[Chimera-users] how to find non-bonded interactions between a protein and a ligand?

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 21 12:42:37 PST 2015


Hi Sam,
There is a “findclash” command for finding favorable contacts and close contacts.  It has the same features as in the “Find Clashes/Contacts” graphical interface, so there are many possibilities of different command-line options and the exact command will depend on the settings you want to use:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

I recommend looking at that page to see the full syntax and the command-line options. You could also first try using the graphical interface (menu: Tools… Structure Analysis… Find Clashes/Contacts) to decide what settings you want to use.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

However, here is one example command using some standard settings for finding contacts, assuming that “protein” and “ligand” specify the desired parts of your structure:

findclash protein test ligand overlap -0.4 hbond 0.0 reveal true

… or if your protein was model #0 and your ligand was model #1:17 and you also want to select the contacting atoms:

findclash #0 test #1:17 overlap -0.4 hbond 0.0 reveal true select true

There are many ways to specify atoms (e.g. protein and ligand) in the command line:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

There is another example of using the “findclash” command in the Opened Interface image tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

… and the “Find Clashes/Contacts” too is used in the Structure Analysis & Comparison tutorial:
<http://www.rbvi.ucsf.edu/chimera/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 Jan 21, 2015, at 2:09 AM, Sam Paul D. <reachsampaul at gmail.com> wrote:

> Hi,
> I need to find non-bonded interactions between a protein and a ligand through command line.
> Could anyone please suggest which chimera command to use with the syntax?
> With regards,
> Sam




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