[Chimera-users] color by RMSD

Daniel Gurnon danielgurnon at depauw.edu
Fri Sep 7 13:19:03 PDT 2012

Hi everyone,

To color a trajectory by RMSD, comparing each frame to the final frame. My
approach was to save the last frame of the trajectory as a pdb, load it as
a separate model, and then run something like this script:

mm #0 #1 show true

rangecolor mavRMSD min white mid pink max red

This works, but of course my screen quickly fills with multialign-viewer
windows. Without "show true" in the script, coloring doesn't work past the
first frame. Is there a way to do this without displaying the MAV window?



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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