[Chimera-users] defining a putative binding site

[Elaine Meng]

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:

<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 
003260.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/ 
003163.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/ 
003183.html>

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.
Best,
Elaine
-----
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
                       http://www.cgl.ucsf.edu/home/meng/index.html




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
>