.525931 >resinfo: 11 10 to 11 10 diff: 0.559115 >resinfo: 10 9 to 10 9 diff: 0.831857 >resinfo: 9 8 to 9 8 diff: 0.94393 >resinfo: 8 7 to 8 7 diff: 0.653129 >resinfo: 7 6 to 7 6 diff: 0.863027 >resinfo: 6 5 to 6 5 diff: 0.803605 >resinfo: 5 4 to 5 4 diff: 0.753019 >resinfo: 4 3 to 4 3 diff: 0.948347 >resinfo: 3 2 to 3 2 diff: 1.08341 >resinfo: 2 1 to 2 1 diff: 7.23927 >resinfo: 1 0 to 1 0 diff: 0.894481 >PASS: NCS deviation info >Entered testcase - NCS Residue Range copy >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb has been read. >Spacegroup: P 21 21 21 >Cell: 64.897 78.323 38.792 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 93/93 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >Molecule 113 read successfully >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_0.pdb.gz >[1m(delete-residue 113 "B" 1 "")[0m >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_1.pdb.gz >[1m(delete-residue 113 "B" 2 "")[0m >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_2.pdb.gz >[1m(delete-residue 113 "B" 3 "")[0m >%%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() >INFO:: NCS chain comparison 90/93 >First atom of 720 in first selection 1/A/1/ASP/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 >First atom of 724 in second selection 1/B/4/GLY/ N altLoc :: segid :: pos: (18.183,22.264,18.93) B-factor: 21.71 >INFO:: LSQ matched 90 atoms >INFO:: 90 matched atoms had: > mean devi: 0.364276 > rms devi: 0.457135 > max devi: 2.1351 > min devi: 0.0880999 > find_ncs_matrix returns (LSQ) >| 0.9705, -0.04634, -0.2366| >| 0.2357, 0.3884, 0.8908| >| 0.05061, -0.9203, 0.3878| >( 37.8, -17.18, 13.82) > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_3.pdb.gz >[1m(setnum-from-serial-number 113 "B" 0)[0m >[1m(setnum-from-serial-number 113 "B" 1)[0m >[1m(setnum-from-serial-number 113 "B" 2)[0m >[1m(setnum-from-serial-number 113 "B" 3)[0m >[1m(setnum-from-serial-number 113 "B" 4)[0m >[1m(setnum-from-serial-number 113 "B" 5)[0m >[1m(setnum-from-serial-number 113 "B" 6)[0m >[1m(setnum-from-serial-number 113 "B" 7)[0m >[1m(setnum-from-serial-number 113 "B" 8)[0m >[1m(setnum-from-serial-number 113 "B" 9)[0m >[1m(setnum-from-serial-number 113 "B" 10)[0m >[1m(setnum-from-serial-number 113 "B" 11)[0m >[1m(setnum-from-serial-number 113 "B" 12)[0m >[1m(setnum-from-serial-number 113 "B" 13)[0m >[1m(setnum-from-serial-number 113 "B" 14)[0m >[1m(setnum-from-serial-number 113 "B" 15)[0m >[1m(setnum-from-serial-number 113 "B" 16)[0m >[1m(setnum-from-serial-number 113 "B" 17)[0m >[1m(setnum-from-serial-number 113 "B" 18)[0m >[1m(setnum-from-serial-number 113 "B" 19)[0m >[1m(setnum-from-serial-number 113 "B" 20)[0m >[1m(setnum-from-serial-number 113 "B" 21)[0m >[1m(setnum-from-serial-number 113 "B" 22)[0m >[1m(setnum-from-serial-number 113 "B" 23)[0m >[1m(setnum-from-serial-number 113 "B" 24)[0m >[1m(setnum-from-serial-number 113 "B" 25)[0m >[1m(setnum-from-serial-number 113 "B" 26)[0m >[1m(setnum-from-serial-number 113 "B" 27)[0m >[1m(setnum-from-serial-number 113 "B" 28)[0m >[1m(setnum-from-serial-number 113 "B" 29)[0m >[1m(setnum-from-serial-number 113 "B" 30)[0m >[1m(setnum-from-serial-number 113 "B" 31)[0m >[1m(setnum-from-serial-number 113 "B" 32)[0m >[1m(setnum-from-serial-number 113 "B" 33)[0m >[1m(setnum-from-serial-number 113 "B" 34)[0m >[1m(setnum-from-serial-number 113 "B" 35)[0m >[1m(setnum-from-serial-number 113 "B" 36)[0m >[1m(setnum-from-serial-number 113 "B" 37)[0m >[1m(setnum-from-serial-number 113 "B" 38)[0m >[1m(setnum-from-serial-number 113 "B" 39)[0m >[1m(setnum-from-serial-number 113 "B" 40)[0m >[1m(setnum-from-serial-number 113 "B" 41)[0m >[1m(setnum-from-serial-number 113 "B" 42)[0m >[1m(setnum-from-serial-number 113 "B" 43)[0m >[1m(setnum-from-serial-number 113 "B" 44)[0m >[1m(setnum-from-serial-number 113 "B" 45)[0m >[1m(setnum-from-serial-number 113 "B" 46)[0m >[1m(setnum-from-serial-number 113 "B" 47)[0m >[1m(setnum-from-serial-number 113 "B" 48)[0m >[1m(setnum-from-serial-number 113 "B" 49)[0m >[1m(setnum-from-serial-number 113 "B" 50)[0m >[1m(setnum-from-serial-number 113 "B" 51)[0m >[1m(setnum-from-serial-number 113 "B" 52)[0m >[1m(setnum-from-serial-number 113 "B" 53)[0m >[1m(setnum-from-serial-number 113 "B" 54)[0m >[1m(setnum-from-serial-number 113 "B" 55)[0m >[1m(setnum-from-serial-number 113 "B" 56)[0m >[1m(setnum-from-serial-number 113 "B" 57)[0m >[1m(setnum-from-serial-number 113 "B" 58)[0m >[1m(setnum-from-serial-number 113 "B" 59)[0m >[1m(setnum-from-serial-number 113 "B" 60)[0m >[1m(setnum-from-serial-number 113 "B" 61)[0m >[1m(setnum-from-serial-number 113 "B" 62)[0m >[1m(setnum-from-serial-number 113 "B" 63)[0m >[1m(setnum-from-serial-number 113 "B" 64)[0m >[1m(setnum-from-serial-number 113 "B" 65)[0m >[1m(setnum-from-serial-number 113 "B" 66)[0m >[1m(setnum-from-serial-number 113 "B" 67)[0m >[1m(setnum-from-serial-number 113 "B" 68)[0m >[1m(setnum-from-serial-number 113 "B" 69)[0m >[1m(setnum-from-serial-number 113 "B" 70)[0m >[1m(setnum-from-serial-number 113 "B" 71)[0m >[1m(setnum-from-serial-number 113 "B" 72)[0m >[1m(setnum-from-serial-number 113 "B" 73)[0m >[1m(setnum-from-serial-number 113 "B" 74)[0m >[1m(setnum-from-serial-number 113 "B" 75)[0m >[1m(setnum-from-serial-number 113 "B" 76)[0m >[1m(setnum-from-serial-number 113 "B" 77)[0m >[1m(setnum-from-serial-number 113 "B" 78)[0m >[1m(setnum-from-serial-number 113 "B" 79)[0m >[1m(setnum-from-serial-number 113 "B" 80)[0m >[1m(setnum-from-serial-number 113 "B" 81)[0m >[1m(setnum-from-serial-number 113 "B" 82)[0m >[1m(setnum-from-serial-number 113 "B" 83)[0m >[1m(setnum-from-serial-number 113 "B" 84)[0m >[1m(setnum-from-serial-number 113 "B" 85)[0m >[1m(setnum-from-serial-number 113 "B" 86)[0m >[1m(setnum-from-serial-number 113 "B" 87)[0m >[1m(setnum-from-serial-number 113 "B" 88)[0m >[1m(setnum-from-serial-number 113 "B" 89)[0m >[1m(setnum-from-serial-number 113 "B" 90)[0m >[1m(setnum-from-serial-number 113 "B" 91)[0m >[1m(setnum-from-serial-number 113 "B" 92)[0m >[1m(setnum-from-serial-number 113 "B" 93)[0m >[1m(setnum-from-serial-number 113 "B" 94)[0m >[1m(setnum-from-serial-number 113 "B" 95)[0m >INFO:: mutate 2 A to a TRP >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_4.pdb.gz >[1m(mutate 2 "A" 113 "TRP")[0m >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_5.pdb.gz >PASS: NCS Residue Range copy >Entered testcase - NCS Residue Range edit to all chains >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1t6q.ent" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1t6q.ent > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1t6q.ent has been read. >Spacegroup: C 2 2 21 >Cell: 60.041 112.491 111.298 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 110/110 >INFO:: NCS chain comparison 110/110 > INFO:: fill_ghost_info Constructed 2 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > Ghost 1 name: "NCS found from matching Chain C onto Chain A" >Molecule 114 read successfully >INFO:: mutate 50 A to a ASP >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb1t6q.ent_Wed_May__5_09:44:21_2010_modification_0.pdb.gz >[1m(mutate 50 "A" 114 "ASP")[0m >[1m(is-solvent-chain-p 114 "C")[0m >%%%%%%%%% calling fill_ghost_info() from c-interface.cc make_ncs_ghosts_maybe() >INFO:: NCS chain comparison 109/110 >First atom of 881 in first selection 1/A/7/GLY/ N altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18 >First atom of 893 in second selection 1/B/6/CYS/ N altLoc :: segid :: pos: (45.362,34.24,30.671) B-factor: 84.36 >INFO:: LSQ matched 110 atoms >INFO:: 110 matched atoms had: > mean devi: 0.20482 > rms devi: 0.265098 > max devi: 1.17072 > min devi: 0.0159991 > find_ncs_matrix returns (LSQ) >| 0.5407, 0.4775, 0.6926| >| -0.4862, -0.4944, 0.7205| >| 0.6865, -0.7263, -0.03511| >( -28.15, 65.89, 42.9) >INFO:: NCS chain comparison 109/110 >First atom of 881 in first selection 1/A/7/GLY/ N altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18 >First atom of 881 in second selection 1/C/7/GLY/ N altLoc :: segid :: pos: (47.664,58.992,25.996) B-factor: 67.72 >INFO:: LSQ matched 110 atoms >INFO:: 110 matched atoms had: > mean devi: 0.227456 > rms devi: 0.303489 > max devi: 1.65495 > min devi: 0.0660944 > find_ncs_matrix returns (LSQ) >| 0.5303, -0.4851, 0.6953| >| 0.4758, -0.5085, -0.7177| >| 0.7017, 0.7114, -0.03884| >( 18.19, 77.78, -25.69) > INFO:: fill_ghost_info Constructed 2 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > Ghost 1 name: "NCS found from matching Chain C onto Chain A" >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb1t6q.ent_Wed_May__5_09:44:21_2010_modification_1.pdb.gz >INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb1t6q.ent_Wed_May__5_09:44:21_2010_modification_2.pdb.gz >result: (#t #t) >PASS: NCS Residue Range edit to all chains >Entered testcase - Manual NCS ghosts generates correct NCS chain ids >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent has been read. >Spacegroup: P 31 2 1 >Cell: 88.32 88.32 115.62 90 90 120 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 62/67 >INFO:: NCS chain comparison 66/67 >INFO:: NCS chain comparison 61/67 >INFO:: NCS chain comparison 0/67 > INFO:: fill_ghost_info Constructed 3 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > Ghost 1 name: "NCS found from matching Chain C onto Chain A" > Ghost 2 name: "NCS found from matching Chain D onto Chain A" >Molecule 115 read successfully >DEBUG ncs_control_change_ncs_master_to_chain_id imol: 115 and chain_id: B > %%%%%% add_ncs_ghosts_using_ncs_master > %%%%%% imaster: 1 > Checking chains for NCS matching to chain B >INFO:: NCS chain comparison 62/62 >First atom of 506 in first selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 >First atom of 540 in second selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 >INFO:: LSQ matched 62 atoms >INFO:: 62 matched atoms had: > mean devi: 2.49888 > rms devi: 2.79624 > max devi: 6.68599 > min devi: 0.440067 > find_ncs_matrix returns (LSQ) >| 0.7026, 0.1278, 0.7| >| 0.6024, 0.4169, -0.6807| >| -0.3788, 0.8999, 0.2159| >( 62.25, -87.53, -9.128) > Adding ghost with name: NCS found from matching Chain A onto Chain B >INFO:: NCS chain comparison 62/62 >First atom of 506 in first selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 >First atom of 535 in second selection 1/C/190/GLN/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76 >INFO:: LSQ matched 62 atoms >INFO:: 62 matched atoms had: > mean devi: 2.6728 > rms devi: 2.9369 > max devi: 6.12 > min devi: 0.248273 > find_ncs_matrix returns (LSQ) >| -0.3504, -0.8022, -0.4834| >| -0.7587, -0.05952, 0.6488| >| -0.5492, 0.594, -0.5878| >( -29.05, 14.61, -72.53) > Adding ghost with name: NCS found from matching Chain C onto Chain B >INFO:: NCS chain comparison 61/62 >First atom of 506 in first selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 >First atom of 497 in second selection 1/D/193/SER/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35 >INFO:: LSQ matched 61 atoms >INFO:: 61 matched atoms had: > mean devi: 1.73174 > rms devi: 1.9769 > max devi: 7.94534 > min devi: 0.52974 > find_ncs_matrix returns (LSQ) >| -0.3815, -0.9208, -0.08098| >| -0.9191, 0.3685, 0.1396| >| -0.09874, 0.1277, -0.9869| >( -11.18, 4.757, -127.2) > Adding ghost with name: NCS found from matching Chain D onto Chain B >INFO:: NCS chain comparison 0/62 >INFO:: set_ncs_master_chain Constructed 3 ghosts > Ghost info:: NCS found from matching Chain A onto Chain B > Ghost info:: NCS found from matching Chain C onto Chain B > Ghost info:: NCS found from matching Chain D onto Chain B >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 115)[0m >INFO:: Matching/moving molecule number 116 to 115 >INFO:: LSQ matched 44 atoms >INFO:: 44 matched atoms had: > mean devi: 0.223919 > rms devi: 0.23495 > max devi: 0.3369 > min devi: 0.0588188 >INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) >INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb1hvv.ent_Wed_May__5_09:44:23_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| 0.3395, 0.5177, 0.7853| >| 0.8624, 0.162, -0.4796| >| -0.3755, 0.8401, -0.3915| >( 90.55, -91.12, -47.52) >INFO:: fractional coordinates matrix: >| 0.8374, 0.1106, 0.6656| >| 0.9958, -0.3359, -0.7249| >| -0.2868, 0.6992, -0.3915| >( 