Coot is also an option.
CCP4 is much better/flexible though. > On Jun 15, 2020, at 3:57 PM, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > > https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724651262&sdata=k9BDzkY3zEahzCUFU5HoykqtqexLpi6AMmoOODmi1mU%3D&reserved=0 > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Re: renumber (Oganesyan, Vaheh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 15 Jun 2020 19:57:14 +0000 > From: "Oganesyan, Vaheh" <vaheh.oganes...@astrazeneca.com> > To: Jared Sampson <jared.samp...@columbia.edu> > Cc: "pymol-users@lists.sourceforge.net" > <pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] renumber > Message-ID: > > <he1pr04mb330757875da8aa6c13dc6a29ed...@he1pr04mb3307.eurprd04.prod.outlook.com> > > Content-Type: text/plain; charset="utf-8" > > Jared, > > Are you saying it cannot be done within PyMOL? The ccp4 option is well known. > > Thanks. > > From: Jared Sampson <jared.samp...@columbia.edu> > Sent: Monday, June 15, 2020 2:41 PM > To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com> > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] renumber > > Hi Vaheh - > > Try `pdbset` from the CCP4 suite. > > https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fpdbset.html%23renumber&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724651262&sdata=xdDIHjozZKMKwAR4hQiO9ghd%2FMXaqmFpSfwkZRJ4r9w%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fpdbset.html%23renumber&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=yMWUgU0gnSgEZkJzOfI09s%2BKz%2FkNh2zpHJ3fqar2qBc%3D&reserved=0> > > ``` > 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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymolwiki.org%2Findex.php%2FRenumber&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=ADMwkPasdKvp5aOaJJhDfI6y2ZmVDQAYIAcr3G1LNTM%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymolwiki.org%2Findex.php%2FRenumber&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=ADMwkPasdKvp5aOaJJhDfI6y2ZmVDQAYIAcr3G1LNTM%3D&reserved=0><https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__pymolwiki.org_index.php_Renumber%26d%3DDwMGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DHQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog%26s%3DziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=VvueI3drZ60f4j3YlTk1fLU2hi%2F3uqE4TED8d3kq%2Bug%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__pymolwiki.org_index.php_Renumber%26d%3DDwMGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DHQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog%26s%3DziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=VvueI3drZ60f4j3YlTk1fLU2hi%2F3uqE4TED8d3kq%2Bug%3D&reserved=0>> > 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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__renumber.py%26d%3DDwQGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DHQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog%26s%3DFHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=OXV62G9zZYBO%2FMfNu9jeVyXqs8bnGxeZPEpAjeumUj4%3D&reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__renumber.py%26d%3DDwQGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DHQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog%26s%3DFHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw%26e%3D&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&sdata=OXV62G9zZYBO%2FMfNu9jeVyXqs8bnGxeZPEpAjeumUj4%3D&reserved=0>> > > 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? > > > Regards, > > Vaheh > > _______________________________________________ > PyMOL-users mailing list > Archives: > 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