[Chimera-users] Contour level animation ?
esserlo at helix.nih.gov
esserlo at helix.nih.gov
Sat Feb 4 09:44:13 PST 2017
I used a modified version of your suggested script:
#-- my version
movie record supersample 3
perframe "volume #0 level 0.2 level $1" range 0.2,0.5 frames 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
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 ?
> 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
> I donât 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 âmovie
> recordâ command at the top ( or after the initial setup commands) and a
> âmovie encodeâ 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
>>> a change in contour level. I have an EM map with noisy features that
>>> 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
>>> question is: can this parameter be changed during an animation?
>> Hi Lothar,
>> Yes, you can use the âvolumeâ command âlevelâ option to change the
>> contour level.
>> The âvolumeâ command doesnât itself have frames option, but you can
>> combine it with the âperframeâ command to perform a gradual change in a
>> single line, as illustrated with this video mini-example:
>> We generally encourage emailing questions to chimera-users (CCâd here)
>> unless they involve private data, since others may like to know the answer.
>> I hope this helps,
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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