[Chimera-users] Definition of residues involved in binding ligand

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 26 10:40:14 PDT 2016


Hi Maarten,
The “smart initial display” just shows sidechains near ligands, as a guess of what might be interesting to see initially.  It uses the same criteria as the ribbons preset:
“... residues within 3.6 Å of a ligand residue or metal ion”

smart initial display is set on/off in the New Molecules preferences:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>

presets:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

 You could certainly display a zone using a different distance cutoff, and/or run contact and H-bond calculations  if you want to seriously analyze the interactions.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

I hope this clarifies,
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 Oct 26, 2016, at 5:56 AM, Maarten Schledorn <m.schledorn at gmail.com> wrote:

> Dear reader,
> 
> I have a pdb file of a protein with bound ADP and the file contains nothing but atomic coordinates and a few CONECT lines. If I open the file, the residues involved in binding ADP are shown, but I would like to know how Chimera knows this. I assume it is some VdW vicinity/overlap perhaps, or all residues within a certain distance from the ADP molecule, but I would like to know exactly how it is defined. I have tried to look for it in the documentation but haven't been successful so far. Does someone know the answer or a link to where it has been discussed previously?
> 
> Many thanks in advance!
> Maarten



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