[Chimera-users] renumbering sequence with gap

[Haghighijoo, Zahra]

Hi Elaine,
Thank you so much for your valuable help.
I did it.
Regards,
Zahra
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, April 22, 2022 6:12 PM
To: Haghighijoo, Zahra <zahaghig at UTMB.EDU>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] renumbering sequence with gap


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Hi Zahra,
I don't know what you mean by "insert the gaps."  If you just want consecutive numbering (does not skip any numbers) you can use  the Renumber Residues tool (in menu under Tools... Structure Editing).  Here is the help for that tool:
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fediting%2Frenumber.html&data=05%7C01%7Czahaghig%40UTMB.EDU%7C0fc5d69341294f425b0608da24b59bd5%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C637862660271582714%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Whlwokoui2SPuCqaP00Ehra3LPQ9R1X1s5bJSDSuoco%3D&reserved=0>

Or you can use the "resrenumber" command to do the same thing.
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fresrenumber.html&data=05%7C01%7Czahaghig%40UTMB.EDU%7C0fc5d69341294f425b0608da24b59bd5%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C637862660271582714%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8l%2FTuUtTWiSwb2F%2BdOp1MhsK%2BozofWoOn3OgxBczM2k%3D&reserved=0>

However, if you need the numbering to skip numbers, e.g. go from 10-15, 20-100 (without any residues 16-19), this tool does not have that option.  You might just want to use some text-editing program to edit the PDB file directly.  Here is some help for PDB format:
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fframepdbintro.html&data=05%7C01%7Czahaghig%40UTMB.EDU%7C0fc5d69341294f425b0608da24b59bd5%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C637862660271582714%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=So%2FJVwTobc%2Be2B%2Fe%2B2coNCvkyYXnyHomrkYmgxUsHNo%3D&reserved=0>

Or to skip one set of numbers, you could text-edit the file into two pieces and use Chimera separately to  number the part before the gap and and part after the gap, and then text-edit the file back together into one file.  Depends how many gaps there are, as this might be too tedious.

There are also some web servers that do PDB file residue renumbering, but probably like Chimera, they don't allow skipping numbers in the middle
<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.canoz.com%2Fsdh%2Frenumberpdbchain.pl&data=05%7C01%7Czahaghig%40UTMB.EDU%7C0fc5d69341294f425b0608da24b59bd5%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C637862660271582714%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=w1nWhswlj%2FFUZQeIrx3Vn6kWDZuxcnpUsmXX4%2F9UIbA%3D&reserved=0>
<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdicsoft2.physics.iisc.ernet.in%2Fpdbgoodies%2Finputpage.html&data=05%7C01%7Czahaghig%40UTMB.EDU%7C0fc5d69341294f425b0608da24b59bd5%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C637862660271582714%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RXWk2UkDOsXdymr9Tvba2aYsO0L7JkqV6Ftf6mZsv2I%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 22, 2022, at 12:01 PM, Haghighijoo, Zahra via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
> I am editing a retrieved pdb from homology modeling that has two gaps, is there a way to insert the gaps and renumbering pdb?
> could you please help me ?
> Thank you,
> Zahra
>
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