i'm just try to start pymol from command line and it say: python: can't open file '/__init__.py': [Errno 2] No such file or directory i've build python with this flag: ssl threads tk ncurses readline gdbm berkdb i've try to rebuild python and pymol...notthing.. Reproducible: Always Steps to Reproduce: 1.echo "dev-lang/python tk" >> /etc/portage/package.use 2.emerge -NuD world 3.emerge -pv pymol emerge --info Portage 2.1.4.4 (default-linux/amd64/2007.0/desktop, gcc-4.2.4, glibc-2.6.1-r0, 2.6.24-gentoo-r8 x86_64) ================================================================= System uname: 2.6.24-gentoo-r8 x86_64 AMD Turion(tm) 64 Mobile Technology ML-32 Timestamp of tree: Mon, 02 Jun 2008 07:15:01 +0000 ccache version 2.4 [disabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r13 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -msse3 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" 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=k8 -msse3 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://ftp.unina.it/pub/linux/distributions/gentoo ftp://ftp.ucsb.edu/pub/mirrors/linux/gentoo ftp://pandemonium.tiscali.de/pub/gentoo ftp://mirror.ing.unibo.it/gentoo ftp://mirror.switch.ch/mirror/gentoo" LANG="it_IT.UTF-8" LC_ALL="it_IT.UTF-8" LINGUAS="it" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="3dnow 3dnowext X acl acpi alsa amd64 audiofile berkdb bzip2 cairo cdr cli cracklib crypt ctype cups dbus dri dvd dvdr dvdread eds emboss encode esd evo fam firefox flac fortran gdbm gif gphoto2 gpm gstreamer gtk hal hddtemp iconv imlib ipod isdnlog jack java jpeg kerberos lame latex libcaca libnotify lzo mad midi mikmod mmx mozilla mp3 mpeg mudflap musepack ncurses nls nptl nptlonly nsplugin ogg opengl openmp oss pcmcia pcre pdf perl png portaudio posix pppd python qt3support quicktime readline reflection sdl session sockets socks5 source sox spell spl sse sse2 ssl svg szip tcpd theora threads tiff truetype unicode usb v4l2 vim-syntax vorbis wavpack wifi x264 xml xorg xscreensaver xv xvid zlib" ALSA_CARDS="atiixp" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="it" USERLAND="GNU" VIDEO_CARDS="fglrx vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
I assume what you mean is: echo "sci-chemistry/pymol python tk" >> /etc/portage/package.use and emerge pymol... which version of pymol are you using? As root try updating the environment variables by running "env-update && source /etc/profile"
0.99_rc10, but with env-update and source /etc/profile now it work. thanks
But now i've an other problem bondet to the same library: PyMOL(TM) Molecular Graphics System, Version 0.99rev10. Copyright (C) 2006 by DeLano Scientific LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. Other Major Authors and Contributors: Ralf W. Grosse-Kunstleve, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command. Hit ESC anytime to toggle between text and graphics. OpenGL graphics engine: GL_VENDOR: ATI Technologies Inc. GL_RENDERER: ATI Radeon Xpress Series GL_VERSION: 2.1.7412 Release /usr/bin/pymol: line 2: 3692 Segmentation fault python ${PYMOL_PATH}/__init__.py $* :\ I get this error when i try to use this when i use: build -> Fragment ----> Segfault
i've execute pymol with gdb for get a backtrace and i've obtained this when i've try to load a pdb file: (gdb) r /usr/lib/python2.5/site-packages/pymol/__init__.py Starting program: /usr/bin/python /usr/lib/python2.5/site-packages/pymol/__init__.py (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) [Thread debugging using libthread_db enabled] [New Thread 0x2b13a6daa120 (LWP 8850)] (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) ---Type <return> to continue, or q <return> to quit--- (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) ---Type <return> to continue, or q <return> to quit--- (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) PyMOL(TM) Molecular Graphics System, Version 1.0r3. Copyright (C) 2007 by DeLano Scientific LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. Other Major Authors and Contributors: Ralf W. Grosse-Kunstleve, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command. Hit ESC anytime to toggle between text and graphics. (no debugging symbols found) (no debugging symbols found) OpenGL graphics engine: GL_VENDOR: ATI Technologies Inc. GL_RENDERER: ATI Radeon Xpress Series GL_VERSION: 2.1.7412 Release (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) [New Thread 0x40800950 (LWP 8851)] [New Thread 0x41001950 (LWP 8852)] (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) parser: no matching files. PyMOL>load 1A00.pdb HEADER OXYGEN TRANSPORT 08-DEC-97 1A00 TITLE HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN (ALPHA CHAIN); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN (BETA CHAIN); COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry-Error: Urecognized space group symbol 'P 21 21 21'. Symmetry-Error: Unable to get matrices from sglite. CmdLoad: "1A00.pdb" loaded as "1A00". ---Type <return> to continue, or q <return> to quit--- Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x2b13a6daa120 (LWP 8850)] 0x00002aaaab4f948b in ?? () i dont know what is this, but it's possible that i get this error because i'm just use gcc (~)4.2.4?
Solved. I've install the new ati driver ~
