[Chimera-users] MD setup from command line?

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 3 09:44:40 PDT 2011

Hi Thomas, 
You can use an MD Movie "metafile" to open your trajectory from the command line -- basically, it's a text file that has all the same info that would otherwise be entered into the MD Movie file input dialog.  Contents of "example.meta" could be something like


and then you could open the trajectory with command: open md:example.meta

See the description of metafiles under MD Movie startup and input:

If by automatic you mean with a command script, you can use the "movie" command for recording, encoding, etc. and the "coordset" command to play through your trajectory during recording.


The "trmovie" example here includes creating a morph trajectory and recording playback of the trajectory.  Of course, you wouldn't be doing the morphing part, but the playback and recording would be analogous:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 3, 2011, at 5:32 AM, Dr. techn. Thomas Mitterfellner wrote:

> Hello!
> I'm using Chimera to view DFT optimizations and vibrational modes. I 
> split the large xyz files into multiple small xyz files and load them 
> with the MD tool.
> Now my question is: can I do the last step from the command line so I 
> could write a script which sets the first and the last frames 
> automatically? Also, is it possible to create the respective movie (as 
> mpeg) in an automated fashion?
> Thank you,
> Thomas

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