[Chimera-users] Contour level animation ?

esserlo at helix.nih.gov esserlo at helix.nih.gov
Sat Feb 4 09:44:13 PST 2017


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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>




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