[Chimera-users] Interface residues in domain-domain contacts

[Elaine Meng]

Hi Amaka,
This is a rather general question, since there are different types or definitions for what is an interaction, with various choices for parameter values. 

The Structure Analysis and Comparison tutorial includes finding protein-ligand contacts with the  tools “Find Clashes/Contacts” and “FindHBond” (which have equivalent commands, “findclash” “findhbond”).  You could generalize and use similar procedures to find interactions between two subunits instead of protein-ligand.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

Either of these Getting Started tutorials (one is for menu, the other for commands) would help you understand how to select different chains (subunits) instead of the ligand. It would be helpful to do this before other tutorial(s).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>

This “Opened Interface” image tutorial includes an example of using the “findclash” command to identify interface residues. 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>

Another related feature is the “measure” command (measure buriedArea, measure contactArea).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 28, 2018, at 3:10 AM, IDIGO Nwamaka <s1322504 at sms.ed.ac.uk> wrote:
> 
> Hi,
> I am quite new to chimera. I was wondering how I can locate interface residues in different domains within the same protein model. For example, my protein has 3 domains and I want to find out the interface residues for the different domains.
> Thanks!
> Amaka Idigo
> PhD Student