Coot is also an option.
CCP4 is much better/flexible though.
> On Jun 15, 2020, at 3:57 PM, pym...@li... wrote:
>
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> Today's Topics:
>
> 1. Re: renumber (Oganesyan, Vaheh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 15 Jun 2020 19:57:14 +0000
> From: "Oganesyan, Vaheh" <vah...@as...>
> To: Jared Sampson <jar...@co...>
> Cc: "pym...@li..."
> <pym...@li...>
> Subject: Re: [PyMOL] renumber
> Message-ID:
> <HE1...@HE...>
>
> 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 <jar...@co...>
> Sent: Monday, June 15, 2020 2:41 PM
> To: Oganesyan, Vaheh <vah...@as...>
> Cc: pym...@li...
> 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 <vah...@as...><mailto:vah...@as...>
> Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...>
> Date: June 15, 2020 at 1:28:23 PM
> To: Mooers, Blaine H.M. (HSC) <bla...@ou...><mailto:bla...@ou...>, Jarrett Johnson <jar...@sc...><mailto:jar...@sc...>
> Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...>
> 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) <Bla...@ou...<mailto:Bla...@ou...>>
> Sent: Monday, June 15, 2020 12:06 PM
> To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>; Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>>
> Cc: pym...@li...<mailto:pym...@li...>
> 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 [vah...@as...]
> Sent: Monday, June 15, 2020 10:49 AM
> To: Jarrett Johnson
> Cc: pym...@li...<mailto:pym...@li...>
> 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 <jar...@sc...<mailto:jar...@sc...>>
> Sent: Monday, June 15, 2020 11:38 AM
> To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>
> Cc: pym...@li...<mailto:pym...@li...>
> 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 <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> 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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> End of PyMOL-users Digest, Vol 169, Issue 18
> ********************************************
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