Hi Dan,

Chimera molecule models take lots of memory, about 2 to 4 Kbytes per atom. If your 200 frame models had 5000 atoms each that would be one million atoms taking about 2-4 Gbytes. You would certainly run out of memory and likely crash with a 32-bit version of Chimera (addressible memory of 4 Gbytes). A 64-bit version of Chimera might get further if your machine has more 8 Gbytes of actual memory. But you can see it won't scale to thousands of models.

So I would suggest opening a small batch of frames (50) as individual PDB models, compute and play the morph, then close that batch of models and open the next (50) and compute and play the morph. All the while you record the movie. The pauses during the morph computations and model opening/closing will not appear in the movie because the Chimera graphics is not being redrawn at those times. This method is a bit more complex though. Maybe it would be slightly simpler to just morph between two frames a time.

Tom

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
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____________________________

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

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