[Chimera-users] mutating amino acid side chain_deleting single atom

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 24 10:01:49 PDT 2007

Hi Gary,
(1) You can mutate an amino acid side chain with the command "swapaa":

We are working on an interface to allow choosing favorable sidechain  
rotamers.  However, that is not yet available, and swapaa does not  
make any effort to choose a favorable conformation.  After swapping  
the residue, you can adjust the torsions if you want,

(2) There is no separate deletion tool, but you can either select the  
atom and use "Actions... Atoms/Bonds... delete" in the menu, or you  
can use the command "delete":

You can see there are functions performed by commands and menu items  
that are not in the "Tools" (which generally have graphical  
interfaces).  You can search for features using "Help... Search  
Documentation" in the Chimera menu, or in addition to the Tools, scan  
the commands index

I hope this helps,
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 Apr 23, 2007, at 5:07 PM, Gary Laco wrote:

> Hi,
> How can I mutate an amino acid side chain in a protein to another  
> residue using Chimera?  Also, how do I delete a single atom on an  
> amino acid (for example a hydrogen).  I looked through all the  
> tools and did not find a way to do it.
> Thanks,
> Gary
> Gary S. Laco, Ph.D.
> Assistant Professor of Biochemistry
> Lake Erie College of Osteopathic Medicine-Bradenton
> 5000 Lakewood Ranch Blvd.
> Bradenton, FL 34211
> Office:  941-782-5666
> Fax:       941-782-5729
> E-mail:  glaco at lecom.edu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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