[Chimera-users] Scripting commands for existing morph

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 23 10:13:03 PDT 2017

Hi Cristina,
Definitely, this is a very common situation of scripting movie content that includes playback of an existing morph trajectory.  The playback part would be done with the “coordset” command, and there are several additional movie-related commands, as listed in the “making movies” page:

Further, the Chimera Animation Gallery has some movies with morph trajectory playback, and includes the command scripts that were used to create them:

(1) Kinase morph, Chimera session kinase-morph3.py with already calculated morph, Chimera command script kinase-morph3.com

(2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation)

This should cover what you want to do, and more.  I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 23, 2017, at 9:37 AM, Cristina Paulino <c.paulino at bioc.uzh.ch> wrote:
> Dear all,
> I would like to create a movie from an existing morph between two pdb coordinates. 
> I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. 
> For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. 
> Can anyone help me out? I couldn't find any good description for this. 
> Many thanks in advance
> Cristina 

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