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

E. Merkley edm4 at u.washington.edu
Tue Oct 2 15:42:10 PDT 2007

Hi Chimera crew,

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?

Also, may I take this occasion to point out that requiring consecutive 
frames to have consecutive  numbers in the file names is inconvenient. 
For instance, 
my simulation is 41 ns long, and the structures are stored (in our 
in-house format) every 1 ps.  So rather then write out 41000 .pdb files, 
I'll write them out every 10 or 100 ps.  To use chimera to view a movie, I 
have to rename the files using a perl script.

Incidentally, I've been using Chimera for 3 years now and love it.

-Eric Merkley
Graduate student
Biochemistry Department
University of Washington

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