Hi Jeff,
I have the incentive version of PyMOL.
It too is saving draw images with ray tracing when using the batch mode and
also when using the pymol api in Jupyter.
As you report, saving a draw image from inside PyMOL works.
This is a very annoying bug.
You should report it as an issue on the PyMOL github site.
Perhaps this is not an issue with an order version of PyMOL.
Try one from before the switch from lines to cartoon as the default molecular
representation (say version 2.1).
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 5:48 AM
To: Mooers, Blaine H.M. (HSC); pymol-users
Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
Hi Blaine,
I've just checked on trial 26 day version of Pymol it use always RAY=1
while I run pymol from script regardless of ray flag (tested with
ray=1, ray=0, without ray as in you case etc :-)
I am going to try open source pymol!
Cheers,
J
вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
<blaine-moo...@ouhsc.edu>:
>
> 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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