Right, thank you! just tested it with the recent Pymol version.
one question - is there any way to plot the name of the loaded pdb on
the image (produced by PNG command) in some automatic fashion (it
could be useful when I use it directly from terminal, without GUI)?
вт, 20 окт. 2020 г. в 14:46, Thomas Holder <thomas.hol...@schrodinger.com>:
>
> 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 !
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives:
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