[Chimera-users] modify structure

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 20 08:49:56 PDT 2010

Hi Francesco,
Tim is totally right -- I just wanted to add that besides the "swapaa" command, there is also a graphical interface, the "Rotamers" tool, if you want to pick the sidechain conformation interactively.


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

On Sep 19, 2010, at 1:04 PM, Tim Travers wrote:

> Hello Francesco,
> If you want to mutate a residue, you can try the swapaa command:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html
> For instance:
> swapaa val #0:12.a lib Dunbrack preserve true
> where val is the target mutation, #0 gives the model number of the peptide
> in Chimera, 12.a says to make the mutation on residue position 12 of chain a,
> lib Dunbrack tells to use the Dunbrack rotamer library, and preserve true tries
> to keep the rotamer of the mutation close to the original one.
> Hope this helps,
> Tim
> On Sun, Sep 19, 2010 at 1:43 PM, Francesco Pietra <chiendarret at gmail.com> wrote:
> Hello:
> New to modify structure. I would like to modify a peptide by changing
> ARG to VAL. As I wanted to start from the conformer containing ARG, I
> tried to delete bonds, in the hope to finally change one H to CH3.
> None worked in my hands.
> Thanks for suggestions.

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