0.4296, -1.191, -0.411) >successfully set cell and symmetry >[1m(close-molecule 116)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 115)[0m >INFO:: Matching/moving molecule number 117 to 115 >INFO:: LSQ matched 44 atoms >INFO:: 44 matched atoms had: > mean devi: 0.194298 > rms devi: 0.211186 > max devi: 0.358313 > min devi: 0.0328719 >INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095) >INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb1hvv.ent_Wed_May__5_09:44:23_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| -0.6203, -0.2279, -0.7505| >| -0.4559, -0.6739, 0.5814| >| -0.6382, 0.7028, 0.3141| >( -22.14, -19.93, 1.626) >INFO:: fractional coordinates matrix: >| -0.8835, -0.09252, -0.543| >| -0.5264, -0.4107, 0.8789| >| -0.4875, 0.7087, 0.3141| >( -0.381, -0.2605, 0.01406) >successfully set cell and symmetry >[1m(close-molecule 117)[0m >Symmetry available for this molecule >[1m(update-go-to-atom-window-on-new-mol)[0m >[1m(copy-molecule 115)[0m >INFO:: Matching/moving molecule number 118 to 115 >INFO:: LSQ matched 44 atoms >INFO:: 44 matched atoms had: > mean devi: 0.417399 > rms devi: 0.453088 > max devi: 0.792632 > min devi: 0.0759332 >INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411) >INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) >INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_pdb1hvv.ent_Wed_May__5_09:44:23_2010_modification_0.pdb.gz >INFO:: coordinates transformed by orthonal matrix: >| -0.2227, -0.9733, -0.05471| >| -0.9662, 0.2129, 0.1454| >| -0.1299, 0.08525, -0.9879| >( -15.82, -0.3228, -130) >INFO:: fractional coordinates matrix: >| -0.7806, -0.3462, 0.03831| >| -1.116, 0.7707, 0.2198| >| -0.09924, 0.106, -0.9879| >( -0.1813, -0.00422, -1.125) >successfully set cell and symmetry >[1m(close-molecule 118)[0m > NCS ghost chain IDs pre: (("B" "A" "C" "D")) > NCS ghost chain IDs post: (("B" "A" "C" "D")) >PASS: Manual NCS ghosts generates correct NCS chain ids >Entered testcase - NCS maps overwrite existing maps >[1m(molecule-name 0)[0m >[1m(molecule-name 1)[0m >[1m(molecule-name 6)[0m >[1m(molecule-name 7)[0m >[1m(molecule-name 8)[0m >[1m(molecule-name 10)[0m >[1m(molecule-name 11)[0m >[1m(molecule-name 12)[0m >[1m(molecule-name 14)[0m >[1m(molecule-name 15)[0m >[1m(molecule-name 16)[0m >[1m(molecule-name 18)[0m >[1m(molecule-name 19)[0m >[1m(molecule-name 20)[0m >[1m(molecule-name 21)[0m >[1m(molecule-name 22)[0m >[1m(molecule-name 24)[0m >[1m(molecule-name 25)[0m >[1m(molecule-name 28)[0m >[1m(molecule-name 35)[0m >[1m(molecule-name 36)[0m >[1m(molecule-name 37)[0m >[1m(molecule-name 38)[0m >[1m(molecule-name 39)[0m >[1m(molecule-name 40)[0m >[1m(molecule-name 41)[0m >[1m(molecule-name 42)[0m >[1m(molecule-name 43)[0m >[1m(molecule-name 44)[0m >[1m(molecule-name 45)[0m >[1m(molecule-name 46)[0m >[1m(molecule-name 48)[0m >[1m(molecule-name 49)[0m >[1m(molecule-name 50)[0m >[1m(molecule-name 51)[0m >[1m(molecule-name 52)[0m >[1m(molecule-name 53)[0m >[1m(molecule-name 54)[0m >[1m(molecule-name 55)[0m >[1m(molecule-name 57)[0m >[1m(molecule-name 58)[0m >[1m(molecule-name 59)[0m >[1m(molecule-name 60)[0m >[1m(molecule-name 61)[0m >[1m(molecule-name 62)[0m >[1m(molecule-name 63)[0m >[1m(molecule-name 64)[0m >[1m(molecule-name 65)[0m >[1m(molecule-name 69)[0m >[1m(molecule-name 70)[0m >[1m(molecule-name 72)[0m >[1m(molecule-name 73)[0m >[1m(molecule-name 74)[0m >[1m(molecule-name 75)[0m >[1m(molecule-name 76)[0m >[1m(molecule-name 77)[0m >[1m(molecule-name 78)[0m >[1m(molecule-name 79)[0m >[1m(molecule-name 80)[0m >[1m(molecule-name 84)[0m >[1m(molecule-name 85)[0m >[1m(molecule-name 86)[0m >[1m(molecule-name 87)[0m >[1m(molecule-name 88)[0m >[1m(molecule-name 89)[0m >[1m(molecule-name 90)[0m >[1m(molecule-name 91)[0m >[1m(molecule-name 92)[0m >[1m(molecule-name 93)[0m >[1m(molecule-name 94)[0m >[1m(molecule-name 95)[0m >[1m(molecule-name 96)[0m >[1m(molecule-name 97)[0m >[1m(molecule-name 98)[0m >[1m(molecule-name 100)[0m >[1m(molecule-name 103)[0m >[1m(molecule-name 104)[0m >[1m(molecule-name 105)[0m >[1m(molecule-name 106)[0m >[1m(molecule-name 107)[0m >[1m(close-molecule 109)[0m >[1m(close-molecule 111)[0m >[1m(molecule-name 113)[0m >[1m(molecule-name 114)[0m >[1m(molecule-name 115)[0m >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent has been read. >Spacegroup: P 31 2 1 >Cell: 88.32 88.32 115.62 90 90 120 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >INFO:: NCS chain comparison 62/67 >INFO:: NCS chain comparison 66/67 >INFO:: NCS chain comparison 61/67 >INFO:: NCS chain comparison 0/67 > INFO:: fill_ghost_info Constructed 3 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > Ghost 1 name: "NCS found from matching Chain C onto Chain A" > Ghost 2 name: "NCS found from matching Chain D onto Chain A" >Molecule 119 read successfully >[1m(make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0)[0m >INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1hvv_sigmaa.mtz >Number of OBSERVED reflections: 20903 >INFO:: finding ASU unique map points with sampling rate 1.5 >INFO grid sampling...Nuvw = ( 112, 112, 150) >INFO:: 0.074 seconds to read MTZ file >INFO:: 0.128 seconds to initialize map >INFO:: 0.135 seconds for FFT >INFO:: 0.008 seconds for statistics > Map mean: ........ -1.58383e-06 > Map sigma: ....... 0.224074 > Map maximum: ..... 1.72187 > Map minimum: ..... -0.881789 >INFO:: 0.016 seconds for contour map >INFO:: 0.361 seconds in total >INFO:: NCS chain comparison 62/67 >First atom of 540 in first selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 >First atom of 506 in second selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 >INFO:: LSQ matched 62 atoms >INFO:: 62 matched atoms had: > mean devi: 2.49888 > rms devi: 2.79624 > max devi: 6.68599 > min devi: 0.440067 > find_ncs_matrix returns (LSQ) >| 0.7026, 0.6024, -0.3788| >| 0.1278, 0.4169, 0.8999| >| 0.7, -0.6807, 0.2159| >( 5.528, 36.75, -101.2) >INFO:: NCS chain comparison 66/67 >First atom of 540 in first selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 >First atom of 535 in second selection 1/C/190/GLN/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76 >INFO:: LSQ matched 66 atoms >INFO:: 66 matched atoms had: > mean devi: 1.97132 > rms devi: 2.1729 > max devi: 4.54109 > min devi: 0.429522 > find_ncs_matrix returns (LSQ) >| -0.4445, -0.8903, -0.09887| >| -0.893, 0.4317, 0.1271| >| -0.07049, 0.1448, -0.9869| >( -8.624, 7.402, -127.7) >INFO:: NCS chain comparison 61/67 >First atom of 540 in first selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 >First atom of 497 in second selection 1/D/193/SER/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35 >INFO:: LSQ matched 61 atoms >INFO:: 61 matched atoms had: > mean devi: 3.70416 > rms devi: 4.0859 > max devi: 9.43828 > min devi: 0.285802 > find_ncs_matrix returns (LSQ) >| -0.7198, -0.6079, 0.3353| >| -0.5986, 0.2989, -0.7432| >| 0.3516, -0.7356, -0.579| >( 36.14, -61.4, -149.3) >INFO:: NCS chain comparison 0/67 > INFO:: fill_ghost_info Constructed 3 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > Ghost 1 name: "NCS found from matching Chain C onto Chain A" > Ghost 2 name: "NCS found from matching Chain D onto Chain A" >INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A >Done install_ghost_map >INFO:: installing ghost map with name :NCS found from matching Chain C onto Chain A >Done install_ghost_map >INFO:: installing ghost map with name :NCS found from matching Chain D onto Chain A >Done install_ghost_map >Reference matcher: 0 and 0 >| 0.7026, 0.6024, -0.3788| >| 0.1278, 0.4169, 0.8999| >| 0.7, -0.6807, 0.2159| >( 5.528, 36.75, -101.2) >inverse of reference matcher transformation: >| 0.7026, 0.1278, 0.7| >| 0.6024, 0.4169, -0.6807| >| -0.3788, 0.8999, 0.2159| >( 62.25, -87.53, -9.128) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >Reference matcher: 0 and 1 >| -0.4445, -0.8903, -0.09887| >| -0.893, 0.4317, 0.1271| >| -0.07049, 0.1448, -0.9869| >( -8.624, 7.402, -127.7) >inverse of reference matcher transformation: >| -0.4445, -0.893, -0.07049| >| -0.8903, 0.4317, 0.1448| >| -0.09887, 0.1271, -0.9869| >( -6.223, 7.613, -127.8) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >Reference matcher: 0 and 2 >| -0.7198, -0.6079, 0.3353| >| -0.5986, 0.2989, -0.7432| >| 0.3516, -0.7356, -0.579| >( 36.14, -61.4, -149.3) >inverse of reference matcher transformation: >| -0.7198, -0.5986, 0.3516| >| -0.6079, 0.2989, -0.7356| >| 0.3353, -0.7432, -0.579| >( 41.75, -69.53, -144.2) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >INFO:: There were 4 maps contributing to the average >INFO:: rescaling by 0.25 >INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A >INFO:: made 1 averaged map(s) >Map statistics: mean: -0.000831256 st.d: 0.176659 >Map statistics: min: -0.997714, max: 1.48656 >-0.935607 4 >-0.811393 18 >-0.687179 139 >-0.562965 686 >-0.438751 3580 >-0.314537 13684 >-0.190323 43824 >-0.0661091 105065 >0.0581048 85978 >0.182319 35332 >0.306533 15215 >0.430747 6067 >0.554961 2422 >0.679174 947 >0.803388 405 >0.927602 206 > 1.05182 85 > 1.17603 38 > 1.30024 9 > 1.42446 8 > 1.54867 0 >INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A >Done install_ghost_map >INFO:: installing ghost map with name :NCS found from matching Chain C onto Chain A >Done install_ghost_map >INFO:: installing ghost map with name :NCS found from matching Chain D onto Chain A >Done install_ghost_map >Reference matcher: 0 and 0 >| 0.7026, 0.6024, -0.3788| >| 0.1278, 0.4169, 0.8999| >| 0.7, -0.6807, 0.2159| >( 5.528, 36.75, -101.2) >inverse of reference matcher transformation: >| 0.7026, 0.1278, 0.7| >| 0.6024, 0.4169, -0.6807| >| -0.3788, 0.8999, 0.2159| >( 62.25, -87.53, -9.128) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >Reference matcher: 0 and 1 >| -0.4445, -0.8903, -0.09887| >| -0.893, 0.4317, 0.1271| >| -0.07049, 0.1448, -0.9869| >( -8.624, 7.402, -127.7) >inverse of reference matcher transformation: >| -0.4445, -0.893, -0.07049| >| -0.8903, 0.4317, 0.1448| >| -0.09887, 0.1271, -0.9869| >( -6.223, 7.613, -127.8) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >Reference matcher: 0 and 2 >| -0.7198, -0.6079, 0.3353| >| -0.5986, 0.2989, -0.7432| >| 0.3516, -0.7356, -0.579| >( 36.14, -61.4, -149.3) >inverse of reference matcher transformation: >| -0.7198, -0.5986, 0.3516| >| -0.6079, 0.2989, -0.7356| >| 0.3353, -0.7432, -0.579| >( 41.75, -69.53, -144.2) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >INFO:: There were 4 maps contributing to the average >INFO:: rescaling by 0.25 >INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A >INFO:: made 1 averaged map(s) >Map statistics: mean: -0.000831256 st.d: 0.176659 >Map statistics: min: -0.997714, max: 1.48656 >-0.935607 4 >-0.811393 18 >-0.687179 139 >-0.562965 686 >-0.438751 3580 >-0.314537 13684 >-0.190323 43824 >-0.0661091 105065 >0.0581048 85978 >0.182319 35332 >0.306533 15215 >0.430747 6067 >0.554961 2422 >0.679174 947 >0.803388 405 >0.927602 206 > 1.05182 85 > 1.17603 38 > 1.30024 9 > 1.42446 8 > 1.54867 0 >INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A >Done install_ghost_map >INFO:: installing ghost map with name :NCS found from matching Chain C onto Chain A >Done install_ghost_map >INFO:: installing ghost map with name :NCS found from matching Chain D onto Chain A >Done install_ghost_map >Reference matcher: 0 and 0 >| 0.7026, 0.6024, -0.3788| >| 0.1278, 0.4169, 0.8999| >| 0.7, -0.6807, 0.2159| >( 5.528, 36.75, -101.2) >inverse of reference matcher transformation: >| 0.7026, 0.1278, 0.7| >| 0.6024, 0.4169, -0.6807| >| -0.3788, 0.8999, 0.2159| >( 62.25, -87.53, -9.128) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >Reference matcher: 0 and 1 >| -0.4445, -0.8903, -0.09887| >| -0.893, 0.4317, 0.1271| >| -0.07049, 0.1448, -0.9869| >( -8.624, 7.402, -127.7) >inverse of reference matcher transformation: >| -0.4445, -0.893, -0.07049| >| -0.8903, 0.4317, 0.1448| >| -0.09887, 0.1271, -0.9869| >( -6.223, 7.613, -127.8) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >Reference matcher: 0 and 2 >| -0.7198, -0.6079, 0.3353| >| -0.5986, 0.2989, -0.7432| >| 0.3516, -0.7356, -0.579| >( 36.14, -61.4, -149.3) >inverse of reference matcher transformation: >| -0.7198, -0.5986, 