[PyMOL] compilation problems on AMD 64-bit running FC5

Hi, I have downloaded and instaled pymol v99_rc6 on my system, AMD X2 processor; following is the corresponding line to the uname -a command: Linux uniparc7 2.6.17-1.2187_FC5 #1 SMP Mon Sep 11 01:16:59 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux However it is really slow, even if it seems to detect

[PyMOL] freeglut problem

Hi, Pymol prebuild executable is running quite slow on my PC (linux FC5). It gives the following error on start up: freeglut (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create direct context rendering for window 'PyMOL Viewer' This may hurt performance. But my system says I have fr

Re: [PyMOL] freeglut problem

Same problem with freeglut2.2.0 Isn't it strange that pymol + freeglut2.4 is NOT compatible, when it is specifically said in pymol distribution that one of the dependences is freeglut2.4 Thanks, Hugo Donnie Berkholz wrote: Hugo Gutiérrez de Teran wrote: freeglut (/home/htera

Re: [PyMOL] freeglut problem

n "Display" Viewport 0 0 Depth 24 Modes"1280x1024" EndSubSection EndSection Section "DRI" Group0 Mode 0666 EndSection DeLano Scientific wrote: Hugo, I believe Donnie is mistaken

Re: [PyMOL] freeglut problem: almost solved!

r graphics driver. Cheers, DeLano Scientific LLC Email Support Services -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Hugo Gutiérrez de Teran Sent: Friday, November 03, 2006 1:30 AM To: Do

Re: [PyMOL] pymol slow on linux PC

Do you have an error like this in your xterm when you launch the program? freeglut (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create direct context rendering for window 'PyMOL Viewer' This may hurt performance. If this is the case (it was my case) the solution is obscure, but it w

Re: [PyMOL] transforming PDB in Pairfit or align

Ravi, Do you use "pairfitting" or "align" command in PyMol? Align works well for me even for different (but homologous) proteins. Another popular alternative is to use Stamp (U. of Dundee) for the alignment of the PDBs (http://www.compbio.dundee.ac.uk/Software/Stamp/stamp.html) Hugo Ravi Boj

Re: [PyMOL] Secondary Structure Matching

I normally use this command with that purpose: align obj1&(ss h)&name ca, obj2&(ss h)&name ca That is, obj2 is structurally aligned onto obj1 on the basis the CA trace on the regions where secondary structure matches alfa helix (ss h) Hugo Kerff Frédéric wrote: > Hello, > > Is there a way to per

Re: [PyMOL] Updates

Hi Jason, I have compiled the last PyMOL code, and tried to used CEalign. What I wanted is to align all proteins using the first entry as reference, as it is possible with the CEalign command "alignto" (following instructions in http://pymolwiki.org/index.php/Cealign#Multiple_Structure_Alignments)

Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under Linux

Dear PyMolers, We are on the process of buying a 3D monitor for stereo rendering. The main software we use for visualization is PyMOL, in Linux (preferably OpenSuse), so it is mandatory that it works well with Pymol. We might use stereo with other programs like Maestro (Schrödinger) or MOE (CC

[PyMOL] pymol dies when switching edit/view modes

Hi, i am experiencing a strange bug in pymol 1.3. It happens when I switch between "Edit" and "View" modes, it dies with the following output: /usr/local/bin/pymol: line 2: 23763 Segmentation fault /usr/bin/python /usr/local/lib64/python2.5/site-packages/pymol/__init__.py "$@" I am usi