[Chimera-users] Contour level animation ?

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 3 16:57:36 PST 2017

Hi Lothar,
It just occurred to me that maybe you meant an animation created with the Animation graphical interface. However, if you save a scene with one contour level and another scene with a different contour level and put them on the timeline as keyframes in the Animation tool, playback does not change gradually between the levels, it just jumps abruptly.  So, to create a movie with a gradual contour level change, it has to be done with a Chimera command script.  

I don’t know if you have experience with that, but basically you come up with a Chimera command file, just a plain text file with a series of commands with your movie content, and once it is to your liking, just put a “movie record” command at the top ( or after the initial setup commands) and a “movie encode” command at the bottom to create the movie file.


I hope this helps,

> On Feb 3, 2017, at 4:33 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> On Feb 3, 2017, at 4:21 PM, esserlo at helix.nih.gov wrote:
>> Hi Elaine,
>> for a small demonstration, I want to make a movie in chimera where I animate
>> a change in contour level. I have an EM map with noisy features that improve
>> upon changing the level. I can do it by hand in the volume section but I
>> cannot figure out what parameter it is even if I wanted to set it on the
>> command line.
>> Setting it on the command line I suppose would be the first step but then my
>> question is: can this parameter be changed during an animation?
>> Thanks,
>>  Lothar
> Hi Lothar,
> Yes, you can use the “volume” command “level” option to change the contour level.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
> The “volume” command doesn’t itself have frames option, but you can combine it with the “perframe” command to perform a gradual change in a single line, as illustrated with this video mini-example:
> <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html#contour>
> We generally encourage emailing questions to chimera-users (CC’d here) unless they involve private data, since others may like to know the answer.
> 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
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