[Chimera-users] substitute single residue

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 4 08:19:34 PDT 2009

Dear Andy,
Yes, there is a much easier way:  use the Rotamers tool (under  
Tools... Structure Editing).  You can specify residue type and rotamer  
library, and that will give you a "bouquet" of rotamers at that  
position.  You can calculate H-bonds and clashes for the rotamers (or  
even how well they fit into a density map!) to help you choose the  
best one, and then have it replace the original sidechain.  This tool  
could be used to generate different rotamers for the same amino acid  
type or to mutate to a different amino acid type.

The "Structure Analysis and Comparison" tutorial includes use of  

There is also a command-line implementation, "swapaa":

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

On Jul 30, 2009, at 2:57 PM, Andrew P. Hinck wrote:

> Dear all,
> I was hoping to make some single amino acid substitutions in the  
> context of a protein binding interface.  I've only briefly poked  
> around, but so far the only way I see to do this is to delete  
> existing atoms/bonds one by one, and then rebuild (the alternate  
> amino acid) atom-by-atom/bond-by-bond.  Is there an easier way  
> (like, telling the program to substitute an Asp for a Lys, or  
> something akin to this)?  Thanks in advance for any suggestions.
> Andy Hinck

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