Thank you Jared. From: Jared Sampson <jared.samp...@columbia.edu> Sent: Monday, June 15, 2020 4:47 PM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com> Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] renumber
Hi Vaheh - I wasn't saying it can't be done, just that pdbset is my preferred way to handle renumbering when going in the insertion code --> integer direction. Within PyMOL, here is one way (you'll have to repeat for each chain you wish to renumber): ``` # see: https://pymolwiki.org/index.php/Pymol.stored<https://pymolwiki.org/index.php/Pymol.stored> from pymol import stored # store the current residue numbers in a list stored.oldresi = [] iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi) # make a list of the new residue numbers stored.newresi = list(range(1, len(stored.oldresi)+1)) # zip them together into a lookup dict stored.hash = dict(zip(stored.oldresi, stored.newresi)) # change the residue numbers for each atom in your chain alter polymer.protein and chain L, resi=stored.hash[resi] ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com><mailto:vaheh.oganes...@astrazeneca.com> Reply: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com><mailto:vaheh.oganes...@astrazeneca.com> Date: June 15, 2020 at 3:57:24 PM To: Jared Sampson <jared.samp...@columbia.edu><mailto:jared.samp...@columbia.edu> Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> <pymol-users@lists.sourceforge.net><mailto:pymol-users@lists.sourceforge.net> Subject: RE: [PyMOL] renumber Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson <jared.samp...@columbia.edu<mailto:jared.samp...@columbia.edu>> Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>> Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber<http://www.ccp4.ac.uk/html/pdbset.html#renumber> ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com><mailto:vaheh.oganes...@astrazeneca.com> Reply: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com><mailto:vaheh.oganes...@astrazeneca.com> Date: June 15, 2020 at 1:28:23 PM To: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu><mailto:blaine-moo...@ouhsc.edu>, Jarrett Johnson <jarrett.john...@schrodinger.com><mailto:jarrett.john...@schrodinger.com> Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> <pymol-users@lists.sourceforge.net><mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] renumber Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a command that will ignore the letters in the number field and renumber the amino acids in the order they appear in the file. Thank you. From: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu<mailto:blaine-moo...@ouhsc.edu>> Sent: Monday, June 15, 2020 12:06 PM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>>; Jarrett Johnson <jarrett.john...@schrodinger.com<mailto:jarrett.john...@schrodinger.com>> Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: RE: [PyMOL] renumber Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. 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: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com] Sent: Monday, June 15, 2020 10:49 AM To: Jarrett Johnson Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: [EXTERNAL] Re: [PyMOL] renumber Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett Johnson <jarrett.john...@schrodinger.com<mailto:jarrett.john...@schrodinger.com>> Sent: Monday, June 15, 2020 11:38 AM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>> Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] renumber Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=>> is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: run renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=>> and then you should be able to use the command as shown on the Wiki page. Hope that helps, Jarrett J. On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com%3cmailto:vaheh.oganes...@astrazeneca.com>>> wrote: Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t recognize it. Is it that Wiki is old, or my PyMOL version is dusty? 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