[Chimera-users] on MD movie and morph conformation by chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 12 10:00:08 PDT 2015

Hi Smith,
If you’re making a fairly simple movie that just plays through the morphing, you can just use MD Movie’s menu: File… Record movie.  See MD Movie documentation, the “recording a movie” section:

However, if you want the morphing to be part of a longer movie with lots of other things, like rotating, zooming, display changes, etc., you would usually use a Chimera command script to do everything.

Probably most people would use the graphical interface of Morph Conformations to calculate the morphing, then save a session that includes the morphing results trajectory.   Then, if you are creating a movie with a Chimera command script, you can open the session and use the “coordset” command to replay the morphing trajectory.

There are examples of Chimera command scripts and resulting movies including morphing in the Chimera Animation Gallery:

(A) "Morphing between the inactive and activated conformations of the FGFR1 kinase domain” 
uses the approach I just described, it opens a session that already includes the previously calculated morphing trajectory.  The session and command file are linked to the description.

(B) "Ball-and-socket motion” 
includes the commands to calculate the morph before starting to record and playing back the morph, so there is only a command file linked, not a session.  However, as mentioned above, it will be more convenient for most people to calculate the morph and then save a session, instead of repeatedly recalculating the same morph.

There may be additional examples in the Animation Gallery, those are just the ones I’m most familiar with since I made them.

You could also use an already calculated morph trajectory in the Animation timeline interface, but I haven’t used that capability except to test it once.  See mentions of “trajectory” in the Animation documentation:

See also the general “making movies” information for Chimera:

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 Jun 12, 2015, at 2:47 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> Will you please introduce to me on how to combine chimera MD movie function and morph conformation function  to make conformation change movie files to insert into PPT files?
> Smith

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