0.3516| >| -0.6079, 0.2989, -0.7356| >| 0.3353, -0.7432, -0.579| >( 41.75, -69.53, -144.2) >boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) >INFO:: There were 4 maps contributing to the average >INFO:: rescaling by 0.25 >INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A >INFO:: made 1 averaged map(s) >Map statistics: mean: -0.000831256 st.d: 0.176659 >Map statistics: min: -0.997714, max: 1.48656 >-0.935607 4 >-0.811393 18 >-0.687179 139 >-0.562965 686 >-0.438751 3580 >-0.314537 13684 >-0.190323 43824 >-0.0661091 105065 >0.0581048 85978 >0.182319 35332 >0.306533 15215 >0.430747 6067 >0.554961 2422 >0.679174 947 >0.803388 405 >0.927602 206 > 1.05182 85 > 1.17603 38 > 1.30024 9 > 1.42446 8 > 1.54867 0 >[1m(molecule-name 0)[0m >[1m(molecule-name 1)[0m >[1m(molecule-name 6)[0m >[1m(molecule-name 7)[0m >[1m(molecule-name 8)[0m >[1m(molecule-name 10)[0m >[1m(molecule-name 11)[0m >[1m(molecule-name 12)[0m >[1m(molecule-name 14)[0m >[1m(molecule-name 15)[0m >[1m(molecule-name 16)[0m >[1m(molecule-name 18)[0m >[1m(molecule-name 19)[0m >[1m(molecule-name 20)[0m >[1m(molecule-name 21)[0m >[1m(molecule-name 22)[0m >[1m(molecule-name 24)[0m >[1m(molecule-name 25)[0m >[1m(molecule-name 28)[0m >[1m(molecule-name 35)[0m >[1m(molecule-name 36)[0m >[1m(molecule-name 37)[0m >[1m(molecule-name 38)[0m >[1m(molecule-name 39)[0m >[1m(molecule-name 40)[0m >[1m(molecule-name 41)[0m >[1m(molecule-name 42)[0m >[1m(molecule-name 43)[0m >[1m(molecule-name 44)[0m >[1m(molecule-name 45)[0m >[1m(molecule-name 46)[0m >[1m(molecule-name 48)[0m >[1m(molecule-name 49)[0m >[1m(molecule-name 50)[0m >[1m(molecule-name 51)[0m >[1m(molecule-name 52)[0m >[1m(molecule-name 53)[0m >[1m(molecule-name 54)[0m >[1m(molecule-name 55)[0m >[1m(molecule-name 57)[0m >[1m(molecule-name 58)[0m >[1m(molecule-name 59)[0m >[1m(molecule-name 60)[0m >[1m(molecule-name 61)[0m >[1m(molecule-name 62)[0m >[1m(molecule-name 63)[0m >[1m(molecule-name 64)[0m >[1m(molecule-name 65)[0m >[1m(molecule-name 69)[0m >[1m(molecule-name 70)[0m >[1m(molecule-name 72)[0m >[1m(molecule-name 73)[0m >[1m(molecule-name 74)[0m >[1m(molecule-name 75)[0m >[1m(molecule-name 76)[0m >[1m(molecule-name 77)[0m >[1m(molecule-name 78)[0m >[1m(molecule-name 79)[0m >[1m(molecule-name 80)[0m >[1m(molecule-name 84)[0m >[1m(molecule-name 85)[0m >[1m(molecule-name 86)[0m >[1m(molecule-name 87)[0m >[1m(molecule-name 88)[0m >[1m(molecule-name 89)[0m >[1m(molecule-name 90)[0m >[1m(molecule-name 91)[0m >[1m(molecule-name 92)[0m >[1m(molecule-name 93)[0m >[1m(molecule-name 94)[0m >[1m(molecule-name 95)[0m >[1m(molecule-name 96)[0m >[1m(molecule-name 97)[0m >[1m(molecule-name 98)[0m >[1m(molecule-name 100)[0m >[1m(molecule-name 103)[0m >[1m(molecule-name 104)[0m >[1m(molecule-name 105)[0m >[1m(molecule-name 106)[0m >[1m(molecule-name 107)[0m >[1m(molecule-name 113)[0m >[1m(molecule-name 114)[0m >[1m(molecule-name 115)[0m >[1m(molecule-name 119)[0m >==== "NCS found from matching Chain B onto Chain A" 2 >[1m(molecule-name 0)[0m >[1m(molecule-name 1)[0m >[1m(molecule-name 6)[0m >[1m(molecule-name 7)[0m >[1m(molecule-name 8)[0m >[1m(molecule-name 10)[0m >[1m(molecule-name 11)[0m >[1m(molecule-name 12)[0m >[1m(molecule-name 14)[0m >[1m(molecule-name 15)[0m >[1m(molecule-name 16)[0m >[1m(molecule-name 18)[0m >[1m(molecule-name 19)[0m >[1m(molecule-name 20)[0m >[1m(molecule-name 21)[0m >[1m(molecule-name 22)[0m >[1m(molecule-name 24)[0m >[1m(molecule-name 25)[0m >[1m(molecule-name 28)[0m >[1m(molecule-name 35)[0m >[1m(molecule-name 36)[0m >[1m(molecule-name 37)[0m >[1m(molecule-name 38)[0m >[1m(molecule-name 39)[0m >[1m(molecule-name 40)[0m >[1m(molecule-name 41)[0m >[1m(molecule-name 42)[0m >[1m(molecule-name 43)[0m >[1m(molecule-name 44)[0m >[1m(molecule-name 45)[0m >[1m(molecule-name 46)[0m >[1m(molecule-name 48)[0m >[1m(molecule-name 49)[0m >[1m(molecule-name 50)[0m >[1m(molecule-name 51)[0m >[1m(molecule-name 52)[0m >[1m(molecule-name 53)[0m >[1m(molecule-name 54)[0m >[1m(molecule-name 55)[0m >[1m(molecule-name 57)[0m >[1m(molecule-name 58)[0m >[1m(molecule-name 59)[0m >[1m(molecule-name 60)[0m >[1m(molecule-name 61)[0m >[1m(molecule-name 62)[0m >[1m(molecule-name 63)[0m >[1m(molecule-name 64)[0m >[1m(molecule-name 65)[0m >[1m(molecule-name 69)[0m >[1m(molecule-name 70)[0m >[1m(molecule-name 72)[0m >[1m(molecule-name 73)[0m >[1m(molecule-name 74)[0m >[1m(molecule-name 75)[0m >[1m(molecule-name 76)[0m >[1m(molecule-name 77)[0m >[1m(molecule-name 78)[0m >[1m(molecule-name 79)[0m >[1m(molecule-name 80)[0m >[1m(molecule-name 84)[0m >[1m(molecule-name 85)[0m >[1m(molecule-name 86)[0m >[1m(molecule-name 87)[0m >[1m(molecule-name 88)[0m >[1m(molecule-name 89)[0m >[1m(molecule-name 90)[0m >[1m(molecule-name 91)[0m >[1m(molecule-name 92)[0m >[1m(molecule-name 93)[0m >[1m(molecule-name 94)[0m >[1m(molecule-name 95)[0m >[1m(molecule-name 96)[0m >[1m(molecule-name 97)[0m >[1m(molecule-name 98)[0m >[1m(molecule-name 100)[0m >[1m(molecule-name 103)[0m >[1m(molecule-name 104)[0m >[1m(molecule-name 105)[0m >[1m(molecule-name 106)[0m >[1m(molecule-name 107)[0m >[1m(molecule-name 113)[0m >[1m(molecule-name 114)[0m >[1m(molecule-name 115)[0m >[1m(molecule-name 119)[0m >==== "NCS found from matching Chain C onto Chain A" 2 >[1m(molecule-name 0)[0m >[1m(molecule-name 1)[0m >[1m(molecule-name 6)[0m >[1m(molecule-name 7)[0m >[1m(molecule-name 8)[0m >[1m(molecule-name 10)[0m >[1m(molecule-name 11)[0m >[1m(molecule-name 12)[0m >[1m(molecule-name 14)[0m >[1m(molecule-name 15)[0m >[1m(molecule-name 16)[0m >[1m(molecule-name 18)[0m >[1m(molecule-name 19)[0m >[1m(molecule-name 20)[0m >[1m(molecule-name 21)[0m >[1m(molecule-name 22)[0m >[1m(molecule-name 24)[0m >[1m(molecule-name 25)[0m >[1m(molecule-name 28)[0m >[1m(molecule-name 35)[0m >[1m(molecule-name 36)[0m >[1m(molecule-name 37)[0m >[1m(molecule-name 38)[0m >[1m(molecule-name 39)[0m >[1m(molecule-name 40)[0m >[1m(molecule-name 41)[0m >[1m(molecule-name 42)[0m >[1m(molecule-name 43)[0m >[1m(molecule-name 44)[0m >[1m(molecule-name 45)[0m >[1m(molecule-name 46)[0m >[1m(molecule-name 48)[0m >[1m(molecule-name 49)[0m >[1m(molecule-name 50)[0m >[1m(molecule-name 51)[0m >[1m(molecule-name 52)[0m >[1m(molecule-name 53)[0m >[1m(molecule-name 54)[0m >[1m(molecule-name 55)[0m >[1m(molecule-name 57)[0m >[1m(molecule-name 58)[0m >[1m(molecule-name 59)[0m >[1m(molecule-name 60)[0m >[1m(molecule-name 61)[0m >[1m(molecule-name 62)[0m >[1m(molecule-name 63)[0m >[1m(molecule-name 64)[0m >[1m(molecule-name 65)[0m >[1m(molecule-name 69)[0m >[1m(molecule-name 70)[0m >[1m(molecule-name 72)[0m >[1m(molecule-name 73)[0m >[1m(molecule-name 74)[0m >[1m(molecule-name 75)[0m >[1m(molecule-name 76)[0m >[1m(molecule-name 77)[0m >[1m(molecule-name 78)[0m >[1m(molecule-name 79)[0m >[1m(molecule-name 80)[0m >[1m(molecule-name 84)[0m >[1m(molecule-name 85)[0m >[1m(molecule-name 86)[0m >[1m(molecule-name 87)[0m >[1m(molecule-name 88)[0m >[1m(molecule-name 89)[0m >[1m(molecule-name 90)[0m >[1m(molecule-name 91)[0m >[1m(molecule-name 92)[0m >[1m(molecule-name 93)[0m >[1m(molecule-name 94)[0m >[1m(molecule-name 95)[0m >[1m(molecule-name 96)[0m >[1m(molecule-name 97)[0m >[1m(molecule-name 98)[0m >[1m(molecule-name 100)[0m >[1m(molecule-name 103)[0m >[1m(molecule-name 104)[0m >[1m(molecule-name 105)[0m >[1m(molecule-name 106)[0m >[1m(molecule-name 107)[0m >[1m(molecule-name 113)[0m >[1m(molecule-name 114)[0m >[1m(molecule-name 115)[0m >[1m(molecule-name 119)[0m >==== "NCS found from matching Chain D onto Chain A" 2 >PASS: NCS maps overwrite existing maps >Ended 07-ncs.scm >Running 08-utils.scm ... >Entered testcase - Test key symbols >WARNING:: could not find key-sym-code for "missing key" >PASS: Test key symbols >Entered testcase - Test running a Python function >error (syntax error) >error (syntax error) >WARNING:: py_clean_internal: incomprehensible argument passed (1, 2, 3) > test_val_2 passed >error (not syntax error) >Traceback (most recent call last): > File "<string>", line 1, in <module> >NameError: name 'rr_not_found_thing' is not defined > test_val_3 passed >PASS: Test running a Python function >Entered testcase - Internal/External Molecule Numbers match >PASS: Internal/External Molecule Numbers match >Entered testcase - spacegroup operators to space group conversion >[1m(handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb" 1)[0m >Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb > PDB file /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb has been read. >Spacegroup: P 1 >Cell: 100 100 100 90 90 90 >INFO:: Found 1 models > Model 1 had 0 links >Symmetry available for this molecule >Molecule 129 read successfully >PASS: spacegroup operators to space group conversion >Ended 08-utils.scm > > === greg-tests Summary === > ># of testcases attempted 95 ># of expected passes 91 ># of expected failures 0 ># of unexpected passes 0 ># of unexpected failures 0 ># of unresolved testcases 1 ># of unsupported testcases 0 ># of untested testcases 3 > > > === Summary of all tests === > ># of tools 1 ># of testcases attempted 95 ># of expected passes 91 ># of expected failures 0 ># of unexpected passes 0 ># of unexpected failures 0 ># of unresolved testcases 1 ># of unsupported testcases 0 ># of untested testcases 3 ># of files abandoned 0 > >[1m(stereo-mode-state)[0m >[1m(save-state)[0m > >Some deprecated features have been used. Set the environment >variable GUILE_WARN_DEPRECATED to "detailed" and rerun the >program to get more information. Set it to "no" to suppress >this message. > * ERROR: sci-chemistry/coot-0.6 failed: > * (no error message) > * > * Call stack: > * ebuild.sh, line 54: Called src_test > * environment, line 5136: Called die > * The specific snippet of code: > * "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die > * > * If you need support, post the output of 'emerge --info =sci-chemistry/coot-0.6', > * the complete build log and the output of 'emerge -pqv =sci-chemistry/coot-0.6'. > * The complete build log is located at '/var/log/portage/build/sci-chemistry/coot-0.6:20100505-073709.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/coot-0.6/temp/environment'. > * S: '/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' > >>>> Install coot-0.6 into /var/tmp/portage/sci-chemistry/coot-0.6/image/ category sci-chemistry >make -j14 DESTDIR=/var/tmp/portage/sci-chemistry/coot-0.6/image/ install >Making install in auxil >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >Making install in catcheck >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/catcheck' >make[3]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/catcheck' >make[3]: Nothing to be done for `install-exec-am'. >make[3]: Nothing to be done for `install-data-am'. >make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/catcheck' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/catcheck' >Making install in rama >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/rama' >make[3]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/rama' >make[3]: Nothing to be done for `install-exec-am'. >make[3]: Nothing to be done for `install-data-am'. >make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/rama' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/rama' >Making install in sec-str >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/sec-str' >make[3]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/sec-str' >make[3]: Nothing to be done for `install-exec-am'. >make[3]: Nothing to be done for `install-data-am'. >make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/sec-str' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/sec-str' >Making install in strand-analysis >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/strand-analysis' >make[3]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/strand-analysis' >make[3]: Nothing to be done for `install-exec-am'. >make[3]: Nothing to be done for `install-data-am'. >make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/strand-analysis' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/strand-analysis' >Making install in vectors >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/vectors' >make[3]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/vectors' >make[3]: Nothing to be done for `install-exec-am'. >make[3]: Nothing to be done for `install-data-am'. >make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/vectors' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil/vectors' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >make[3]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >make[3]: Nothing to be done for `install-exec-am'. >make[3]: Nothing to be done for `install-data-am'. >make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/auxil' >Making install in scheme >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme' >make[2]: Nothing to be done for `install-exec-am'. >test -z "/usr/share/coot/scheme" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme" > /usr/bin/install -c -m 644 '0-auto-rot.