Dear all,
I'm trying to render PNG from -A LOT OF- pdb files (up to 1000!).
Fortunately, I can use a Linux cluster with a PBS server. I have create
a small script that :
1- loads PDB files (coming from a MD trajectory)
2- set up the scene (light, color etc.)
3- renders the movie
at the end of my script I have thus:
mset 1 -1000
set ray_trace_frames, 1
set cache_frames, 0
mclear
mpng /tmp/nsapay_pymol/foo
However, it seems that PyMOL doesn't clear its cache since the process
fills the memory until crash. No picture is rendered and PyMOL clearly
tells me that it ran out of memory. It seems to me that with the cache
turned off, frames should be rendered successively and not stored in the
memory. I have make some tests, it seems that PyMOL indeed loads all PDB
but crashes just after the mpng command line. So, is the problem could
be due to an error in my script? Or may be because my system is quite
large (> 15000 atoms * > 1000 frames!).
Any suggestion will be welcome!
Nicolas
PS : congratulation to PyMOL authors! It's a well-conceived and well
documented software.
--
_ Nicolas Sapay ____________________________________________
Ph.D sudent in structural bioinformatics
Institut de Biologie et Chimie des Proteines
CNRS - Claude Bernard University, Lyon I
> contact :
7, Passage du Vercors Tel: +33 (0)4 72 72 26 46
69367-F Lyon cedex 07 Fax: +33 (0)4 72 72 26 04
France Web: http://pbil.ibcp.fr/
