[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:

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.  

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:

There is another example of using the “findclash” command in the Opened Interface image tutorial:

… and the “Find Clashes/Contacts” too is used in the Structure Analysis & Comparison tutorial:

I hope this helps,
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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