[Chimera-users] "extended" Zone specifier

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 8 13:52:22 PDT 2008

Hi Francesco,
Maybe I misunderstood your question.  At first I thought you wanted  
all residues in one structure within some distance of *specific*  
residues in another.  However, maybe you meant you would just like to  
know all the residue-residue contacts between two structures.  In that  
case, just use the Find Clashes/Contacts tool (or the command  
"findclash").  These can write out a list of all the contacting atom  
pairs, their VDW overlaps (which could be negative where the atoms are  
not touching), and distances.  Depending on how you set the cutoffs,  
you can list only very close contacts ("clashes") or also include atom  
pairs that are farther apart.

Besides cutoffs, there are several other options such as saving to a  
file, drawing lines to show the contacts, etc.


for example:

open 1zik
findclash :.a log true

checks for clashes between chain A and all other atoms, and sends the  
following information to the Reply Log:

4 contacts
atom1  atom2  overlap  distance
LEU 5.A CD1   MET 2.B CE    0.769  2.991
MET 2.A CE    MET 2.B CE    0.761  2.999
MET 2.A CA    MET 2.B CE    0.707  3.053
VAL 23.A CG2  VAL 23.B CG2  0.707  3.053

In your example, you could just open your two models and specify #0 to  
find all the contacts between #0 and everything else.   If you use the  
GUI instead of the command, you would select all atoms of #0 and  
"Designate" them for checking against all other atoms.

This tutorial includes use of Find Clashes/Contacts:
- the "Distances, H-Bonds Contacts" part uses the tool to identify  
binding site residues, and then does some other stuff to write out a  
list of the residues instead of atom pairs
- the "Angles, Rotamers, Clashes" part uses the tool to identify  
clashes while rotating a side chain interactively

I hope this helps,
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 Oct 8, 2008, at 10:23 AM, Francesco Pietra wrote:

> What I would like to do is a global search of which residues of model
> #0 are within a certain distance from which residues of model #1.
> Where "model" stands for a protein in both cases. That would save time
> in simulations of docking (not using DOCK) between proteins. I can
> locate with Chimera key residues, but their number is large.
> Thanks
> francesco pietra
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