[Chimera-users] pause during morph conformations

Eric Pettersen pett at cgl.ucsf.edu
Wed May 4 13:07:30 PDT 2011

Hi Charles,
	Alternatively, you can also do this with the graphical interface.   
Just add each conformation twice when you are adding conformations.   
Then, choose the second conformation in the final list you've made  
(i.e. the second copy of your first conformation) and change  
"interpolation steps" to 15 (for a half-second pause).  Then choose  
the third state and change the interpolation steps to however many you  
want when it's moving.  Then choose the fourth state and use 15 again,  
	I notice that the final list of conformations wants you to click in  
with the mouse to change which one you're working on -- the up/down  
arrows keys seem to change the conformation chosen but don't update  
the rest of the interface, so beware of that.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On May 4, 2011, at 12:57 PM, Elaine Meng wrote:

> 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.
> Elaine
> 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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