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 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.
<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@cgl.ucsf.edu> wrote:
On Feb 3, 2017, at 4:21 PM, esserlo@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 âvolumeâ command âlevelâ 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 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:
<http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html...>
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 ----- 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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