Hi, I ran into an installation bug after upgrading to sci-chemistry/coot-0.7.1 from sci-chemistry/coot-0.7. Unfortunately, the symmetry information library syminfo.lib is not copied to /usr/share/coot/ during installation. As a consequence, spacegroup/symmetry information in the PDB file header is ignored when reading such files into Coot and it is also not possible to apply the space group information manually. This cripples the functionality of the program. syminfo.lib is contained coot source package file coot-0.7.1.tar.gz. Functionality is completely restored by copying syminfo.lib manually to /usr/share/coot/ There is no error message or reference to syminfo.lib during package build. ----------------------------- Coot output while reading a PDB file: DEBUG:: filename: build6_refmac1.pdb (handle-read-draw-molecule-with-recentre "build6_refmac1.pdb" 0) Reading coordinate file: build6_refmac1.pdb PDB file build6_refmac1.pdb has been read. No Spacegroup found for this PDB file Cell: 107.755 75.049 74.672 90 96.07 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary ----------------------------- Trying to set the space group manually using Python script: Command: set_space_group(0, "C 1 2 1") Coot output: BL INFO:: command input is: set_space_group(0, "C 1 2 1") BL INFO:: result is 0 Command: show_spacegroup(0) Coot output: BL INFO:: command input is: show_spacegroup(0) INFO:: spacegroup: No spacegroup BL INFO:: result is No spacegroup -- Thanks! Best regards, Markus
Portage 2.1.12.2 (default/linux/amd64/13.0, gcc-4.6.3, glibc-2.15-r3, 3.8.13-gentoo x86_64) ================================================================= System uname: Linux-3.8.13-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_5150_@_2.66GHz-with-gentoo-2.2 KiB Mem: 8169824 total, 2006804 free KiB Swap: 8385924 total, 8102956 free Timestamp of tree: Mon, 26 Aug 2013 16:15:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.5-r2, 3.2.5-r2 dev-util/cmake: 2.8.10.2-r2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.6.3-r1, 1.10.3, 1.11.6, 1.12.6 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.6.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.7 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo x-portage ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA AdobeFlash-11.x dlj-1.1 Oracle-BCLA-JavaSE skype-4.0.0.7-copyright" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -mfpmath=sse -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -mfpmath=sse -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://gentoo.arcticnetwork.ca/pub/gentoo/ " LANG="en_CA.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac aalib acl acpi aim alsa amd64 amr amrnb amrwb apache2 audio avahi bash-completion bidi blas bluray branding bzip2 cairo cdda cddb cdparanoia cdr cjk cli consolekit cracklib cups curl curlwrappers cxx daap dbus dmi doc dri dts dv dvb dvd dvdr dvdread emacs emboss emf encode exif faac faad fam ffmpeg fftw firefox flac fontconfig foomaticdb fortran ftp gcj gd gdbm gdm gif gimp ginac glade glut gmp gnome-keyring gnutls gphoto2 gpm graphviz gstreamer gtk gtk3 gtkhtml guile iconv icq idn ieee1394 imagemagick imap imlib ipod ipv6 jabber java javascript jbig jpeg jpeg2k lapack lcms ldap lesstif libcaca libnotify libsamplerate lm_sensors m17n-lib mad matroska mikmod mime mmap mmx mng modplug modules mono mozilla mp3 mpeg mpi mplayer msn mtp mudflap multilib musepack ncurses netcdf nls nntp nptl nptlonly ogg opengl openmp osc oscar pam pcre pdf perl php plotutils png policykit posix povray ppds pulseaudio python qt3support quicktime readline recode rtmp samba sdl session sharedmem smp sndfile sox speex spell sqlite sse sse2 sse3 ssl ssse3 startup-notification svg syslog taglib tcl tcpd theora threads threadsafe thunar tiff timidity tk truetype udev unicode upnp usb v4l v4l2 vcd video vorbis wav win32codecs wmf wxwindows x264 xattr xcb xcomposite xft xine xinerama xml xmp xosd xpm xscreensaver xulrunner xv xvid zeroconf zlib" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="actions alias asis auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de de_CH de_DE en en_CA en_GB fr fr_CA fr_FR" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" XFCE_PLUGINS="brightness menu trash" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
+*coot-0.7.1-r1 (28 Aug 2013) + + 28 Aug 2013; Justin Lecher <jlec@gentoo.org> -coot-0.7.1.ebuild, + +coot-0.7.1-r1.ebuild: + Install missing syminfo, #482734 +
