[Chimera-users] Trajectory analysis: hbond

[Elaine Meng]

Hi George,
For dumping results to a file, please see this previous post:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007044.html>

For plotting, I don't know what you wanted on the Y axis, but the MD Movie plotting currently only includes distances, angles, and dihedrals.   Of course, you could plot the distance between the H-bonding atoms.

Regards,
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 Mar 26, 2012, at 9:14 AM, George Tzotzos wrote:

> I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works.
> 
> Or dumb values to a file.
> 
> Many thanks in advance for any suggestions
> 
> Regards
> 
> George