[Chimera-users] Contour level animation ?

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 4 11:34:27 PST 2017


Hi Lothar,
Using the “level” keyword twice sets up two isosurfaces, so with the command in your script, there is a bigger isosurface at 0.2 which is enclosing and hiding the other one that is gradually shrinking as it goes from 0.2 to 0.5: 

> perframe "volume #0 level 0.2 level $1" range 0.2,0.5 frames 100

 If you just want one isosurface that is changing from 0.2 to 0.5 the command would instead be:

 perframe "volume #0 level $1" range 0.2,0.5 frames 100

I hope that solves it!  I can understand it was a little confusing because the mini video example uses “level” twice.  You can see in that video there is an inner isosurface that stays the same while the outer transparent one increases in size as the contour level decreases.
<http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html#contour>

Best,
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 Feb 4, 2017, at 9:44 AM, esserlo at helix.nih.gov wrote:
> 
> Hi
>  I used a modified version of your suggested script:
> 
> movie-howto-mar2012/scripts/contour.cmd
> 
> #-- my version
> 
> 
> movie record supersample 3
> 
> perframe "volume #0 level 0.2 level $1" range 0.2,0.5 frames 100
> wait 100
> 
> movie encode em_contour_1.mp4 quality high
> 
> #---
> 
> My assumption was that within 100 frames the values between 0.2 and 0.5 are
> linearly interpolated and fed as $1 into volume #0 level (with starting level
> 0.2).
> However this does not work. I see some changes on the surface but it certainly
> does not contour from 0.2 up to 0.5.
> 
> Interestingly, when I reverse the values: (pseudo code)
>  level 0.5 level $1 range 0.5,0.2 frame 100
> 
> it works perfectly well.
> Are we working with a lower and upper boundary as two level bars appear in the
> volume viewer control menu ?
> 
> How can I contour from low to high ?
> 
> Thanks,
> 
>  Lothar
> 
> 
> 
> 
>> 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.
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>
>> 
>> I hope this helps,
>> Elaine
>> 
>>> 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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>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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>> 
> 
> 
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