[Chimera-users] Identifying surface residues

[Elaine Meng]

Dear Soumya,
Matchmaker is for superimposing related structures, not for finding  
interactions.

To find interactions in Chimera, the two proteins would already need  
to be in the correct positions.  Chimera will not predict how one  
protein should be positioned to interact with the other; for that you  
would need to use some other program or web server.

However, if the proteins are already in their correct interacting  
position, you can use the following tools in Chimera:

(a) FindHBond (or command "findhbond")
(b) Find Contacts/Clashes (or command "findclash")

Both are under Tools... Structure Analysis.  They are also used in the  
"Structure Analysis and Comparison" tutorial.

Please see:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>

"Help... Search Documentation" in the Chimera menu can be used to  
search for topics, for example "find interactions".  It will give you  
a list of links to the relevant manual pages.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On May 16, 2009, at 1:16 PM, Soumya Ghosh (Systembiologie) wrote:

> Dear Dr. Elaine Meng,
> sorry to bother you once again. Actually after you explain me the  
> things it become very much easier , otherwise the user's guide is  
> too hard for me to decipher the solution of the specific problem.I  
> am asking you a small problem. I have protein called GID1a whose 3D  
> model I retrieved from the SWISS MODEL.I know that this  particular  
> protein interacts via alpha helices and ß sheets with the  
> interacting protein GAI. I also retrieved the 3D model of GAI. Now  
> in simple words I want to see at what points these two proteins  
> interact.What are the interacting domains involved in the  
> interaction with bonds and every thing. When I took these two  
> proteins on the CHIMERA and using the command Tools-Structural  
> comparison- Match maker, these two proteins does not show the points  
> of interaction. Can I do this here?
> Eagerly waiting for your kind reply.
>
> Thanks with regards,
> Soumya