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
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UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco