[Chimera-users] Fwd: Help needed

[Elaine Meng]

>
> Begin forwarded message:
>> From: "Bagchi,  Angshuman" <abagchi at iupui.edu>
>> Date: May 13, 2008 8:58:15 AM PDT
>> To: chimera-users at 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 at 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