Hi Jeff,
I do not know the answer to your question. This is a work around.
Try dropping ray=0 and adding the draw command with the dimensions in pixels
(width, height).
cmd.draw(1600,1600);cmd.png('test1600.png')
I would not use the Educational PyMOL for the kind of serious work that you are
trying to do.
The PyMOL Wiki has several pages about open source versions of PyMOL.
Use one of those instead.
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 [jmsstarli...@gmail.com]
Sent: Tuesday, October 20, 2020 5:24 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
hello,
I am using educational version of Pymol to generate png image of
protein-ligand complex
First, there are no problems in the case of PNG command from pymol's
GUI. However if I run the same from script from terminal:
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
"
it does not produce an image with the following message:
! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
! has a reduced set of features compared to the full Incentive PyMOL version.
! Please visit
https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=
for details. If you want to generate
! figures for publication, then please obtain an academic license,
! see
https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
note that ray is disabled in my command (since I do not need a HQ
image) and as I've mentioned there were no problems to create an image
from gui session using the same command. Could it be fixed for my case
or I need another version of Pymol ?
Thank you !
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