[Chimera-users] is the connection present?

[Elaine Meng]

Dear Dmitry,
There is a “findclash” command that has the same capabilities as the “Find Clashes/Contacts” tool.  Depending on the cutoffs, you can find just clashes (bad, too-close contacts) or also include longer-range favorable contacts.  You could just use the command, or use the GUI to first figure out what settings you want to use with the command.

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

command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

I recommend the links above for seeing all the options and recommended values, but below are a couple of command examples. To find clashes between molecule models #1 and #3, show as red lines, and write results to Reply Log:

findclash #1 test #3 pbColor red log true

…and to find contacts between chains A and B of model #0:

findclash #0:.A test #0:.B overlap -0.5 hb 0 log true

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 Aug 25, 2015, at 5:10 AM, Dmitry <semchonok at gmail.com> wrote:
> 
> Dear Colleagues,
> I have 3d tetramer volume density where I fitted known x-ray structure of monomer (to each unit of tetramer).
> I want to check the inter-monomeric space, whether there is connections between 2 monomers.
> Is there a command or script that checks the presence of contacts between bounds of 2 structures?
> Thank you
> Sincerely,
> Dmitry