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@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@lecom.edu

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