[Chimera-users] make one chain from two chains ID in PDB

[Dong, Jianbo]

Elaine,

I think I got it now, by trying the first link. The residue numbering
was not a problem, since although the peptide was made as two chains,
the residues was numbered as one chain (chain B: 4-246, chain
C:252-416). I simply changed C to B, and test it on PISA, it looks work.

Thank you so much for the help!

Jianbo


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Sent: Tue 3/2/2010 3:03 PM
To: Dong, Jianbo
Cc: Chimera BB
Subject: Re: [Chimera-users] make one chain from two chains ID in PDB
 
I forgot to mention that when you change chain ID, you usually also  
need to change the residue numbering so that residues will be uniquely  
specifiable.  For example, if you have two residues both numbered 10  
in chain B, it may be difficult to do something to only one or the  
other in Chimera.  Those editing servers allow renumbering in addition  
to changing the chain ID.
Elaine

On Mar 2, 2010, at 2:12 PM, Elaine Meng wrote:

> Dear Jianbo,
> You may want to try one of these PDB-editing web servers:
>
> <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
>
> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
>
> Both make you choose the file before you can see the options, but  
> can do several things, including changing chain ID and renumbering.   
> I haven't tried exactly what you describe, but it is probably worth  
> trying before using a text editor.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Mar 2, 2010, at 1:35 PM, Dong, Jianbo wrote:
>
>> Hello,
>>
>> I'm working with a PDB file, in this file, one protein peptide was
>> recognized as two chains (B and C), I want to make it as one chain,  
>> so
>> it will be easier to do some interface analysis and modeling. I  
>> guess I
>> can open the file as WORD file and change all the C to B one by  
>> one, but
>> it's too much work to edit it that way.
>>
>> May I get some help for this? Is there a easier way to do this?
>>
>> Many thanks,
>>
>> Jianbo
>
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