[Chimera-users] Chimera commands to record MD movies

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 18 13:10:11 PDT 2013


Dear Henry,
You would use the "movie" command to start/stop recording and assemble the movie file, and the "coordset" command to play the trajectory.  I.e. in your Chimera command script, you'd have some setup commands, then "movie start" to start recording, then all the stuff you want in the movie (trajectory playback with "coordset" etc.), and then "movie stop" and "movie encode" (most likely with various command options such as file name, format, and location).

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>

List of movie-related commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>

There are some examples of using coordset to play back trajectories from morphing, but trajectories from MD are handled the same way once they have been loaded.  The only tricky thing is that some MD formats don't load all the coordinate sets until you have actually played the whole trajectory using the MD Movie dialog.  Examples include:
(1) video mini-example
<http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html#coordset>
(2) "ball-and-socket motion" video in the Animation Gallery (about halfway down the page)... there is also a link to the corresponding Chimera script file, trmovie.com
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html>

The above only addresses how it could be done in a Chimera command script.  Others would have to respond if you have questions about using "headless" remote Chimera or something like that.
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

On Sep 18, 2013, at 12:11 PM, psu4 at uic.edu wrote:

> Dear Chimera,
>     Since we run a lot of Amber MD simulation in remote clusters,  we wonder if there is any Chimera command that can record the Amber MD trajectories remotely and save them as avi (or any other movie file formats)?   If this is feasible, then we don't have to download all the trajectories to local and make the trajectory movies manually.    We have searched the Chimera user manual but didn't see any command.   If there are related commands which we didn't see, please forgive us : )   Thanks. 
> 
>    * There is a way to activate X11 forwarding and use remote Chimera GUI to do this, but it's extremely slow and prone to freeze the computer.   
>     Cheers,
>     Henry




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