See last question here ("Ray tracing does not work"):
https://pymol.org/edu/faq.php
Cheers,
Thomas
On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
<blaine-moo...@ouhsc.edu> wrote:
>
> 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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