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/0-auto-rot.scm' > /usr/bin/install -c -m 644 'coot-utils.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/coot-utils.scm' > /usr/bin/install -c -m 644 'get-ebi.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/get-ebi.scm' > /usr/bin/install -c -m 644 'mutate.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/mutate.scm' > /usr/bin/install -c -m 644 'background-demo.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/background-demo.scm' > /usr/bin/install -c -m 644 'demo-script.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/demo-script.scm' > /usr/bin/install -c -m 644 'gtkin.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/gtkin.scm' > /usr/bin/install -c -m 644 'my-readline.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/my-readline.scm' > /usr/bin/install -c -m 644 'bit.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/bit.scm' > /usr/bin/install -c -m 644 'extra-top-level.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/extra-top-level.scm' > /usr/bin/install -c -m 644 'hello.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/hello.scm' > /usr/bin/install -c -m 644 'raster3d.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/raster3d.scm' > /usr/bin/install -c -m 644 'brute-lsqman.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/brute-lsqman.scm' > /usr/bin/install -c -m 644 'file-utils.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/file-utils.scm' > /usr/bin/install -c -m 644 'junk.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/junk.scm' > /usr/bin/install -c -m 644 'refmac.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/refmac.scm' > /usr/bin/install -c -m 644 'coot-gui.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/coot-gui.scm' > /usr/bin/install -c -m 644 'filter.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/filter.scm' > /usr/bin/install -c -m 644 'libcheck.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/libcheck.scm' > /usr/bin/install -c -m 644 'simple.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/simple.scm' > /usr/bin/install -c -m 644 'coot.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/coot.scm' > /usr/bin/install -c -m 644 'get-ebi.save.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/get-ebi.save.scm' > /usr/bin/install -c -m 644 'local-code.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/local-code.scm' > /usr/bin/install -c -m 644 'trivial.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/trivial.scm' > /usr/bin/install -c -m 644 'gap.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/gap.scm' > /usr/bin/install -c -m 644 'remote-control.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/remote-control.scm' > /usr/bin/install -c -m 644 'povray.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/povray.scm' > /usr/bin/install -c -m 644 'coot-lsq.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/coot-lsq.scm' > /usr/bin/install -c -m 644 'shelx.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/shelx.scm' > /usr/bin/install -c -m 644 'group-settings.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/group-settings.scm' > /usr/bin/install -c -m 644 'fitting.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/fitting.scm' > /usr/bin/install -c -m 644 'americanisms.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/americanisms.scm' > /usr/bin/install -c -m 644 'tips.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/tips.scm' > /usr/bin/install -c -m 644 'tips-gui.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/tips-gui.scm' > /usr/bin/install -c -m 644 'generic-objects.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/generic-objects.scm' > /usr/bin/install -c -m 644 'cns2coot.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/cns2coot.scm' > /usr/bin/install -c -m 644 'extensions.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/extensions.scm' > /usr/bin/install -c -m 644 'ncs.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/ncs.scm' > /usr/bin/install -c -m 644 'create-server.scsh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/create-server.scsh' > /usr/bin/install -c -m 644 'coot-crash-catcher.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/coot-crash-catcher.scm' > /usr/bin/install -c -m 644 'snarf-coot-docs.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/snarf-coot-docs.scm' > /usr/bin/install -c -m 644 'clear-backup.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/clear-backup.scm' > /usr/bin/install -c -m 644 'bones-reader.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/bones-reader.scm' > /usr/bin/install -c -m 644 'matrices.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/matrices.scm' > /usr/bin/install -c -m 644 'fascinating-things.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/fascinating-things.scm' > /usr/bin/install -c -m 644 'shelx-extensions.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/shelx-extensions.scm' > /usr/bin/install -c -m 644 'parse-pisa-xml.scm' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/scheme/parse-pisa-xml.scm' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/scheme' >Making install in python >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python' >make[2]: Nothing to be done for `install-exec-am'. >test -z "/usr/share/coot/python" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python" > /usr/bin/install -c -m 644 'coot_utils.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot_utils.py' > /usr/bin/install -c -m 644 'get_ebi.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/get_ebi.py' > /usr/bin/install -c -m 644 'mutate.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/mutate.py' > /usr/bin/install -c -m 644 'background_demo.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/background_demo.py' > /usr/bin/install -c -m 644 'hello.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/hello.py' > /usr/bin/install -c -m 644 'raster3d.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/raster3d.py' > /usr/bin/install -c -m 644 'brute_lsqman.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/brute_lsqman.py' > /usr/bin/install -c -m 644 'refmac.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/refmac.py' > /usr/bin/install -c -m 644 'coot_gui.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot_gui.py' > /usr/bin/install -c -m 644 'filter.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/filter.py' > /usr/bin/install -c -m 644 'libcheck.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/libcheck.py' > /usr/bin/install -c -m 644 'coot_load_modules.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot_load_modules.py' > /usr/bin/install -c -m 644 'local_code.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/local_code.py' > /usr/bin/install -c -m 644 'gap.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/gap.py' > /usr/bin/install -c -m 644 'remote_control.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/remote_control.py' > /usr/bin/install -c -m 644 'povray.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/povray.py' > /usr/bin/install -c -m 644 'coot_lsq.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot_lsq.py' > /usr/bin/install -c -m 644 'shelx.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/shelx.py' > /usr/bin/install -c -m 644 'group_settings.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/group_settings.py' > /usr/bin/install -c -m 644 'fitting.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/fitting.py' > /usr/bin/install -c -m 644 'americanisms.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/americanisms.py' > /usr/bin/install -c -m 644 'tips.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/tips.py' > /usr/bin/install -c -m 644 'tips_gui.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/tips_gui.py' > /usr/bin/install -c -m 644 'generic_objects.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/generic_objects.py' > /usr/bin/install -c -m 644 'cns2coot.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/cns2coot.py' > /usr/bin/install -c -m 644 'extensions.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/extensions.py' > /usr/bin/install -c -m 644 'ncs.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/ncs.py' > /usr/bin/install -c -m 644 'create_server.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/create_server.py' > /usr/bin/install -c -m 644 'python_coot_docs.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/python_coot_docs.py' > /usr/bin/install -c -m 644 'clear_backup.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/clear_backup.py' > /usr/bin/install -c -m 644 'bones_reader.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/bones_reader.py' > /usr/bin/install -c -m 644 'shelx_extensions.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/shelx_extensions.py' > /usr/bin/install -c -m 644 'parse_pisa_xml.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/parse_pisa_xml.py' > /usr/bin/install -c -m 644 'coot_toolbuttons.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot_toolbuttons.py' > /usr/bin/install -c -m 644 'coot-python-functions.texi' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot-python-functions.texi' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python' >Making install in macros >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/macros' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/macros' >make[2]: Nothing to be done for `install-exec-am'. >make[2]: Nothing to be done for `install-data-am'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/macros' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/macros' >Making install in compat >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/compat' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/compat' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-compat.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-compat.la' > /usr/bin/install -c -m 644 'coot-getopt.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-getopt.h' >libtool: install: /usr/bin/install -c .libs/libcoot-compat.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-compat.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so.0 || { rm -f libcoot-compat.so.0 && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so || { rm -f libcoot-compat.so && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-compat.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-compat.la >libtool: install: /usr/bin/install -c .libs/libcoot-compat.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-compat.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-compat.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-compat.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/compat' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/compat' >Making install in utils >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-utils.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-utils.la' > /usr/bin/install -c -m 644 'coot-utils.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-utils.hh' > /usr/bin/install -c -m 644 'coot-fasta.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-fasta.hh' >libtool: install: /usr/bin/install -c .libs/libcoot-utils.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-utils.