[Chimera-users] finding residues in distance zone

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 3 10:06:13 PST 2015


Hi Angshuman,
Sure, it just requires knowing how to do a more complicated command.  Could be something like:

select :.B-C & :78.A z<5
~select ~ protein

The first command would select residues in chains B,C that are also within 5 angstroms of residue 78 in chain A.  The second one would un-select any residues that are not protein (because B and C might also include water, ions, etc.).  See the documentation for how to specify atoms in the command line, including distance zones and combinations.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Also you wouldn't have to use selection (command "select" in the examples above). You could do something else like show residue labels ("rlabel") or color the residues (e.g. "color red").

Or instead of an atomic center to atomic center distance cutoff, you could use the Find Clashes/Contacts tool (in menu under Tools… Structure Analysis, or the "findclash" command) to find all the contacts based on distances between the VDW surfaces of atoms.  That tool can draw lines to show the contacts.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

There is a similar tool and command specifically for finding H-bonds:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

This tutorial has examples of using both FindHBond and Find Clashes/Contacts:
<http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/tutorials/squalene.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 3, 2015, at 2:17 AM, angshu at klyuniv.ac.in wrote:

> Hi,
> I need a small help. I need to find out the amino acid residues from one chain of a protein which are within 5A of a specific amino acid residue of some another chain of the same protein.
> For example: Say I have a protein 1XYZ.pdb containing A, B, C chains. I want to find which amino acids from chain B and C are within 5A distance from ALA 78 belonging to chain A.
> Please let me know.
> Thanks.
> Angshuman




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