[Chimera-users] Chimera commands to record MD movies

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 18 14:23:06 PDT 2013

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.   

Hi Henry,
	The trick is to get the trajectory loaded without using the graphical user interface.  When dinosaurs roamed the earth and the MD Movie tool was being designed, we didn't recognize the importance of providing command-line versions of all important functions and therefore the MD Movie is very much unfriendly to non-GUI usage like what you are trying to do.  Nonetheless, in Python almost anything is possible and indeed non-GUI loading of trajectories is possible using a short Python script.  I've attached such a script.  You would need to edit the second line of the script to specify where the topology and coordinate files are.  Then you can run it simply by opening it with the "open"command.
	The other trick is that you will need to get the "headless" version of Chimera from the download page in order to be able to save images/movies without using the GUI.
	Let me know if you run into any problems.


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