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(
I think you can superimpose the name externally after the image is produced
using GD libraries of python.
Also I am not sure that Pymol labels could help,
https://pymolwiki.org/index.php/Label
---
I also have a question.
I am also trying to achieve something similar, but with docking output
f
Hi Saurabh,
I recommend that you start a new thread because your goal is not identical to
Jeff's.
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 Biomedic
Hi Jeff,
Yes, there are many ways to add customized labels in PyMOL.
The labels will be saved to your png file.
As Saurabh suggested, Please see the examples here
https://pymolwiki.org/index.php/Label.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and
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
thank you, Blaine!
actually this problem only exists for the saving image of the system
consisted of many models loaded into save pymol session after its
splitting
I've already tried with dpi=50 (keeping the same resolution) but It
did not produce any differences :-)
Cheers,
J.
ср, 21 окт. 2020 г.
Here are some benchmarks
1)This is an example for rendering of the image based on a multi-model
pdb of 240 frames (all states splitted into the same model)
Ray: render time: 698.52 sec. = 5.2 frames/hour (698.52 sec. accum.).
2) This is the same for 20 model pdb
Ray: render time: 19.26 sec. = 186
