[Chimera-users] How to assign a unique chain ID to a receptor with two chains

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 12 14:00:00 PST 2011

Hello Dr. Shao,
The problem you want to avoid is having two or more residues with the  
same number and chain ID.  It is OK if one or the other is the same,  
but not both.  Here are two possible approaches to changing residue  
numbers and/or chain IDs:

(A) If you are familiar with text-editing PDB files, you could just  
put the two chains in two separate files before opening in Chimera.   
You don't have to to anything else unless you want a corrected single  
PDB file for the receptor.

Then if you want to make a corrected single PDB file, Chimera can fix  
numbering and/or chain IDs for you: start the Model Panel (under  
Favorites) then choose the two models from your two input files on the  
left, then use "copy/combine" on the right to make them into a single  
model, and then use "File... Save PDB" in the main menu to save the  
single file.

(B) If you are not comfortable text-editing PDB files yourself, you  
could instead use one of these PDB-editing web servers to make a  
corrected single file from your original single file:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 11, 2011, at 7:09 AM, Qin Shao, Mr. wrote:

> Hello
> I am currently using Chimera 1.5 to analysis docking simulation  
> results from HadDock, because  one of my receptor has two chains, it  
> cannot be accepted directly. Through a communication to HadDock, I  
> was advised that I should avoid overlapping numbering between the  
> two chains and use a unique chain ID. Could you tell me whether I  
> can do it on Chimera based on Windows platform, how to do it. Thank  
> you very much.
> Best regards
> Dr. Qin Shao

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