Hi Jeff,
10 minutes is a long time for a 800 by 800 pixel image.
Maybe you need to use a computer with more memory.
You can set the dpi in the argument to the png command to a lower value like
300 or 200 to speed up writing the png file.
You can also turn off the casting of shadows: cmd.do("set ray_shadows,off"),
which might save a few seconds.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Jeff Saxon [[email protected]]
Sent: Wednesday, October 21, 2020 4:03 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Generation of images using png
Dear PyMol users,
I am generating png images of protein-ligand complex using png command
of pymol. This is the syntax that I am using from my bash script:
image=800
pdb='my.pdb'
# load pdb, split states, make image
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.split_states('complex*')
cmd.bg_color('white')
cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
"
Briefly, it works well but the time of the production of each image is
up to 10 minutes (in the case if I have many models in my.pdb). Is it
possible to speed PNG, while keeping the same resolution of image
(800x800)?
Cheers,
J.
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