* 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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_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 -o protein-geometry.lo protein-geometry.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../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 -o protein-geometry-mmdb.lo protein-geometry-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../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 test-geometry.o -MD -MP -MF .deps/test-geometry.Tpo -c -o test-geometry.o test-geometry.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../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 test-read-components.o -MD -MP -MF .deps/test-read-components.Tpo -c -o test-read-components.o test-read-components.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../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 -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 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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../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 -o coot-rama.lo coot-rama.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../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 -o coot-shelx-ins.lo coot-shelx-ins.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 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-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=\"\" 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-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 .deps/coot-map-utils.Tpo .deps/coot-map-utils.Plo mv -f .deps/coot-shelx-ins.Tpo .deps/coot-shelx-ins.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 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coot-map-heavy.o coot-fffear.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-map-heavy.a libtool: link: ( cd ".libs" && rm -f "libcoot-map-heavy.la" && ln -s "../libcoot-map-heavy.la" "libcoot-map-heavy.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils' Making all in surface make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/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../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe 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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../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 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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../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 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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../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 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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../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=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_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 -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../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 -o cos-sin.lo cos-sin.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../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 -o mmdb-extras.lo mmdb-extras.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../skeleton -I../utils -I../coot-utils 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-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_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. 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-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_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 -o BuildCas.lo BuildCas.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 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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 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"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. 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-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 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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../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 -o simple-restraint.lo simple-restraint.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 -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 -o pepflip.lo pepflip.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 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/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 /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/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-ideal.so.0 -o 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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 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-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 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-DHAVE_MEMORY_H=1 -DHAVE_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 ../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 ../db-main/.libs/libcoot-db-main.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-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-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 ../mini-mol/.libs/libcoot-mini-mol.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 -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 ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/coot-utils/.libs/libcoot-shelx.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so 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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 -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 -o high-res.lo high-res.cc /bin/sh ../libtool --tag=CXX 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-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 -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/CalphaBuild.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles/.libs ../angles/.libs/libcoot-AngleInfo.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 /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,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 -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -o .libs/testcabuild testcabuild.o ./.libs/libcoot-cabuild.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.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/build' Making all in greg-tests make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/greg-tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/greg-tests' Making all in python-tests make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/python-tests' 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-tests' Making all in analysis make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6/work/coot-0.6/analysis' /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 -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c -o bfkurt.lo bfkurt.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/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 -DHAVE_MEMORY_H=1 -DHAVE_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 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-DVERSION=\"0.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_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 -DHAVE_MEMORY_H=1 -DHAVE_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-demo.o -MD -MP -MF .deps/cootaneer-demo.Tpo -c -o cootaneer-demo.o cootaneer-demo.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/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 -fPIC -DPIC -o .libs/buccaneer-prot.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-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 -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 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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-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 /;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 /;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. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) 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. (set-display-intro-string "Good Morning None, Welcome to Coot.") 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 (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) 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. (set-display-intro-string "Good morning root. Welcome to Coot") 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" (set-display-lists-for-maps 0) (filter-fileselection-filenames-state) (get-active-map-drag-flag) === 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() (post-go-to-atom-window) PASS: Post Go To Atom no molecules Entered testcase - Close bad molecule (close-molecule -2) PASS: Close bad molecule Entered testcase - Read coordinates test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (info-dialog "Oops, failed to create fragment. No atoms selected Incorrect atom specifier? "//A/100"") 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/ins-code-fragment-pre.pdb" 0) 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 (set-go-to-atom-molecule 1) 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 (change-residue-number 1 "A" 68 "" 68 "A") 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 (change-residue-number 1 "A" 69 "" 68 "B") 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 (change-residue-number 1 "A" 67 "" 68 "") 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 (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) 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 (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) (another-level-from-map-molecule-number 2) PASS: Another Level Test Entered testcase - Sharpen map from map (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) 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 (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.50) PASS: Set Atom Attribute Test Entered testcase - Add Terminal Residue Test (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) 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 (add-terminal-residue 6 "A" 1 1) (write-pdb-file 6 "regression-test-terminal-residue.pdb") In new_molecule_by_atom_selection has contains chain id A Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) 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 (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) PASS: Add Terminal Residue Test Entered testcase - Select by Sphere Symmetry available for this molecule (n-chains 8) (chain_id 8 0) Sphere mol: there are 4 residues in chain "B" (resname-from-serial-number 8 "B" 0) (setnum-from-serial-number 8 "B" 0) (insertion-code-from-serial-number 8 "B" 0) (resname-from-serial-number 8 "B" 1) (setnum-from-serial-number 8 "B" 1) (insertion-code-from-serial-number 8 "B" 1) (resname-from-serial-number 8 "B" 2) (setnum-from-serial-number 8 "B" 2) (insertion-code-from-serial-number 8 "B" 2) (resname-from-serial-number 8 "B" 3) (setnum-from-serial-number 8 "B" 3) (insertion-code-from-serial-number 8 "B" 3) Found 20 sphere atoms PASS: Select by Sphere Entered testcase - Test Views (go-to-view-number 0 1) 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 (update-go-to-atom-window-on-new-mol) (set-rotation-centre 31.46 21.41 14.82) 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 (delete-residue 9 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:28_2010_modification_1.pdb.gz (delete-residue 9 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Wed_May__5_09:43:28_2010_modification_2.pdb.gz (delete-residue 9 "B" 12 "") PASS: Label Atoms and Delete Entered testcase - Rotamer outliers (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rotamer-test-fragment.