[Chimera-users] Renaming chain directly in Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 27 12:03:51 PST 2009

Hi Damien,
For a more reliable response, please send mail to chimera-users at cgl.ucsf.edu 
  rather than to me directly -- sometimes the others know the answer  
when I don't, and sometimes I'm away from work.

Chimera doesn't provide a way to just choose some set of residues and  
give them any chain ID you want.  It can reassign chain IDs if you are  
merging models, for example if you had two models that were both chain  
A, it could combine them into another model with chains A and B.   
However, I can't think of how that process could be used to do what  
you want in this situation.

I've come across a few PDB-editing web servers, but I don't know which  
of these might do what you want.  You may need to use SPDBV for pre- 
processing in this case.  Here are the web servers in case they are of  
general interest:


Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 27, 2009, at 9:40 AM, Damien Larivière wrote:

> Dear Elaine,
> If a PDB structure contains 2 chains A and B, is it possible to  
> rename chain B as for example chain A directly in Chimera in order  
> to get one only chain ? Also, is it possible to rename part of  
> residues of a chain A (residues 256 to 312 for example) as chain B ?
> I ask this question because I often export low resolution surfaces  
> (obtained with Multiscale Models tool) in the vrml format or obj  
> format. However, I often have to color all the model (chains A and  
> B) in only one color and highlight a set of residues in another color.
> I know that I can do this by selecting the residues of interest,  
> coloring them by using Color zone, but the result is not exportable  
> in VRML (problem of vertex color or something like that). To avoid  
> export problem, it is very simple to rather rename chains and/or  
> reassign a letter to part of chain, which I do by using  
> SwissPDBviewer. So, can I do this in Chimera ?
> Thanks for your help
> Damien

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