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Hi Dan,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
<blockquote
cite="mid:CAMLvGrvkCAFSt=wCBnOb71G0RecvSUcFA63F-A7VgToM94RBxA@mail.gmail.com"
type="cite">Hi everyone,
<div>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. </div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>Is there a better way to add transitions in between (ideally
thousands of) frames of an MD trajectory?<br clear="all">
<div><br>
</div>
<div>Thanks</div>
<div>Dan</div>
-- <br>
____________________________<br>
<br>
Daniel Gurnon, Ph. D.<br>
Associate Professor of Chemistry and Biochemistry<br>
DePauw University<br>
Greencastle, IN 46135<br>
<br>
p: 765-658-6279<br>
e: <a moz-do-not-send="true"
href="mailto:danielgurnon@depauw.edu" target="_blank">danielgurnon@depauw.edu</a><br>
</div>
<br>
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<br>
<br>
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