[Chimera-users] Chimera - Surface Residue Identification

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 7 07:05:41 PDT 2008

On Apr 6, 2008, at 4:53 PM, Thiruvarangan Ramaraj wrote:
> Hello,
> I am new to Chimera, I am trying to identify the residues that lie  
> on the surface of a antigen complex that are within certain  
> distance from the antibody.

Hi Thiruvarangan,
If you want just a certain distance, you can select the residues with  
a command that includes a "zone" specification.  For example, this  
command would select residues in chain A with any atom within 4.5  
angstroms of any atom in chain B:

select :.a & :.b zr<4.5

zr is for residue-based cutoff, za for atom-based, and you can use <  
for less than and > for more than.  Once the residues are selected  
you could do other things to them with the Actions menu including  
coloring and writing a list of their names to a file.  (You can also  
do the selecting with the menu, but it takes more words to explain.)

However, there are other ways to find contacts that do not use a  
single cutoff distance:  "Find Clashes/Contacts" and  
"Intersurf" (both under Tools... Surface/Binding Analysis).  For more  
details on using zone specification or these other tools, please see  
this previous message:


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
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