[Chimera-users] Trajectory analysis: hbond

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 26 13:31:51 PDT 2012

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


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.

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

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