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

Sam Paul D reachsampaul at gmail.com
Wed Jan 21 17:50:58 PST 2015

Hi Elaine, 
First of all thanks for all the suggestions.
 I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand.

Sent from my iPhone

> On 22-Jan-2015, at 02:12, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Sam,
> There is a “findclash” command for finding favorable contacts and close contacts.  It has the same features as in the “F
> ind 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/tut
> orials/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

More information about the Chimera-users mailing list