[Chimera-users] Scripting commands for existing morph

Cristina Paulino c.paulino at bioc.uzh.ch
Tue Mar 28 23:02:12 PDT 2017

Dear Elaine, 
Thanks for the quick answer.
Coordset was exactly was I was looking for!
However, I’m missing the possibility of controlling how fast the morph trajectory goes as I cannot indicate how many frames it should take to get from frame #start to #end. I can indicate the step size, but the smallest is obviously 1 and this is still to quick for me. 

I guess I need to redo the morph and indicate to create the trajectory with the double amount of frames?

On another note I have some trouble with the option loop [N] for the coordset command.
I cannot get to loop smoothly back and forward. It instead goes from start to end and than instead of going backward it jumps back to start. 


> On Mar 23, 2017, at 6:17 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> P.S. the scripts are linked to the Animation Gallery entries, the full URLs given in my message.   I see that the Mail tool made the script names ending in “.com”  look like links in my message, but they are not and won’t work if you click them.
>> On Mar 23, 2017, at 10:13 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 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:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
>> 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
>> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph>
>> (2) Ball-and-socket motion of thioredoxin, Chimera command script trmovie.com (includes morph calculation)
>> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>
>> This should cover what you want to do, and more.  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 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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