From: Matt Franklin <mattf@ge...> - 2003-02-05 23:17:26
Hi all -
I'm trying to use pymol to render a large number of complex images in
order to make a molecular movie. This already takes a long time (1-2
minutes per frame) on my Octane due to the large molecular surfaces I'm
drawing, but I'm now going to need to raise the surface quality,
increase the number of frames, and possibly raytrace the images as well.
Rather than tie up my computer for a week doing this, I thought I'd
try a suggestion that Warren made, and run my pymol scripts in batch
mode on a 24-CPU Origin2000 compute server that we have.
However, I'm having trouble getting the command mode to function. It
appears that one should launch pymol like so:
pymol.com -c < pymol_script
where "pymol_script" is a script file that you could otherwise invoke
from the GUI's command line by "@pymol_script". However, when I try
this with a simple script like:
load egf.pdb, egf
color orange, egf
show surface, egf
the program starts and then exits immediately without doing anything.
There's no .png file generated; if I give an incorrect filename in the
script, there's no error message; the script takes no time to execute.
The screen output that I do get is:
(the usual pymol startup message)
Command mode. No graphics front end.
Memory: 0 blocks expected, 0 found, 46 maximum allocated.
Memory: current memory allocated 0 bytes (0.0 MB).
PyMOL: normal program termination.
Soooo, what am I doing wrong? Am I invoking pymol correctly? Do I need
things in the script that I wouldn't normally (like window size)?
I'm using pymol 0.86 on an SGI Octane running Irix 6.5, if it matters.
Matthew Franklin Phone:(650)225-4596
Postdoctoral Researcher Fax:(650)225-3734
1 DNA Way, South San Francisco, CA 94080
From: Kristian Rother <kristian.rother@ch...> - 2003-02-06 08:34:23
There is a straighter way to do it. Try just=20
(This works at least on my Linux machine).
You can also try
cat pymol_script.pml | pymol.com -p
tail -f pymol_script.pml | pymol.com -p
The latter allows one to append lines to the pymol script from an externa=
program, which will be executed immediately.
> I'm trying to use pymol to render a large number of complex images in
> order to make a molecular movie.=20
> However, I'm having trouble getting the command mode to function. It
> appears that one should launch pymol like so:
> pymol.com -c < pymol_script
> where "pymol_script" is a script file that you could otherwise invoke
> from the GUI's command line by "@pymol_script". However, when I try
> this with a simple script like: