Hi Jeff, Yes, there are many ways to add customized labels in PyMOL. The labels will be saved to your png file. As Saurabh suggested, Please see the examples here https://pymolwiki.org/index.php/Label.
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: Saurabh Gayali [saurabh.gay...@gmail.com] Sent: Wednesday, October 21, 2020 5:54 AM To: Jeff Saxon Cc: pymol-users Subject: Re: [PyMOL] [EXTERNAL] png command in Educational Pymol 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Label&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=DrgJ6lV_1gdnhXA-GZQcnykt60-aQBIrBqPr9Irv6Pg&e=> ------- 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. ________________________________ [https://i.imgur.com/KatpbrU.jpg] Saurabh Gayali / Post Doctoral Fellow saurabh.gay...@gmail.com<mailto:saurabh.gay...@gmail.com> / +91 8800412916 CSIR-IGIB <https://urldefense.proofpoint.com/v2/url?u=http-3A__example.com_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=uWtW0pw2aLchvAV3eOX1UFjoMNMC1QnC8twXa7EFP7k&e=>New Delhi, India On Tue, Oct 20, 2020 at 9:17 PM Jeff Saxon <jmsstarli...@gmail.com<mailto: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<mailto:thomas.hol...@schrodinger.com>>: > > See last question here ("Ray tracing does not work"): > https://pymol.org/edu/faq.php<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_edu_faq.php&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=UQ4HfX4kGVvTsIoXylaT19Or6Xzlk6UjUJUkVvAKKws&e=> > > Cheers, > Thomas > > On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC) > <blaine-moo...@ouhsc.edu<mailto: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<mailto: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<mailto: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<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=qDvoQ4fQobq5o0Gm3kNL2jSFxG737Q4K-WS-Bw2wxrM&e=> > > Unsubscribe: > > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=w7XKWcijJ9qnOQ2CmbqcwsN-n66FY3bJz9lgvVRg8WI&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=qDvoQ4fQobq5o0Gm3kNL2jSFxG737Q4K-WS-Bw2wxrM&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=w7XKWcijJ9qnOQ2CmbqcwsN-n66FY3bJz9lgvVRg8WI&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