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so.0 || { rm -f libcoot-utils.so.0 && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so || { rm -f libcoot-utils.so && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-utils.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-utils.la >libtool: install: /usr/bin/install -c .libs/libcoot-utils.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-utils.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-utils.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-utils.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils' >Making install in geometry >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /usr/bin/install -c -m 644 'protein-geometry.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/protein-geometry.hh' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-geometry.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-geometry.la' >libtool: install: warning: relinking `libcoot-geometry.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo ../utils/libcoot-utils.la -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-utils -L/usr -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lmmdb -lsrfftw -lsfftw -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-geometry.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-geometry.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so.0 || { rm -f libcoot-geometry.so.0 && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so || { rm -f libcoot-geometry.so && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-geometry.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-geometry.la >libtool: install: /usr/bin/install -c .libs/libcoot-geometry.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-geometry.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-geometry.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-geometry.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry' >Making install in mini-mol >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-mini-mol.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-mini-mol.la' > /usr/bin/install -c -m 644 'mini-mol.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/mini-mol.hh' > /usr/bin/install -c -m 644 'mini-mol-utils.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/mini-mol-utils.hh' > /usr/bin/install -c -m 644 'atom-quads.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/atom-quads.hh' >libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-mini-mol.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0 || { rm -f libcoot-mini-mol.so.0 && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so || { rm -f libcoot-mini-mol.so && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-mini-mol.la >libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-mini-mol.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-mini-mol.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-mini-mol.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol' >Making install in coot-utils >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-coord-utils.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-utils.la' > /usr/bin/install -c -m 644 'peak-search.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/peak-search.hh' > /usr/bin/install -c -m 644 'coot-trim.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-trim.hh' > /usr/bin/install -c -m 644 'coot-coord-utils.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-coord-utils.hh' > /usr/bin/install -c -m 644 'coot-map-utils.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-map-utils.hh' > /usr/bin/install -c -m 644 'coot-coord-extras.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-coord-extras.hh' > /usr/bin/install -c -m 644 'coot-map-heavy.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-map-heavy.hh' > /usr/bin/install -c -m 644 'coot-lsq-types.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-lsq-types.h' >libtool: install: warning: relinking `libcoot-coord-utils.la' > /usr/bin/install -c -m 644 'coot-shelx.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-shelx.hh' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-coord-utils.la -rpath /usr/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) > /usr/bin/install -c -m 644 'coot-rama.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-rama.hh' > /usr/bin/install -c -m 644 'xmap-stats.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/xmap-stats.hh' >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-utils.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0 || { rm -f libcoot-coord-utils.so.0 && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so || { rm -f libcoot-coord-utils.so && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-utils.la >libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-utils.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-utils.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-utils.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-shelx.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-shelx.la' >libtool: install: warning: relinking `libcoot-shelx.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-shelx.la -rpath /usr/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-shelx-ins.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-coord-utils -L/usr -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-shelx.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-shelx.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so.0 || { rm -f libcoot-shelx.so.0 && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so || { rm -f libcoot-shelx.so && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-shelx.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-shelx.la >libtool: install: /usr/bin/install -c .libs/libcoot-shelx.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-shelx.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-shelx.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-shelx.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-coord-extras.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-extras.la' >libtool: install: warning: relinking `libcoot-coord-extras.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-coord-extras.la -rpath /usr/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-coord-utils -L/usr -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-extras.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0 || { rm -f libcoot-coord-extras.so.0 && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so || { rm -f libcoot-coord-extras.so && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-extras.la >libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-extras.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-extras.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coord-extras.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-map-utils.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-utils.la' >libtool: install: warning: relinking `libcoot-map-utils.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-map-utils.la -rpath /usr/lib coot-map-utils.lo peak-search.lo trim.lo xmap-stats.lo libcoot-coord-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-map-utils.o .libs/peak-search.o .libs/trim.o .libs/xmap-stats.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-coord-utils -L/usr -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-utils.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0 || { rm -f libcoot-map-utils.so.0 && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so || { rm -f libcoot-map-utils.so && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-utils.la >libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-utils.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-utils.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-utils.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-map-heavy.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-heavy.la' >libtool: install: warning: relinking `libcoot-map-heavy.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-map-heavy.la -rpath /usr/lib coot-map-heavy.lo coot-fffear.lo ../mini-mol/libcoot-mini-mol.la libcoot-map-utils.la libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-map-heavy.o .libs/coot-fffear.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-mini-mol -L/usr -lcoot-map-utils -lcoot-coord-utils -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lmmdb -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-heavy.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0 || { rm -f libcoot-map-heavy.so.0 && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so || { rm -f libcoot-map-heavy.so && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-heavy.la >libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-heavy.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-heavy.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-map-heavy.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils' >Making install in surface >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >make[2]: Nothing to be done for `install-data-am'. > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libccp4mg-surface.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-surface.la' >libtool: install: /usr/bin/install -c .libs/libccp4mg-surface.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-surface.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libccp4mg-surface.so.0.0.0 libccp4mg-surface.so.0 || { rm -f libccp4mg-surface.so.0 && ln -s libccp4mg-surface.so.0.0.0 libccp4mg-surface.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libccp4mg-surface.so.0.0.0 libccp4mg-surface.so || { rm -f libccp4mg-surface.so && ln -s libccp4mg-surface.so.0.0.0 libccp4mg-surface.so; }; }) >libtool: install: /usr/bin/install -c .libs/libccp4mg-surface.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-surface.la >libtool: install: /usr/bin/install -c .libs/libccp4mg-surface.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-surface.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-surface.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-surface.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface' >Making install in coot-surface >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >make[2]: Nothing to be done for `install-data-am'. > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-surface.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-surface.la' >libtool: install: warning: relinking `libcoot-surface.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lccp4mg-surface -L/usr -lglut -lGL -lXxf86vm -lXi -lXmu -lXt -lSM -lICE -luuid -lXext -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lresolv -lpangocairo-1.0 -lpangoft2-1.0 -lcairo -lpixman-1 -lglitz -lpng12 -lxcb-render-util -lxcb-render -lXrender -lX11 -lxcb -lXau -lXdmcp -lpango-1.0 -lfontconfig -lfreetype -lexpat -lgobject-2.0 -lgmodule-2.0 -ldl -lglib-2.0 -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-surface.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-surface.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so.0 || { rm -f libcoot-surface.so.0 && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so || { rm -f libcoot-surface.so && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-surface.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-surface.la >libtool: install: /usr/bin/install -c .libs/libcoot-surface.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-surface.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-surface.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-surface.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-surface' >Making install in coords >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-coords.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coords.la' > /usr/bin/install -c -m 644 'Bond_lines.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/Bond_lines.h' > /usr/bin/install -c -m 644 'Cartesian.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/Cartesian.h' > /usr/bin/install -c -m 644 'cos-sin.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/cos-sin.h' > /usr/bin/install -c -m 644 'mmdb.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/mmdb.h' > /usr/bin/install -c -m 644 'mmdb-extras.