On Jun 30, 2004, at 11:39, Gabriel C. Lander wrote:
Anyone know if pymol can in any way handle rendering very large
molecules (like viral capsids)? I've got a molecule with 392,095
atoms, and an additional 78,406 - atom molecule with 155 different
states. Pymol loads the line rendering just fine, but when I go to
cartoon rendering, Pymol crashes. I'm using 2 dual-processor G5's.
Is there any way to get this to work?
thanks,
-gabe
Hi Gabe,
I don't know about viral capsids, but I could render the whole 50S
subunit (~90000 atoms) with no problems (see
http://www.mssm.edu/students/jovinl02/images/50s_large.jpg ) - that is,
after reducing the hash_max parameter to 70 (default is 120) to prevent
PyMOL from crashing.
Another two parameters you might want to reduce are stick_quality
(default is 8) and cartoon_sampling (default is 7); lowering these will
save a lot of memory and not highly affect the quality of an overall
view of something as large as a virus... I doubt people will check
individual strands within such a picture!
Hope this helps, good luck - Luca
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Luca Jovine, Ph.D.
Brookdale Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620 FAX: +1.509.356-2832
E-Mail: lucajov...@mac.com - luca.jov...@mssm.edu
W3: http://www.mssm.edu/students/jovinl02
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