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/res098.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (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) 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 (auto-fit-best-rotamer 93 "A" "" "A" 12 13 1 0.01) PASS: Correct occupancies after auto-fit rotamer on alt-confed residue Entered testcase - Pepflip flips the correct alt confed atoms (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-pepflip-test.pdb" 1) 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 (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) 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 (go-to-view-number 1 1) 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 (mutate 11 "A" 15 "GLY") 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 (mutate 11 "A" 15 "LEU") ==== 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 (auto-fit-best-rotamer 11 "" "" "A" 15 2 1 1.00) 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... (write-pdb-file 15 "tmp-fixed-cis.pdb") /bin/grep CISPEPs: "3" PASS: Correction of CISPEP test Entered testcase - Refine Zone with Alt conf (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (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) 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 (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) 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 (set-go-to-atom-molecule 18) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-waters.pdb" 1) 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 (update-go-to-atom-window-on-other-molecule-chosen) (set-go-to-atom-molecule 0) (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B") PASS: Tweak Alt Confs on Active Residue Entered testcase - Backrub rotamer (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb" 0) 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 (update-go-to-atom-window-on-new-mol) (copy-molecule 20) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/coords-B3A.pdb" 1) 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 (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) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/test-TER-OXT.pdb" 1) 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 (add-OXT-to-residue 24 14 "" "A") WARNING:: This residue already has an OXT - aborting (add-OXT-to-residue 24 14 "" "A") (write-pdb-file 24 "test-TER-OXT-added.pdb") 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/val.pdb" 1) 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 (mutate 3 "C" 25 "HIS") (write-pdb-file 25 "his.pdb") 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: (delete-residue-with-altconf 0 "A" 88 "" "A") PASS: Deleting (non-existing) Alt conf and Go To Atom [JED] Entered testcase - Mask and difference map (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) 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 (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) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 0) 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 (atom-info-string 28 "A" 20 "" " CA " "") (atom-info-string 28 "A" 21 "" " CA " "") (atom-info-string 28 "A" 22 "" " CA " "") (atom-info-string 28 "A" 23 "" " CA " "") (atom-info-string 28 "A" 24 "" " CA " "") (atom-info-string 28 "A" 25 "" " CA " "") (atom-info-string 28 "A" 26 "" " CA " "") (atom-info-string 28 "A" 27 "" " CA " "") (atom-info-string 28 "A" 28 "" " CA " "") (atom-info-string 28 "A" 29 "" " CA " "") (atom-info-string 28 "A" 30 "" " CA " "") (atom-info-string 28 "A" 1 "" " CA " "") (atom-info-string 28 "A" 2 "" " CA " "") (atom-info-string 28 "A" 3 "" " CA " "") (atom-info-string 28 "A" 4 "" " CA " "") (atom-info-string 28 "A" 5 "" " CA " "") (atom-info-string 28 "A" 6 "" " CA " "") (atom-info-string 28 "A" 7 "" " CA " "") (atom-info-string 28 "A" 8 "" " CA " "") (atom-info-string 28 "A" 9 "" " CA " "") (atom-info-string 28 "A" 10 "" " CA " "") 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 (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) 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 (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) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/multi-carbo-coot-2.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-VAL.pdb" 1) 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 (set-undo-molecule 36) 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 (apply-undo) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3ins-6B-3.0.pdb" 1) 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 (update-go-to-atom-window-on-new-mol) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (n-chains 40) (chain_id 40 0) (chain_id 40 1) (chain_id 40 2) (chain_id 40 3) (chain_id 40 4) (chain_id 40 5) (chain_id 40 6) (chain_id 40 7) (chain_id 40 8) PASS: Change Chain IDs and Chain Sorting Entered testcase - Replace Fragment Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) 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 (update-go-to-atom-window-on-new-mol) 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. (replace-fragement 41 "//A70-80") 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") in new_molecule_by_residue_type_selection Something bad happened - No residues selected (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (backup-state 44) (turn-off-backup 44) (rotamer-score 44 "A" 28 "") Rotamer 0 : "m-85" 100.0 (rotamer-score 44 "A" 28 "") Rotamer 1 : "t80" 90.1668395996094 (rotamer-score 44 "A" 28 "") Rotamer 2 : "p90" 