[Chimera-users] updating hydrogen bonds in an MD movie

[Elaine Meng]

On Oct 2, 2007, at 3:42 PM, E. Merkley wrote:

> I am using chimera to visualize an MD trajectory.  I want to look at  
> the
> fluctuations of hydrogen bonding patterns in a helix over the course of
> the trajectory.  Is there a way to use Find HBonds on each frame and
> display the updated pseudobonds as I view the movie in Chimera?

Hi Eric,
Yes, there is a way, and it is even shown in one of the tutorials.   
With the MD Movie tool, you can define a simple script to be run at  
each step during playback.

Part 1 of the "Trajectory and Ensemble Analysis" tutorial has examples  
of using either Chimera commands or python to run findhbond at each  
frame:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
ensembles2.html#part1

(that's the tutorial at our web site, but you can also get to the copy  
you downloaded with Chimera from the Help menu)  You can generalize  
what is done in the tutorial, for example by using different options to  
the findhbond command.

Thanks for your feedback and suggestions, we appreciate them -
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html