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

[Elaine Meng]

Hi Gary,
(1) You can mutate an amino acid side chain with the command "swapaa":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html

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,
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
structuremeas/structuremeas.html#adjust

(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":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html

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
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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
>
>
>
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