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/mmdb-extras.h' > /usr/bin/install -c -m 644 'utils.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/utils.h' > /usr/bin/install -c -m 644 'mmdb-crystal.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/mmdb-crystal.h' > /usr/bin/install -c -m 644 'Bond_lines_ext.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/Bond_lines_ext.h' >libtool: install: warning: relinking `libcoot-coords.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -Wl,-O1 -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) > /usr/bin/install -c -m 644 'coot-close.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-close.hh' >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-geometry -L/usr -lcoot-shelx -lcoot-coord-utils -lcoot-utils -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-coords.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coords.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so.0 || { rm -f libcoot-coords.so.0 && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so || { rm -f libcoot-coords.so && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-coords.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coords.la >libtool: install: /usr/bin/install -c .libs/libcoot-coords.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coords.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coords.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-coords.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords' >Making install in angles >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-AngleInfo.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-AngleInfo.la' > /usr/bin/install -c -m 644 'AngleInfo.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/AngleInfo.h' > /usr/bin/install -c -m 644 'ncube.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/ncube.h' > /usr/bin/install -c -m 644 'wrapped-ncube.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/wrapped-ncube.h' >libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-AngleInfo.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0 || { rm -f libcoot-AngleInfo.so.0 && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so || { rm -f libcoot-AngleInfo.so && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-AngleInfo.la >libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-AngleInfo.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-AngleInfo.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-AngleInfo.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles' >Making install in skeleton >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-skeleton.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-skeleton.la' > /usr/bin/install -c -m 644 'graphical_skel.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/graphical_skel.h' > /usr/bin/install -c -m 644 'dm-utils.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/dm-utils.h' > /usr/bin/install -c -m 644 'BuildCas.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/BuildCas.h' >libtool: install: warning: relinking `libcoot-skeleton.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-AngleInfo -L/usr -lcoot-coords -lcoot-geometry -lcoot-shelx -lcoot-coord-utils -lcoot-utils -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-skeleton.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0 || { rm -f libcoot-skeleton.so.0 && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so || { rm -f libcoot-skeleton.so && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-skeleton.la >libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-skeleton.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-skeleton.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-skeleton.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/skeleton' >Making install in ccp4mg-utils >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libccp4mg-utils.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-utils.la' > /usr/bin/install -c -m 644 'geomutil.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/geomutil.h' > /usr/bin/install -c -m 644 'mgtree.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/mgtree.h' > /usr/bin/install -c -m 644 'cartesian.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/cartesian.h' > /usr/bin/install -c -m 644 'matrix.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/matrix.h' > /usr/bin/install -c -m 644 'quat.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/quat.h' > /usr/bin/install -c -m 644 'ppmutil.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/ppmutil.h' >libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-utils.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0 || { rm -f libccp4mg-utils.so.0 && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so || { rm -f libccp4mg-utils.so && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so; }; }) >libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-utils.la >libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-utils.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-utils.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libccp4mg-utils.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils' >Making install in density-contour >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-isosurface.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-isosurface.la' > /usr/bin/install -c -m 644 'Vectors.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/Vectors.h' > /usr/bin/install -c -m 644 'CIsoSurface.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/CIsoSurface.h' >libtool: install: warning: relinking `libcoot-isosurface.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-isosurface.la -rpath /usr/lib Vectors.lo CIsoSurface.lo ../coords/libcoot-coords.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/Vectors.o .libs/CIsoSurface.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-coords -L/usr -lcoot-geometry -lcoot-shelx -lcoot-coord-utils -lcoot-utils -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lmmdb -lsrfftw -lsfftw -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-isosurface.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0 || { rm -f libcoot-isosurface.so.0 && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so || { rm -f libcoot-isosurface.so && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-isosurface.la >libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-isosurface.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-isosurface.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-isosurface.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/density-contour' >Making install in db-main >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /usr/bin/install -c -m 644 'db-main.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/db-main.hh' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-db-main.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-db-main.la' > /usr/bin/install -c -m 644 'db-strands.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/db-strands.hh' >libtool: install: warning: relinking `libcoot-db-main.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -Wl,-O1 -o libcoot-db-main.la -rpath /usr/lib db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/db-main.o .libs/db-strands.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-mini-mol -L/usr -lcoot-coord-utils -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-db-main.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-db-main.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so.0 || { rm -f libcoot-db-main.so.0 && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so || { rm -f libcoot-db-main.so && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-db-main.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-db-main.la >libtool: install: /usr/bin/install -c .libs/libcoot-db-main.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-db-main.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-db-main.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-db-main.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main' >Making install in ideal >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-ideal.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ideal.la' > /usr/bin/install -c -m 644 'test-indexing.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/test-indexing.hh' > /usr/bin/install -c -m 644 'simple-restraint.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/simple-restraint.hh' > /usr/bin/install -c -m 644 'pepflip.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/pepflip.hh' > /usr/bin/install -c -m 644 'regularize-minimol.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/regularize-minimol.hh' > /usr/bin/install -c -m 644 'lograma.h' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/lograma.h' >libtool: install: warning: relinking `libcoot-ideal.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -Wl,-O1 -o libcoot-ideal.la -rpath /usr/lib simple-restraint.lo pepflip.lo regularize-minimol.lo lograma.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/simple-restraint.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -lcoot-coord-extras -lcoot-geometry -lcoot-coord-utils -lcoot-utils -lcoot-mini-mol -lgsl -lcblas -latlas -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lmmdb -lsrfftw -lsfftw -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-ideal.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ideal.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so.0 || { rm -f libcoot-ideal.so.0 && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so || { rm -f libcoot-ideal.so && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-ideal.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ideal.la >libtool: install: /usr/bin/install -c .libs/libcoot-ideal.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ideal.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ideal.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ideal.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal' >Making install in ligand >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-ligand.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ligand.la' > /usr/bin/install -c 'findwaters' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/findwaters' > /usr/bin/install -c -m 644 'ligand.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/ligand.hh' > /usr/bin/install -c 'findligand' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/findligand' > /usr/bin/install -c -m 644 'residue_by_phi_psi.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/residue_by_phi_psi.hh' > /usr/bin/install -c -m 644 'wligand.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/wligand.hh' > /usr/bin/install -c -m 644 'monomer-utils.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/monomer-utils.hh' > /usr/bin/install -c -m 644 'chi-angles.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/chi-angles.hh' > /usr/bin/install -c -m 644 'dunbrack.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/dunbrack.hh' > /usr/bin/install -c -m 644 'helix-placement.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/helix-placement.hh' >libtool: install: warning: relinking `libcoot-ligand.la' > /usr/bin/install -c -m 644 'fast-ss-search.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/fast-ss-search.hh' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -o libcoot-ligand.la -rpath /usr/lib ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo ../ideal/libcoot-ideal.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) > /usr/bin/install -c -m 644 'rigid-body.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/rigid-body.hh' > /usr/bin/install -c -m 644 'ideal-rna.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/ideal-rna.hh' > /usr/bin/install -c -m 644 'rotamer.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/rotamer.hh' > /usr/bin/install -c -m 644 'richardson-rotamer.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/richardson-rotamer.hh' > /usr/bin/install -c -m 644 'torsion-general.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/torsion-general.hh' > /usr/bin/install -c -m 644 'primitive-chi-angles.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/primitive-chi-angles.hh' > /usr/bin/install -c -m 644 'dipole.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/dipole.hh' > /usr/bin/install -c -m 644 'base-pairing.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/base-pairing.hh' > /usr/bin/install -c -m 644 'backrub-rotamer.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/backrub-rotamer.hh' >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-ideal -L/usr/lib/blas/threaded-atlas -L/usr -lgsl -lcblas -latlas -lcoot-db-main -lccp4mg-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-geometry -lcoot-mini-mol -lcoot-map-utils -lcoot-coord-utils -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-ligand.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ligand.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so.0 || { rm -f libcoot-ligand.so.0 && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so || { rm -f libcoot-ligand.so && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-ligand.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ligand.la >libtool: install: /usr/bin/install -c .libs/libcoot-ligand.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ligand.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ligand.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-ligand.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'findligand-real' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/findligand-real' >libtool: install: warning: `./libcoot-ligand.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib' >libtool: install: /usr/bin/install -c .libs/findligand-real /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/findligand-real > /bin/sh ../libtool --mode=install /usr/bin/install -c 'findwaters-real' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/findwaters-real' >libtool: install: warning: `./libcoot-ligand.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib' >libtool: install: /usr/bin/install -c .libs/findwaters-real /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/findwaters-real >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand' >Making install in high-res >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-high-res.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-high-res.la' > /usr/bin/install -c -m 644 'high-res.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/high-res.hh' > /usr/bin/install -c -m 644 'coot-atom-graph.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-atom-graph.hh' > /usr/bin/install -c -m 644 'coot-node-info.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-node-info.hh' > /usr/bin/install -c -m 644 'sequence-assignment.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/sequence-assignment.hh' >libtool: install: warning: relinking `libcoot-high-res.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -O2 -pipe -Wl,-O1 -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -L/usr -lcoot-ligand -L/usr/lib/blas/threaded-atlas -lcoot-ideal -lgsl -lcblas -latlas -lcoot-db-main -lccp4mg-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-geometry -lcoot-mini-mol -lcoot-map-utils -lcoot-coord-utils -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-high-res.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-high-res.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so.0 || { rm -f libcoot-high-res.so.0 && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so || { rm -f libcoot-high-res.so && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-high-res.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-high-res.la >libtool: install: /usr/bin/install -c .libs/libcoot-high-res.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-high-res.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-high-res.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-high-res.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/high-res' >Making install in build >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/build' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/build' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-cabuild.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-cabuild.la' > /usr/bin/install -c -m 644 'CalphaBuild.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/CalphaBuild.hh' >libtool: install: warning: relinking `libcoot-cabuild.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/build; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-cabuild.la -rpath /usr/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/CalphaBuild.o -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-AngleInfo -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr -lmmdb -lsrfftw -lsfftw -lz -lpthread -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-cabuild.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0 || { rm -f libcoot-cabuild.so.0 && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so || { rm -f libcoot-cabuild.so && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-cabuild.la >libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-cabuild.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-cabuild.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-cabuild.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/build' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/build' >Making install in greg-tests >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/greg-tests' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/greg-tests' >make[2]: Nothing to be done for `install-exec-am'. >make[2]: Nothing to be done for `install-data-am'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/greg-tests' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/greg-tests' >Making install in python-tests >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python-tests' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python-tests' >make[2]: Nothing to be done for `install-exec-am'. >make[2]: Nothing to be done for `install-data-am'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python-tests' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python-tests' >Making install in analysis >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-analysis.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-analysis.la' > /usr/bin/install -c -m 644 'bfkurt.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/bfkurt.hh' >libtool: install: warning: relinking `libcoot-analysis.la' >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis; /bin/sh /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/libtool --tag CXX --mode=relink i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o libcoot-analysis.la -rpath /usr/lib bfkurt.lo ../coot-utils/libcoot-coord-utils.la -L/usr/lib -L/usr -lmmdb -lm -inst-prefix-dir /var/tmp/portage/sci-chemistry/coot-0.6/image/) >libtool: relink: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtbeginS.o .libs/bfkurt.o -L/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib -L/usr/lib -lcoot-coord-utils -L/usr -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -lsrfftw -lsfftw -lz -lpthread -lmmdb -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.5.0/../../../crtn.o -Wl,-O1 -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 >libtool: install: /usr/bin/install -c .libs/libcoot-analysis.so.0.0.0T /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-analysis.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so.0 || { rm -f libcoot-analysis.so.0 && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so || { rm -f libcoot-analysis.so && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-analysis.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-analysis.la >libtool: install: /usr/bin/install -c .libs/libcoot-analysis.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-analysis.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-analysis.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-analysis.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'bfactan' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/bfactan' >libtool: install: warning: `libcoot-analysis.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: /usr/bin/install -c .libs/bfactan /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/bfactan >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis' >Making install in tw >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/tw' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/tw' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/include/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcoot-tw.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-tw.la' > /usr/bin/install -c -m 644 'coot-tw.hh' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/include/coot/coot-tw.hh' >libtool: install: /usr/bin/install -c .libs/libcoot-tw.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-tw.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so.0 || { rm -f libcoot-tw.so.0 && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so || { rm -f libcoot-tw.so && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcoot-tw.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-tw.la >libtool: install: /usr/bin/install -c .libs/libcoot-tw.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-tw.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-tw.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcoot-tw.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/tw' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/tw' >Making install in cootaneer >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootaneer' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootaneer' >test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib" >test -z "/usr/share/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot" > /bin/sh ../libtool --mode=install /usr/bin/install -c 'libcootaneer.la' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcootaneer.la' > /usr/bin/install -c -m 644 'cootaneer-llk-2.40.dat' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/cootaneer-llk-2.40.dat' >libtool: install: /usr/bin/install -c .libs/libcootaneer.so.0.0.0 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcootaneer.so.0.0.0 >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so.0 || { rm -f libcootaneer.so.0 && ln -s libcootaneer.so.0.0.0 libcootaneer.so.0; }; }) >libtool: install: (cd /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so || { rm -f libcootaneer.so && ln -s libcootaneer.so.0.0.0 libcootaneer.so; }; }) >libtool: install: /usr/bin/install -c .libs/libcootaneer.lai /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcootaneer.la >libtool: install: /usr/bin/install -c .libs/libcootaneer.a /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcootaneer.a >libtool: install: chmod 644 /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcootaneer.a >libtool: install: i686-pc-linux-gnu-ranlib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/lib/libcootaneer.a >libtool: install: warning: remember to run `libtool --finish /usr/lib' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootaneer' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/cootaneer' >Making install in src >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/src' >cp coot_gtk2.py coot.py >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/src' >test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin" >test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin" >test -z "/usr/share/coot/python" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python" > /usr/bin/install -c 'coot' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/coot' > /usr/bin/install -c 'coot.py' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/python/coot.py' > /bin/sh ../libtool --mode=install /usr/bin/install -c 'coot-real' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/coot-real' > /usr/bin/install -c 'density-score-by-residue' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/density-score-by-residue' >libtool: install: warning: `../ligand/libcoot-ligand.la' has not been installed in `/usr/lib' >libtool: install: warning: `../density-contour/libcoot-isosurface.la' has not been installed in `/usr/lib' >libtool: install: warning: `../build/libcoot-cabuild.la' has not been installed in `/usr/lib' >libtool: install: warning: `../skeleton/libcoot-skeleton.