[Chimera-users] modify structure

[Elaine Meng]

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.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>

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 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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