[Chimera-users] mutating residues

[Elaine Meng]

Dear Hussain MR,
The chimera-users at cgl.ucsf.edu address (not the others) is recommended for asking questions about using Chimera.

To change an amino acid in a protein structure, you can use the Rotamers tool (in menu under Tools… Structure Editing) or the "swapaa" command.  Please see the manual:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

There are "swapaa" examples in the link above, and examples of using Rotamers in the "Structure Analysis and Comparison Tutorial":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

You can find tutorials and search the documentation using the Help menu in Chimera.
I hope this helps,
Elaine 
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 8, 2014, at 5:07 AM, MUHAMMAD RAMZAN MANWAR <geniouschemist26 at gmail.com> wrote:

> Dear Dr. Ferrin,
> Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible.
> With regards
> Hussain MR
> PACER-HD, KAU, KSA