Re: [Chimera-users] Contour level animation ?
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 “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...> 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
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@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 “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...>
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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...> 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@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@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 “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...>
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, thanks that makes sense. I misinterpreted the first level command as level at which to start. Kind regards, Lothar
Hi Lothar, Using the âlevelâ 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 âlevelâ 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...>
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@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 donââ¬â¢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 ââ¬Åmovie recordââ¬Â command at the top ( or after the initial setup commands) and a ââ¬Åmovie encodeââ¬Â 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 ââ¬Åvolumeââ¬Â command ââ¬Ålevelââ¬Â 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 ââ¬Åvolumeââ¬Â command doesnââ¬â¢t itself have frames option, but you can combine it with the ââ¬Åperframeââ¬Â 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 (CCââ¬â¢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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, thanks. Sorry it was late and I used your e-mail instead of chimera-users. Have a nice day. Lothar
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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