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: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002425.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