50.7077865600586 (rotamer-score 44 "A" 28 "") Rotamer 3 : "m -30 " 21.4231548309326 (rotamer-score 44 "A" 28 "") Rotamer 4 : "m -30 " 21.4231548309326 (turn-on-backup 44) PASS: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions (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) 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 (write-pdb-file 45 "mutated.pdb") ::::: (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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb3hfl.ent" 1) 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 (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) 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 (auto-fit-best-rotamer 52 "" "A" "H" 46 47 0 0.00) 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 (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") 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 (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") 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 (update-go-to-atom-window-on-new-mol) (copy-molecule 0) 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 (mutate 32 "A" 50 "LYS") PASS: SegIDs are correct after mutate Entered testcase - TER on water chain is removed on adding a water by hand (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/some-waters-with-ter.pdb" 1) 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 (set-rotation-centre 3.00 4.00 5.00) 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 (place-typed-atom-at-pointer "Water") (write-pdb-file 51 "tmp-with-new-water.pdb") 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tm+some-waters.pdb" 1) 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 (write-pdb-file 52 "auto-waters.pdb") (write-pdb-file 52 "tmp-with-new-water.pdb") PASS: TER on water chain is removed on adding waters automatically Entered testcase - Arrange waters round protein (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/water-test-no-cell.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pathological-water-test.pdb" 1) 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 (write-pdb-file 54 "waters-moved-failure.pdb") PASS: Arrange waters round protein Entered testcase - Correct Segid After Add Terminal Residue Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) (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) 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 (add-terminal-residue 55 "A" 93 1) PASS: Correct Segid After Add Terminal Residue Entered testcase - Correct Segid after NCS residue range copy Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) PASS: Correct Segid after NCS residue range copy Entered testcase - Merge Water Chains (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (backup-state 58) (turn-off-backup 58) 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) (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 43.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 45.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 47.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 49.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 51.60 8.69 12.91) (renumber-residue-range 58 "D" 1 5 10) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 53.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 55.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 57.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 59.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 61.60 8.69 12.91) (renumber-residue-range 58 "E" 11 15 5) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 63.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 65.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 67.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 69.60 8.69 12.91) 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 (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 71.60 8.69 12.91) (renumber-residue-range 58 "F" 16 20 2) (n-chains 58) (chain_id 58 0) (chain_id 58 1) (chain_id 58 2) (chain_id 58 3) (chain_id 58 4) (is-solvent-chain-p 58 "A") (is-solvent-chain-p 58 "B") (is-solvent-chain-p 58 "D") (is-solvent-chain-p 58 "E") (is-solvent-chain-p 58 "F") (setnum-from-serial-number 58 "D" 4) (renumber-residue-range 58 "E" 1 5 5) (setnum-from-serial-number 58 "D" 9) (renumber-residue-range 58 "F" 1 10 10) (turn-on-backup 58) (n-chains 58) (chain_id 58 2) (setnum-from-serial-number 58 "D" 0) (setnum-from-serial-number 58 "D" 14) PASS: Merge Water Chains Entered testcase - LSQ by atom Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1py3.ent" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2goz-manip.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/HOF.RES" 1) 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 (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/HOF.RES") PASS: Read small molecule .res file Entered testcase - Read hollander small molecule .res file (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/hollander.ins" 1) 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 (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/hollander.ins") INFO:: spacegroup: I 41 2 2 PASS: Read hollander small molecule .res file Entered testcase - read shelx insulin with fcf (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res" 1) 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 (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res") /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 (update-go-to-atom-window-on-new-mol) 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 (update-go-to-atom-window-on-new-mol) 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 (add-terminal-residue 70 "B" 2020 1) PASS: Addition of Terminal Residue on SHELX molecule has correct occupancy Entered testcase - Add water to SHELX molecule (set-rotation-centre 3.00 -1.00 60.00) 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 (place-typed-atom-at-pointer "Water") (resname-from-serial-number 66 "D" 68) (setnum-from-serial-number 66 "D" 68) (insertion-code-from-serial-number 66 "D" 68) PASS: Add water to SHELX molecule Entered testcase - Find Waters for a SHELXL molecule (n-chains 66) 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 (n-chains 66) (resname-from-serial-number 66 "D" 126) (setnum-from-serial-number 66 "D" 126) (insertion-code-from-serial-number 66 "D" 126) PASS: Find Waters for a SHELXL molecule Entered testcase - NPD Anisotropic Atom [Mitch Miller] (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) 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 (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/miller/shelx-test4-NPD-mini.res") (close-molecule 71) PASS: NPD Anisotropic Atom [Mitch Miller] Entered testcase - close shelx molecules (close-molecule 67) (close-molecule 66) PASS: close shelx molecules Entered testcase - Aniso Bs in P21 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/horma-p21.res" 1) 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 (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/horma-p21.res") INFO :: padding UNIT card from size 6 to 6 INFO:: SHELXL file new-horma.ins written. (handle-read-draw-molecule-with-recentre "new-horma.ins" 1) 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 (read-shelx-ins-file "new-horma.ins") 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/ ? //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: /A/N - Y - hydrogen atoms where they are : # A - with all hydrogen atoms : # N - without hydrogen atoms : #IND: /Y - Y - create index of mon_lib.cif : # output file: "new_mon_lib_ind.cif" : #FILE_O: - 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: /S/L - S short output, L - long, M - medium : #REF: /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: /Y - use Vobs from coords instead Videal : #LCOOR: /N - Y use coords from lib description : #NODIST: /Y - Y not read the distributed library : # (only with FILE_L) : #SRCH: /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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" 0) 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 (update-go-to-atom-window-on-new-mol) (copy-molecule 74) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 74) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 74) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 74) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 74) (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1) 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 (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) 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 (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) 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) (handle-read-draw-molecule-with-recentre "coot-ccp4/monomer-3GP.pdb" 1) 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 (update-go-to-atom-window-on-new-mol) (copy-molecule 94) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/dipole-residues.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (assign-pir-sequence 97 "A" ">test ACDEFGHIKLMNPQ*") debug seq: ("A" . "ACDEFGHIKLMNPQ") in assign_pir_sequence storing sequence: ACDEFGHIKLMNPQRST for chain id: A (assign-pir-sequence 97 "A" ">test ACDEFGHIKLMNPQRST*") PASS: Assignment of new PIR sequence overwrites old assignment Entered testcase - Cootaneer Beta Strand (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/crashes_on_cootaneering.pdb" 1) 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 (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) 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 (assign-pir-sequence 98 "A" "> tutorial-modern chain A RNASE DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * ") (set-rotation-centre 64.27 7.04 14.42) 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 (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") !! Warning:: No symmetry available for this molecule No Symmetry for this model (update-go-to-atom-window-on-new-mol) (copy-molecule 100) (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 76.27 10.04 14.42) (go-to-view-number 2 1) (n-chains 101) (chain_id 101 0) (chain_id 101 1) (is-solvent-chain-p 101 "A") There are 8 residues in chain "A" (resname-from-serial-number 101 "A" 0) (setnum-from-serial-number 101 "A" 0) (insertion-code-from-serial-number 101 "A" 0) (resname-from-serial-number 101 "A" 1) (setnum-from-serial-number 101 "A" 1) (insertion-code-from-serial-number 101 "A" 1) (resname-from-serial-number 101 "A" 2) (setnum-from-serial-number 101 "A" 2) (insertion-code-from-serial-number 101 "A" 2) (resname-from-serial-number 101 "A" 3) (setnum-from-serial-number 101 "A" 3) (insertion-code-from-serial-number 101 "A" 3) (resname-from-serial-number 101 "A" 4) (setnum-from-serial-number 101 "A" 4) (insertion-code-from-serial-number 101 "A" 4) (resname-from-serial-number 101 "A" 5) (setnum-from-serial-number 101 "A" 5) (insertion-code-from-serial-number 101 "A" 5) (resname-from-serial-number 101 "A" 6) (setnum-from-serial-number 101 "A" 6) (insertion-code-from-serial-number 101 "A" 6) (resname-from-serial-number 101 "A" 7) (setnum-from-serial-number 101 "A" 7) (insertion-code-from-serial-number 101 "A" 7) (is-solvent-chain-p 101 "B") There are 8 residues in chain "B" (resname-from-serial-number 101 "B" 0) (setnum-from-serial-number 101 "B" 0) (insertion-code-from-serial-number 101 "B" 0) (resname-from-serial-number 101 "B" 1) (setnum-from-serial-number 101 "B" 1) (insertion-code-from-serial-number 101 "B" 1) (resname-from-serial-number 101 "B" 2) (setnum-from-serial-number 101 "B" 