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From: "Bagchi, Angshuman" <abagchi@iupui.edu> Date: May 13, 2008 8:58:15 AM PDT To: chimera-users@cgl.ucsf.edu Subject: Help needed Hi, I am a student of IUPUI (indiana-University-Purdue University- Indianapolis). I would like to know how chimera can be used to select the amino acid residues of one chain of a protein, which are within a certain distance (say 10A) of another chain of the same protein. For example, the pdb 1o6s has two chains A and B. I would like to find what amino acid residues of A chain of 1o6s are within 10A of B chain of 1o6s. I am eagerly expecting a reply from your end. Thanks Ang
Hi Ang, Sure, it is quite simple. You can do it with a command or with menu operations. (A) Command (show command line with "Favorites... Command Line" in the menu): select :.a & :.b z<10 (use "z" to get whole residues, "za" to get just atoms) Command-line specifications including zones are documented here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html (B) Menu: Select... Chain... B Select... Zone (specify <10 angstroms and whether you want whole residues or not, click OK) Select... Selection Mode (change to "intersect") Select... Chain... A (change selection mode back to "replace" so you don't get confused later) Either way, you can then write a list of the residues in the current selection with "Actions... Write List" in the menu - in the resulting dialog, indicate you want "selected residues." In fact you can do more sophisticated things such as identify contacts using VDW radii and identify H-bonding residues, and write out atom-atom distances. I am in the middle of writing a tutorial that includes all this stuff, but it is not done yet. In the meanwhile, this previous chimera-users message has some additional information: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002425.html See also "Find Clashes/Contacts" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html and "FindHBond" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.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