[Chimera-users] Smoothing a trajectory

Daniel Gurnon danielgurnon at depauw.edu
Tue Sep 20 09:40:31 PDT 2011

Hi everyone,
For the purpose of making educational content, I'm interested in smoothing
out the often jumpy transitions from frame to frame in a MD trajectory. My
approach was to write two python scripts (with critical help from Eric of
course); one goes through the trajectory and saves pdbs of each desired
frame, while the second opens these pdbs and creates a morph, interpolating
from one pdb to the next.

It seemed like I was almost there, and it looked great when I tried 50
frames.....but Chimera crashed when I tried morphing 200 frames, adding 3
frames of interpolation between each.

Is there a better way to add transitions in between (ideally thousands of)
frames of an MD trajectory?


Daniel Gurnon, Ph. D.
Associate Professor of Chemistry and Biochemistry
DePauw University
Greencastle, IN 46135

p: 765-658-6279
e: danielgurnon at depauw.edu
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