2) (insertion-code-from-serial-number 101 "B" 2) (resname-from-serial-number 101 "B" 3) (setnum-from-serial-number 101 "B" 3) (insertion-code-from-serial-number 101 "B" 3) (resname-from-serial-number 101 "B" 4) (setnum-from-serial-number 101 "B" 4) (insertion-code-from-serial-number 101 "B" 4) (resname-from-serial-number 101 "B" 5) (setnum-from-serial-number 101 "B" 5) (insertion-code-from-serial-number 101 "B" 5) (resname-from-serial-number 101 "B" 6) (setnum-from-serial-number 101 "B" 6) (insertion-code-from-serial-number 101 "B" 6) (resname-from-serial-number 101 "B" 7) (setnum-from-serial-number 101 "B" 7) (insertion-code-from-serial-number 101 "B" 7) 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 (update-go-to-atom-window-on-new-mol) (copy-molecule 100) 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. (close-molecule 102) (close-molecule 101) (go-to-view-number 3 1) PASS: RNA NCS Ghosts Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1wly.pdb" 0) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1yb5.pdb" 1) 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 (graphics-to-ca-plus-ligands-representation 103) do_Ca_plus_ligands_bonds with atom_colour_type 0 (graphics-to-ca-plus-ligands-representation 104) 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% (set-rotation-centre 65.65 -3.00 -4.00) (go-to-view-number 4 1) PASS: SSM - Frank von Delft's Example Entered testcase - SSM - Alice Dawson's Example (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1pyd.pdb" 0) Error reading /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1pyd.pdb (graphics-to-ca-plus-ligands-representation -1) (set-graphics-window-size 687 452) (molecule-name 0) 0 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 1) 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" (molecule-name 6) 6 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb" (molecule-name 7) 7 "atom selection from tutorial-add-terminal-1-test.pdb" (molecule-name 8) 8 "sphere selection from tutorial-modern.pdb" (molecule-name 10) 10 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rotamer-test-fragment.pdb" (molecule-name 11) 11 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/res098.pdb" (molecule-name 12) 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" (molecule-name 14) 14 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-pepflip-test.pdb" (molecule-name 15) 15 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" (molecule-name 16) 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" (molecule-name 18) 18 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-add-terminal-1-test.pdb" (molecule-name 19) 19 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/alt-conf-waters.pdb" (molecule-name 20) 20 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb" (molecule-name 21) 21 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/backrub-fragment.pdb" (molecule-name 22) 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" (molecule-name 24) 24 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/test-TER-OXT.pdb" (molecule-name 25) 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" (molecule-name 28) 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" (molecule-name 35) 35 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/multi-carbo-coot-2.pdb" (molecule-name 36) 36 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-VAL.pdb" (molecule-name 37) 37 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/3ins-6B-3.0.pdb" (molecule-name 38) 38 "atom selection from tutorial-modern.pdb" (molecule-name 39) 39 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb" (molecule-name 40) 40 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 41) 41 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 42) 42 "atom selection from tutorial-modern.pdb" (molecule-name 43) 43 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 44) 44 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 45) 45 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/rnase-A-needs-an-insertion.pdb" (molecule-name 46) 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" (molecule-name 48) 48 "Ideal-A-form-RNA" (molecule-name 49) 49 "Ideal-A-form-DNA" (molecule-name 50) 50 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 51) 51 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/some-waters-with-ter.pdb" (molecule-name 52) 52 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tm+some-waters.pdb" (molecule-name 53) 53 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/water-test-no-cell.pdb" (molecule-name 54) 54 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pathological-water-test.pdb" (molecule-name 55) 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" (molecule-name 57) 57 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 58) 58 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 59) 59 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 60) 60 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 61) 61 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 62) 62 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1py3.ent" (molecule-name 63) 63 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2goz-manip.pdb" (molecule-name 64) 64 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/HOF.RES" (molecule-name 65) 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" (molecule-name 69) 69 "atom selection from insulin.res" (molecule-name 70) 70 "atom selection from insulin.res" (molecule-name 72) 72 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/horma-p21.res" (molecule-name 73) 73 "new-horma.ins" (molecule-name 74) 74 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" (molecule-name 75) 75 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" (molecule-name 