Hi Alex -
I'm not surprised you're having memory issues. I just tried this test
with one of my molecules. Simply generating and displaying the symmetry
mates in a 250 A radius required 4 G of memory, and the raytracing would
have needed a lot more (I only have 8 G on this computer, so I didn't
finish that job). Unless you're running your job on a server-scale
computer with 32 G or more of memory, I think you'll have trouble with
so many molecules.
However, that's with cartoon rendering. I assume you're trying to show
unit cell packing, and the molecules will be so tiny that it doesn't
matter what they look like. Use ribbon rendering instead, and the
memory demands are greatly reduced. I was able to raytrace a 2000 x
2000 pixel image (which should be more than adequate for a poster -
that's 10 x 10 inches at 200 dpi) in 40 seconds with peak memory usage
under 2 G.
This is with the Fink compiled version of Pymol - version 1.6.9.0.
Hope that helps,
Matt
On 1/28/14 10:27 AM, A K wrote:
Hi all,
I am trying to generate a high resolution figure of a molecule
together with its symmetry mates (250 A readius) for a poster. If I
try to ray it, the pymol session crashes (perhaps too many molecules
are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make
any difference; the image is still kind of low resolution for A0 or
A1. Any idea how I can generate this in pymol? (I am using the free
version of pymol)
Thank you in advance,
Alex
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
