[Chimera-users] pause during morph conformations

Elaine Meng meng at cgl.ucsf.edu
Wed May 4 12:57:28 PDT 2011

Sigh, the coordset commands in my previous reply are not quite right, you would put the model number before the frames.  Sorry about that.  However, the commands are all correct within the "trmovie" example command file discussed in that message. 

On May 4, 2011, at 12:51 PM, Elaine Meng wrote:

> Hi Charles,
> It can be done with commands.  First you would create the morph trajectory, then use a Chimera command script (just open a plain text file containing the commands) of the general form:
> movie record [options]
> coordset 1,20 #3; wait 20
> wait 10
> coordset 21,40 #3; wait 20
> wait 10
> coordset 41,60 #3; wait 20
> movie stop
> movie encode [options]
> where [options] is not meant literally but would give your desired movie settings, and you would also change other things depending on which model is your trajectory and which frames cover the transitions, and how long you would like the pauses to be.  I would also recommend saving the session with your morph trajectory in the desired orientation so you can revisit it later and easily re-make the movie with any needed variations.
> There is an example command file showing a similar procedure...
> the "trmovie" example includes morphing and uses coordset to play parts of the trajectory and does other stuff between the uses of coordset (it actually does the morph creation too, but it may be easier for you to do that part beforehand):
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>
> ... and the resulting movie is in the Animation Gallery, currently third on this page:
> <http://www.cgl.ucsf.edu/chimera/animations/animations.html>
> More info on movies and movie-related commands:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On May 4, 2011, at 11:51 AM, Charles Greenberg wrote:
>> I have a 3-state structure and I'm currently using morph conformations  
>> to interpolate between them.  This works very nicely, but I'd like the  
>> output movie to pause for half a second (a few frames) during each of  
>> the three key states.  Anyone know how to do this?  I know you can add  
>> behaviors during particular frames, but I don't know how to make it  
>> pause.  Thanks!
>> --Charles
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