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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