[Chimera-users] Smoothing a trajectory

[Eric Pettersen]

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 at depauw.edu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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