Hi Philippe, Pymol isn't very good at handling many spheres. However, Povray is extremely efficient with raytracing scenes consisting of spheres and if you know the perspective you want to have the image from, you can convert your atom set to spheres (with desired radii) and apply the view from Pymol. If you would like, I can send you the script (Povray macro) to export the Pymol view to Povray.
Best regards, Tsjerk On 7/25/06, philippe.garteise...@ou.edu <philippe.garteise...@ou.edu> wrote:
Hi again, list. I need help on how to render an unconventional (non-protein) pdb file with a big number of atoms in it. Even with no display (console mode), pymol still crashes due to insufficient memory. A different hardware is out of the question and a smaller file would defeat my purpose, so I would like to simplify the representation. What i do is to 'show sphere', then 'set sphere_scale,0.01'. However, it seems it takes the same amount of memory for pymol to display small or large spheres (i thought that by using very small sphere_scale, pymol would tend to treat each atom more and more as a single pixel). The dots representation is also very complex to display I believe. In my case the line display can not be used either. Are there some settings to increase the memory allocated to pymol ? Are there settings of the dots representation so that only one dot is represented for each atom ? Any additional ideas are of course welcome ! Thanks in advance ! Garteiser Philippe OMRF, Cardiovascular Biology dpt. Doctoral candidate, OU Bioengineering Advisors: Dr. Tim Mather, Dr M. Uli Nollert 12600 N Macarthur Crown Pointe apt. #1423 Oklahoma City, OK 73142 home: (405) 603 7091 work: (405) 271 4924 "It does not pay to leave a live dragon out of your calculations" - Tolkien ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
-- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
