[Chimera-users] Contacts

[Elaine Meng]

Hi George,
It can be done directly, although that may generate more data than you really want.

First, show your trajectory in Chimera - start MD Movie (under Tools... MD/Ensemble analysis), then enter the file types and file locations.  The MD Movie tool lets you play back your trajectory and do a bunch of other stuff, such as running commands at each step. The commands "findhbond" and/or "findclash" could be run for each frame -- these are the command-line implementations of the FindHBond and Find Clashes/Contacts tools.  Depending on the command options you use, all the info could be sent to the Reply Log, or written to a different text file for each frame.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

Before plunging into running the commands at each frame, you would try them out on the Command Line (show the command line using the Chimera Favorites menu) to figure out what options to use.  Here are their man pages:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>

Then, choose Per-Frame... Define Script from the MD Movie menu, and enter a Chimera command script containing the desired command(s).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

The "trajectory and ensemble analysis" tutorial includes using MD Movie and per-frame scripting,
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1>

and here is a related chimera-users post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004736.html>

All the data for each frame may be more than you want.  You might ultimately decide only to run the commands for representative frames.  MD Movie can also do clustering:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#clustering>

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 Jun 7, 2011, at 10:12 AM, George Tzotzos wrote:

> Hi everybody,
> I'm trying to analyse AMBER trajectories of protein/ligand complexes. The objective of my exercise is to find out contacts/interactions between the ligand and the receptor in the course of the trajectory.
> 
> Is there a way of doing this DIRECTLY in Chimera? Or one has to first perform clustering of structures and then work out clashes/contacts on the representative structures that are dumped from the trajectory.
> 
> Best regards
> George