76) 76 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" (molecule-name 77) 77 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" (molecule-name 78) 78 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" (molecule-name 79) 79 "Copy of /var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-NPO.pdb" (molecule-name 80) 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)" (molecule-name 84) 84 "Fitted ligand #0" (molecule-name 85) 85 "Fitted ligand #1" (molecule-name 86) 86 "Fitted ligand #2" (molecule-name 87) 87 "Fitted ligand #3" (molecule-name 88) 88 "Fitted ligand #4" (molecule-name 89) 89 "Fitted ligand #5" (molecule-name 90) 90 "Fitted ligand #6" (molecule-name 91) 91 "Fitted ligand #7" (molecule-name 92) 92 "Fitted ligand #8" (molecule-name 93) 93 "Fitted ligand #9" (molecule-name 94) 94 "coot-ccp4/monomer-3GP.pdb" (molecule-name 95) 95 "Copy of coot-ccp4/monomer-3GP.pdb" (molecule-name 96) 96 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/dipole-residues.pdb" (molecule-name 97) 97 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" (molecule-name 98) 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" (molecule-name 100) 100 "Ideal-A-form-RNA" (molecule-name 103) 103 "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1wly.pdb" (molecule-name 104) 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 (graphics-to-ca-plus-ligands-representation 104) PASS: SSM - Alice Dawson's Example Entered testcase - SSM by atom selection [JED Example] (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2qd9.pdb" 1) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/2gtn.pdb" 1) 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 ... (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res" 1) 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 (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/insulin.res") Entered testcase - NCS maps test (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) 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/tutorial-modern.pdb" 1) 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 (delete-residue 113 "B" 1 "") INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-0.6_work_data_greg-data_tutorial-modern.pdb_Wed_May__5_09:44:20_2010_modification_1.pdb.gz (delete-residue 113 "B" 2 "") 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 (delete-residue 113 "B" 3 "") %%%%%%%%% 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 (setnum-from-serial-number 113 "B" 0) (setnum-from-serial-number 113 "B" 1) (setnum-from-serial-number 113 "B" 2) (setnum-from-serial-number 113 "B" 3) (setnum-from-serial-number 113 "B" 4) (setnum-from-serial-number 113 "B" 5) (setnum-from-serial-number 113 "B" 6) (setnum-from-serial-number 113 "B" 7) (setnum-from-serial-number 113 "B" 8) (setnum-from-serial-number 113 "B" 9) (setnum-from-serial-number 113 "B" 10) (setnum-from-serial-number 113 "B" 11) (setnum-from-serial-number 113 "B" 12) (setnum-from-serial-number 113 "B" 13) (setnum-from-serial-number 113 "B" 14) (setnum-from-serial-number 113 "B" 15) (setnum-from-serial-number 113 "B" 16) (setnum-from-serial-number 113 "B" 17) (setnum-from-serial-number 113 "B" 18) (setnum-from-serial-number 113 "B" 19) (setnum-from-serial-number 113 "B" 20) (setnum-from-serial-number 113 "B" 21) (setnum-from-serial-number 113 "B" 22) (setnum-from-serial-number 113 "B" 23) (setnum-from-serial-number 113 "B" 24) (setnum-from-serial-number 113 "B" 25) (setnum-from-serial-number 113 "B" 26) (setnum-from-serial-number 113 "B" 27) (setnum-from-serial-number 113 "B" 28) (setnum-from-serial-number 113 "B" 29) (setnum-from-serial-number 113 "B" 30) (setnum-from-serial-number 113 "B" 31) (setnum-from-serial-number 113 "B" 32) (setnum-from-serial-number 113 "B" 33) (setnum-from-serial-number 113 "B" 34) (setnum-from-serial-number 113 "B" 35) (setnum-from-serial-number 113 "B" 36) (setnum-from-serial-number 113 "B" 37) (setnum-from-serial-number 113 "B" 38) (setnum-from-serial-number 113 "B" 39) (setnum-from-serial-number 113 "B" 40) (setnum-from-serial-number 113 "B" 41) (setnum-from-serial-number 113 "B" 42) (setnum-from-serial-number 113 "B" 43) (setnum-from-serial-number 113 "B" 44) (setnum-from-serial-number 113 "B" 45) (setnum-from-serial-number 113 "B" 46) (setnum-from-serial-number 113 "B" 47) (setnum-from-serial-number 113 "B" 48) (setnum-from-serial-number 113 "B" 49) (setnum-from-serial-number 113 "B" 50) (setnum-from-serial-number 113 "B" 51) (setnum-from-serial-number 113 "B" 52) (setnum-from-serial-number 113 "B" 53) (setnum-from-serial-number 113 "B" 54) (setnum-from-serial-number 113 "B" 55) (setnum-from-serial-number 113 "B" 56) (setnum-from-serial-number 113 "B" 57) (setnum-from-serial-number 113 "B" 58) (setnum-from-serial-number 113 "B" 59) (setnum-from-serial-number 113 "B" 60) (setnum-from-serial-number 113 "B" 61) (setnum-from-serial-number 113 "B" 62) (setnum-from-serial-number 113 "B" 63) (setnum-from-serial-number 113 "B" 64) (setnum-from-serial-number 113 "B" 65) (setnum-from-serial-number 113 "B" 66) (setnum-from-serial-number 113 "B" 67) (setnum-from-serial-number 113 "B" 68) (setnum-from-serial-number 113 "B" 69) (setnum-from-serial-number 113 "B" 70) (setnum-from-serial-number 113 "B" 71) (setnum-from-serial-number 113 "B" 72) (setnum-from-serial-number 113 "B" 73) (setnum-from-serial-number 113 "B" 74) (setnum-from-serial-number 113 "B" 75) (setnum-from-serial-number 113 "B" 76) (setnum-from-serial-number 113 "B" 77) (setnum-from-serial-number 113 "B" 78) (setnum-from-serial-number 113 "B" 79) (setnum-from-serial-number 113 "B" 80) (setnum-from-serial-number 113 "B" 81) (setnum-from-serial-number 113 "B" 82) (setnum-from-serial-number 113 "B" 83) (setnum-from-serial-number 113 "B" 84) (setnum-from-serial-number 113 "B" 