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:
> 
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> Today's Topics:
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>   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&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724651262&amp;sdata=xdDIHjozZKMKwAR4hQiO9ghd%2FMXaqmFpSfwkZRJ4r9w%3D&amp;reserved=0<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fpdbset.html%23renumber&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=yMWUgU0gnSgEZkJzOfI09s%2BKz%2FkNh2zpHJ3fqar2qBc%3D&amp;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&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=ADMwkPasdKvp5aOaJJhDfI6y2ZmVDQAYIAcr3G1LNTM%3D&amp;reserved=0<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymolwiki.org%2Findex.php%2FRenumber&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=ADMwkPasdKvp5aOaJJhDfI6y2ZmVDQAYIAcr3G1LNTM%3D&amp;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&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=VvueI3drZ60f4j3YlTk1fLU2hi%2F3uqE4TED8d3kq%2Bug%3D&amp;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&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=VvueI3drZ60f4j3YlTk1fLU2hi%2F3uqE4TED8d3kq%2Bug%3D&amp;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&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=OXV62G9zZYBO%2FMfNu9jeVyXqs8bnGxeZPEpAjeumUj4%3D&amp;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&amp;data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724661218&amp;sdata=OXV62G9zZYBO%2FMfNu9jeVyXqs8bnGxeZPEpAjeumUj4%3D&amp;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
> 
> _______________________________________________
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> 
> 
> --
> 
> Jarrett Johnson | Senior Developer
> 
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