Hi Dan, As per this previous message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-April/002496.html it might be better to rewrite the trajectory with averaged coordinates, using a "smoothing window" of nearby frames to compute an average for each frame. The script attached to that original message still works, though I'm attaching it again to this message (see the original message for running it). Let me know if this doesn't meet your needs. --Eric On Sep 20, 2011, at 9:40 AM, Daniel Gurnon wrote:
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?
Thanks Dan -- ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
p: 765-658-6279 e: danielgurnon@depauw.edu _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users