[Chimera-users] Scripting commands for existing morph

Cristina Paulino c.paulino at bioc.uzh.ch
Wed Mar 29 09:18:52 PDT 2017


Hi Elaine,

> (1)  I don’t know if you mean it is too fast when it executes in Chimera, or in a saved movie file.  Those are two different things.  
I meant while saving the movie. Sorry for not being specific enough. 

> When you encode the movie there is an option for its playback frame rate. You could try setting that lower and see what you think.  If you are using the Movie Recorder GUI it is in the Movie options.  If using the command see “movie encode” option “framerate”
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-options>

This will not help, as I just t change the speed of the trajectory to be slower and not in general for all the other commands in my script which I would otherwise have to change. 
I just help myself out by creating the morph new, but now being composed out of 61 instead of 21 frames. Does when using coordset later in my movie script it was 3 times slower then before :)


> 
> (2) coordset “loop” means to jump from the end to the start, not play it backwards.  However, you would simply use coordset again to play backwards, for example:
> coordset #2 1,21; wait 21
> coordset #2 21,1; wait 21
That is what I ended up doing. Thought there would be a ‘loop’ command option for scripting. In the movie encode gui there is the option of the loop for back and forth. 

> 
> Or probably easier, just use the “movie encode” option “roundtrip true” (see link above). 
> 
> (In our new software ChimeraX the “coordset” command now has a “pause” option so that you can specify more image update frames per trajectory frame, but this program is still in early development, with many missing features.)
Looking forward to testing it :)

Best,
Cristina



> 
> 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 28, 2017, at 11:02 PM, Cristina Paulino <c.paulino at bioc.uzh.ch> wrote:
>> 
>> 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. 
>> 
>> Best,
>> Cristina
>> 
>>> 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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>> 
>> 
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