[Chimera-users] Contour level animation ?

esserlo at helix.nih.gov esserlo at helix.nih.gov
Sat Feb 4 12:20:55 PST 2017


Hi,

  thanks that makes sense. I misinterpreted the first level command as level
at which to start.
  Kind regards,

    Lothar


> 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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>>
>>
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