It is probably easiest to do this with a python script. Example render.py
script:
from pymol import cmd
import glob
files = glob.glob("*.pdb")
for f in files:
cmd.load(f, "tmp")
cmd.show("sticks", "tmp") ## or whatever you display, color, etc.
cmd.ray(320,240) ## or a different size
cmd.png(f+".png") ## or a different filename/location
cmd.delete("tmp")
Then run pymol as 'pymol -c render.py' (-c option is for command mode... no
gui)
Hope this helps.
Ken
---
Kenneth E. Lind, Ph.D.
Scientist, Computational Chemistry
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
South San Francisco, CA 94080
(650) 266-3662
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of Torin Huzil
Sent: Wednesday, December 10, 2003 4:09 PM
To: pymol
Subject: [PyMOL] Pymol batch question
I have a quick question regarding pymol and batch files.
First, I am using pymol to render images of a membrane simulation that uses
point particles, as opposed to molecules.
My problem arises when making movies of the simulation. My computer
(either mac or PC) will not allow pymol to handle the large number of
points in the simulation to render more than 1 or 2 frames (the simulation
currently has 25,000 particles in it). So I have been ray tracing each
frame individually and saving the png files.
I currently have a script that does everything as far as set up, ray
tracing and saving. but I still need to load each pdb file (represents an
iteration of the simulation) into pymol and execute the script.
I have a folder with, say, 3000 pdb files in it. I would like to have
pymol open the first file, run the script and save the image as the
original file name, then open the second file and do the same thing ....
3000 times. It would be preferable to run this without the GUI.
Any help would be greatly appreciated.
-------
Dr. Torin Huzil
Department of Physics
444 Avadh Bhatia Physics Laboratory
University of Alberta
Edmonton, Alberta
Canada
T6G 2J1
Office: (780) 492-1064
Cell: (780)721-7222
email: j...@scibuzz.com
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