I think you can superimpose the name externally after the image is produced using GD libraries of python. Also I am not sure that Pymol labels could help, https://pymolwiki.org/index.php/Label
------- I also have a question. I am also trying to achieve something similar, but with docking output files where models are saved as frames and I want a particular frame. I dont know the question should be in the same thread or I should start a new one. ------------------------------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India On Tue, Oct 20, 2020 at 9:17 PM Jeff Saxon <jmsstarli...@gmail.com> wrote: > 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: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e= > > > > Unsubscribe: > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e= > > > > > > > > > _______________________________________________ > > > PyMOL-users mailing list > > > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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