[Chimera-users] Smoothing a trajectory

Daniel Gurnon danielgurnon at depauw.edu
Tue Sep 20 11:10:55 PDT 2011


Here it is:

from chimera import openModels, Molecule, runCommand
i=1
runCommand ("morph start #0 frames 2")
totalModels=len(openModels.list(modelTypes=[Molecule]))
for m in openModels.list(modelTypes=[Molecule]):
    while i < totalModels:
        runCommand ("morph interpolate #" +str(i)+ " frames 2")
        i=int(i)+1

runCommand ("morph movie")



On Tue, Sep 20, 2011 at 1:54 PM, Darren Weber <dweber at cgl.ucsf.edu> wrote:

>
> Hi,
>
> Can we see the interpolation code?
>
> -- Darren
>
>
>
> On 09/20/2011 09:40 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 <mailto: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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>



-- 
____________________________

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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