In the last 3 maybe 4 version of pymol (>0.96) it's not possible to generate symmetry-related molecules, because the space group is not recognized. The error is not related to the space group itself (I tested at least 5 different ones and they all fail). Donnie Berkholz suggested on the pymol-users list this could be due to FHS-compatible locations and default paths in pymol. Reproducible: Always Steps to Reproduce: 1. Compile newest pymol version 2. Load any pdb 3. symexp operations fail Actual Results: It's not possible to create symmetry-related molecules. Expected Results: Symmetry-related molecules should be created. Portage 2.1.3.19 (default-linux/amd64/2007.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.23-tuxonice-r6 x86_64) ================================================================= System uname: 2.6.23-tuxonice-r6 x86_64 Intel(R) Core(TM)2 Duo CPU T7100 @ 1.80GHz Timestamp of tree: Sun, 13 Jan 2008 13:46:01 +0000 app-shells/bash: 3.2_p17-r1 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r8, 2.5.1-r5 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.10-r5 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.23-r2 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -Os -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -Os -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/ http://pandemonium.tiscali.de/pub/gentoo/ " LANG="en_US.utf8" LC_ALL="en_US.utf8" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/science" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X acl amd64 berkdb bitmap-fonts cli cracklib crypt cups dri fortran gdbm gpm iconv isdnlog kdeenablefinal kdehiddenvisibility midi mmx mudflap ncurses nls nptl nptlonly openmp pam pcre perl pppd python readline reflection session spl sse sse2 ssl tcpd truetype-fonts type1-fonts unicode xorg zlib" ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
The problem is fixed in the svn revision 3151 of pymol. If you change the svn path in the 1.0-r1 ebuild to: "https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol" you can use this ebuild to build the latest version, which is a beta of 1.1. Regards, Mark
confirmed, should be marked as solved.
Fixed as noted above, thanks for the report!