85) (setnum-from-serial-number 113 "B" 86) (setnum-from-serial-number 113 "B" 87) (setnum-from-serial-number 113 "B" 88) (setnum-from-serial-number 113 "B" 89) (setnum-from-serial-number 113 "B" 90) (setnum-from-serial-number 113 "B" 91) (setnum-from-serial-number 113 "B" 92) (setnum-from-serial-number 113 "B" 93) (setnum-from-serial-number 113 "B" 94) (setnum-from-serial-number 113 "B" 95) 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 (mutate 2 "A" 113 "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_5.pdb.gz PASS: NCS Residue Range copy Entered testcase - NCS Residue Range edit to all chains (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1t6q.ent" 1) 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 (mutate 50 "A" 114 "ASP") (is-solvent-chain-p 114 "C") %%%%%%%%% 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent" 1) 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 (update-go-to-atom-window-on-new-mol) (copy-molecule 115) 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 (close-molecule 116) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 115) 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 (close-molecule 117) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 115) 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 (close-molecule 118) 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 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 14) (molecule-name 15) (molecule-name 16) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 21) (molecule-name 22) (molecule-name 24) (molecule-name 25) (molecule-name 28) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 45) (molecule-name 46) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 54) (molecule-name 55) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 62) (molecule-name 63) (molecule-name 64) (molecule-name 65) (molecule-name 69) (molecule-name 70) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 78) (molecule-name 79) (molecule-name 80) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 96) (molecule-name 97) (molecule-name 98) (molecule-name 100) (molecule-name 103) (molecule-name 104) (molecule-name 105) (molecule-name 106) (molecule-name 107) (close-molecule 109) (close-molecule 111) (molecule-name 113) (molecule-name 114) (molecule-name 115) (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/pdb1hvv.ent" 1) 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 (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) 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 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 14) (molecule-name 15) (molecule-name 16) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 21) (molecule-name 22) (molecule-name 24) (molecule-name 25) (molecule-name 28) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 45) (molecule-name 46) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 54) (molecule-name 55) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 62) (molecule-name 63) (molecule-name 64) (molecule-name 65) (molecule-name 69) (molecule-name 70) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 78) (molecule-name 79) (molecule-name 80) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 96) (molecule-name 97) (molecule-name 98) (molecule-name 100) (molecule-name 103) (molecule-name 104) (molecule-name 105) (molecule-name 106) (molecule-name 107) (molecule-name 113) (molecule-name 114) (molecule-name 115) (molecule-name 119) ==== "NCS found from matching Chain B onto Chain A" 2 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 14) (molecule-name 15) (molecule-name 16) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 21) (molecule-name 22) (molecule-name 24) (molecule-name 25) (molecule-name 28) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 45) (molecule-name 46) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 54) (molecule-name 55) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 62) (molecule-name 63) (molecule-name 64) (molecule-name 65) (molecule-name 69) (molecule-name 70) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 78) (molecule-name 79) (molecule-name 80) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 96) (molecule-name 97) (molecule-name 98) (molecule-name 100) (molecule-name 103) (molecule-name 104) (molecule-name 105) (molecule-name 106) (molecule-name 107) (molecule-name 113) (molecule-name 114) (molecule-name 115) (molecule-name 119) ==== "NCS found from matching Chain C onto Chain A" 2 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 14) (molecule-name 15) (molecule-name 16) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 21) (molecule-name 22) (molecule-name 24) (molecule-name 25) (molecule-name 28) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 45) (molecule-name 46) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 54) (molecule-name 55) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 62) (molecule-name 63) (molecule-name 64) (molecule-name 65) (molecule-name 69) (molecule-name 70) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 78) (molecule-name 79) (molecule-name 80) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 96) (molecule-name 97) (molecule-name 98) (molecule-name 100) (molecule-name 103) (molecule-name 104) (molecule-name 105) (molecule-name 106) (molecule-name 107) (molecule-name 113) (molecule-name 114) (molecule-name 115) (molecule-name 119) ==== "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 "", line 1, in 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 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-0.6/work/data/greg-data/monomer-ACT.pdb" 1) 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 (stereo-mode-state) (save-state) 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