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles/libcoot-AngleInfo.la' has not been installed in `/usr/lib' >libtool: install: warning: `../angles/libcoot-AngleInfo.la' has not been installed in `/usr/lib' >libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `../high-res/libcoot-high-res.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ligand/libcoot-ligand.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-surface/libcoot-surface.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/surface/libccp4mg-surface.la' has not been installed in `/usr/lib' >libtool: install: warning: `../surface/libccp4mg-surface.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../analysis/libcoot-analysis.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../cootaneer/libcootaneer.la' has not been installed in `/usr/lib' >libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib' >libtool: install: /usr/bin/install -c .libs/coot-real /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/coot-real > /bin/sh ../libtool --mode=install /usr/bin/install -c 'density-score-by-residue-real' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/density-score-by-residue-real' >libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib' >libtool: install: /usr/bin/install -c .libs/density-score-by-residue-real /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/density-score-by-residue-real > /bin/sh ../libtool --mode=install /usr/bin/install -c 'fix-nomenclature-errors' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/fix-nomenclature-errors' >libtool: install: warning: `../ligand/libcoot-ligand.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/geometry/libcoot-geometry.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib' >libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib' >libtool: install: /usr/bin/install -c .libs/fix-nomenclature-errors /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/bin/fix-nomenclature-errors >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/src' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/src' >Making install in data >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/data' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/data' >make[2]: Nothing to be done for `install-exec-am'. >test -z "/usr/share/coot/data" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/data" > /usr/bin/install -c -m 644 'tutorial-modern.pdb' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/data/tutorial-modern.pdb' > /usr/bin/install -c -m 644 'rnasa-1.8-all_refmac1.mtz' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/data/rnasa-1.8-all_refmac1.mtz' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/data' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/data' >Making install in rama-data >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/rama-data' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/rama-data' >make[2]: Nothing to be done for `install-exec-am'. >test -z "/usr/share/coot/rama-data" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data" > /usr/bin/install -c -m 644 'rota500-arg.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-arg.data' > /usr/bin/install -c -m 644 'rota500-asn.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-asn.data' > /usr/bin/install -c -m 644 'rota500-asp.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-asp.data' > /usr/bin/install -c -m 644 'rota500-cys.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-cys.data' > /usr/bin/install -c -m 644 'rota500-gln.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-gln.data' > /usr/bin/install -c -m 644 'rota500-glu.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-glu.data' > /usr/bin/install -c -m 644 'rota500-his.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-his.data' > /usr/bin/install -c -m 644 'rota500-ile.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-ile.data' > /usr/bin/install -c -m 644 'rota500-leu.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-leu.data' > /usr/bin/install -c -m 644 'rota500-lys.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-lys.data' > /usr/bin/install -c -m 644 'rota500-met.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-met.data' > /usr/bin/install -c -m 644 'rota500-phetyr.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-phetyr.data' > /usr/bin/install -c -m 644 'rota500-pro.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-pro.data' > /usr/bin/install -c -m 644 'rota500-ser.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-ser.data' > /usr/bin/install -c -m 644 'rota500-thr.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-thr.data' > /usr/bin/install -c -m 644 'rota500-trp.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-trp.data' > /usr/bin/install -c -m 644 'rota500-val.data' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/rama-data/rota500-val.data' >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/rama-data' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/rama-data' >Making install in doc >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/doc' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/doc' >make[2]: Nothing to be done for `install-exec-am'. >make[2]: Nothing to be done for `install-data-am'. >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/doc' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/doc' >make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' >make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' >make[2]: Nothing to be done for `install-exec-am'. >if test -d ./pixmaps; then \ > /bin/sh ./mkinstalldirs /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/pixmaps; \ > for pixmap in ./pixmaps/*; do \ > if test -f $pixmap; then \ > /usr/bin/install -c -m 644 $pixmap /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/pixmaps; \ > fi \ > done \ > fi >test -z "/usr/share/coot" || /bin/mkdir -p "/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot" >mkdir -p -- /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/pixmaps > /usr/bin/install -c -m 644 'cootrc' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/cootrc' > /usr/bin/install -c -m 644 'standard-residues.pdb' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/standard-residues.pdb' > /usr/bin/install -c -m 644 'colours.def' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/colours.def' > /usr/bin/install -c -m 644 'mtrix-to-ncs-matrix.awk' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/mtrix-to-ncs-matrix.awk' > /usr/bin/install -c -m 644 'theor-helix-70.pdb' '/var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot/theor-helix-70.pdb' >if test -z "" ; then \ > /usr/bin/install -c -m 644 ./syminfo.lib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot; \ > else \ > /usr/bin/install -c -m 644 ./windows/syminfo.lib /var/tmp/portage/sci-chemistry/coot-0.6/image//usr/share/coot; \ > fi >make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' >make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6' >>>> Completed installing coot-0.6 into /var/tmp/portage/sci-chemistry/coot-0.6/image/ > >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-tw.la already clean, skipping update. >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-AngleInfo.la already clean, skipping update. >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libccp4mg-utils.la already clean, skipping update. >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-surface.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-high-res.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcootaneer.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-map-heavy.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-coords.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-db-main.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-shelx.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-ideal.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-map-utils.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-geometry.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-compat.la already clean, skipping update. >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libccp4mg-surface.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-isosurface.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-utils.la already clean, skipping update. >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-analysis.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-ligand.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-mini-mol.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-coord-utils.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-coord-extras.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-cabuild.la: Updating... >/var/tmp/portage/sci-chemistry/coot-0.6/image/usr/lib/libcoot-skeleton.la: Updating... >strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment > usr/lib/libcoot-isosurface.so.0.0.0 > usr/lib/libcoot-coords.so.0.0.0 > usr/lib/libcoot-coord-extras.so.0.0.0 > usr/lib/libcoot-skeleton.so.0.0.0 > usr/lib/libcoot-ideal.so.0.0.0 > usr/lib/libcoot-high-res.so.0.0.0 > usr/lib/libcoot-AngleInfo.so.0.0.0 > usr/lib/libcoot-surface.so.0.0.0 > usr/lib/libcoot-cabuild.so.0.0.0 > usr/lib/libcoot-mini-mol.so.0.0.0 > usr/lib/libcootaneer.so.0.0.0 > usr/lib/libccp4mg-surface.so.0.0.0 > usr/lib/libcoot-compat.so.0.0.0 > usr/lib/libcoot-geometry.so.0.0.0 > usr/lib/libccp4mg-utils.so.0.0.0 > usr/lib/libcoot-db-main.so.0.0.0 > usr/lib/libcoot-tw.so.0.0.0 > usr/lib/libcoot-map-heavy.so.0.0.0 > usr/lib/libcoot-coord-utils.so.0.0.0 > usr/lib/libcoot-map-utils.so.0.0.0 > usr/lib/libcoot-ligand.so.0.0.0 > usr/lib/libcoot-utils.so.0.0.0 > usr/lib/libcoot-analysis.so.0.0.0 > usr/lib/libcoot-shelx.so.0.0.0 > usr/bin/findwaters-real > usr/bin/findligand-real > usr/bin/bfactan > usr/bin/density-score-by-residue-real > usr/bin/coot-real > usr/bin/fix-nomenclature-errors > usr/lib/libcoot-cabuild.a > usr/lib/libcoot-high-res.a > usr/lib/libcoot-utils.a > usr/lib/libcoot-coord-utils.a > usr/lib/libcoot-db-main.a > usr/lib/libcoot-isosurface.a > usr/lib/libcoot-skeleton.a > usr/lib/libcoot-tw.a > usr/lib/libcoot-map-heavy.a > usr/lib/libcoot-geometry.a > usr/lib/libcootaneer.a > usr/lib/libcoot-ideal.a > usr/lib/libcoot-mini-mol.a > usr/lib/libcoot-coord-extras.a > usr/lib/libccp4mg-utils.a > usr/lib/libcoot-ligand.a > usr/lib/libcoot-surface.a > usr/lib/libcoot-compat.a > usr/lib/libcoot-analysis.a > usr/lib/libccp4mg-surface.a > usr/lib/libcoot-coords.a > usr/lib/libcoot-AngleInfo.a > usr/lib/libcoot-map-utils.a > usr/lib/libcoot-shelx.a >removing executable bit: usr/lib/libccp4mg-surface.la >removing executable bit: usr/lib/libccp4mg-utils.la >removing executable bit: usr/lib/libcoot-analysis.la >removing executable bit: usr/lib/libcootaneer.la >removing executable bit: usr/lib/libcoot-AngleInfo.la >removing executable bit: usr/lib/libcoot-cabuild.la >removing executable bit: usr/lib/libcoot-compat.la >removing executable bit: usr/lib/libcoot-coord-extras.la >removing executable bit: usr/lib/libcoot-coords.la >removing executable bit: usr/lib/libcoot-coord-utils.la >removing executable bit: usr/lib/libcoot-db-main.la >removing executable bit: usr/lib/libcoot-geometry.la >removing executable bit: usr/lib/libcoot-high-res.la >removing executable bit: usr/lib/libcoot-ideal.la >removing executable bit: usr/lib/libcoot-isosurface.la >removing executable bit: usr/lib/libcoot-ligand.la >removing executable bit: usr/lib/libcoot-map-heavy.la >removing executable bit: usr/lib/libcoot-map-utils.la >removing executable bit: usr/lib/libcoot-mini-mol.la >removing executable bit: usr/lib/libcoot-shelx.la >removing executable bit: usr/lib/libcoot-skeleton.la >removing executable bit: usr/lib/libcoot-surface.la >removing executable bit: usr/lib/libcoot-tw.la >removing executable bit: usr/lib/libcoot-utils.la
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