[Chimera-users] defining a putative binding site

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 18 12:06:52 PST 2009

Hi Francesco,
If you want detailed information about which atoms contact which, and  
the distances between them, use the "Find Clashes/Contacts" tool, or  
its command version "findclash", as discussed in several previous posts:


There are links in those posts to the manual pages and a tutorial  
with an example.

Some of those discussions were about finding contacts for a ligand,  
but the findclash feature is general and can be used on whatever set  
of atoms/residues you want.  Again, you can save results to a file or  
write them to the Reply Log.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 18, 2009, at 10:55 AM, Francesco Pietra wrote:

> Hi Elaine:
> By doing as indicate in your and my post, only residues (45 residues)
> for model 0 (the bigger protein) are listed. Then I also commanded:
> sel #1:1701-1793 & 0:20,30-40,55 z<5
> i.e., inverting the order of the two models. That gave a list of
> residues (18 residues) for only model 1 (the smaller protein).
> Probably all that is useful information. But, is any way (one touch,
> as above) to get information about which-to-which?
> I am not too lazy, I am prepared on the basis of the above two
> listings, to use the zone command residue per residue, should this be
> the way.
> (the numbers for the above residues are just for a split example;
> actually I set all residues - even for areas that I knoe are not
> involved - in the zone command for both proteins)
> Thanks
> francesco

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