[PyMOL] Running pymol over SSH and setting LIBGL_ALWAYS_INDIRECT
Hi pymolers. I was trying to test our lab pymol installation from home. But i ran into an error in freeglut, when executing over SSH. I have found a solution, but is unsure what it does, and if means something for speed and 3D rendering. *When I ran:* *[software@elvis ~]$ pymol* *freeglut (pymol): ERROR: Internal error FBConfig with necessary capabilities not found in function fgOpenWindow* *X Error of failed request: BadWindow (invalid Window parameter)* * Major opcode of failed request: 4 (X_DestroyWindow)* * Resource id in failed request: 0x0* * Serial number of failed request: 33* * Current serial number in output stream: 36* * PyMOL: abrupt program termination.* I found a solution here: http://superuser.com/questions/203587/remotely-connecting-to-ubuntu-server-from-a-macbook-cant-run-pymol http://unix.stackexchange.com/questions/1437/what-does-libgl-always-indirect-1-actually-do http://ubuntuforums.org/showthread.php?t=1682020 *I then changed the pymol exexution script.* * * *[software@elvis ~/pymolsvn]$ ls* *modules pymol pymolMPEG.sh pymolplugins Pymol-script-repo pymolsvn.desktop svnfreemol svnpymol updatepymol.sh* *[software@elvis ~/pymolsvn]$ cat pymolMPEG.sh * *#!/bin/bash* *if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ];* *then* *ln -s /sbinlab2/software/pymolsvn/pymolsvn.desktop $HOME/.local/share/applications/pymolsvn.desktop* *fi* * * *export FREEMOL=/sbinlab2/software/pymolsvn/svnfreemol/freemol* *export PYMOL_GIT_MOD=/sbinlab2/software/pymolsvn/Pymol-script-repo/modules* *export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL * *export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-tk * *export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload * *export PYTHONPATH=/sbinlab2/software/pymolsvn:$PYTHONPATH* *export PYTHONPATH=/sbinlab2/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH * *export PYTHONPATH=/sbinlab2/software/pymolsvn/Pymol-script-repo:$PYTHONPATH * *export PYMOL_PATH=/sbinlab2/software/pymolsvn/modules/pymol/pymol_path* *export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib * *export LIBGL_ALWAYS_INDIRECT=no* * * */usr/bin/python /sbinlab2/software/pymolsvn/modules/pymol/__init__.py $@* It now works fine when running pymol. And it also works when i set: *export LIBGL_ALWAYS_INDIRECT=yes* * * But what is the fastest solution, so pymol can use Direct rendering? Locally, when sitting at the computer and over SSH. Best Troels -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New to PyMol. Want to extract sequence from .pse file w/ colors.
Hi Pymol Network, I would appreciate someones help in extracting the sequence in the viewer above the protein. I have gone through the sequence and changed AAs to different colors based on their position. I would ideally like to be able to copy that sequence with the colors that they are coded so that I could export it to an excel file. Is this possible? Thanks very much. Shane -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
