[Chimera-users] movie recorder command file help

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 5 11:55:43 PDT 2005

Hi Lee,
The full list of commands with short descriptions is

and the subset with frame arguments (so that you can spread  
something, such as a motion, over several frames) are listed in
(this also links to an example command file, 1gfl.com)

These manual pages pertain to recent releases (Sept/Oct 2005).

To address your question more specifically,
   display - turns on display of the specified atoms (~display turns  
them off)
   show - turns on display of the specified atoms, turns off other atoms
   modeldisplay - toggles display of the whole model without changing  
atom display status (e.g., if you had only the backbone shown, you  
could hide the model with ~modeldisplay and turn it back on with  
modeldisplay, which would not turn on all the other atoms)
   represent - changes amongst wire/stick/ball&stick/sphere
   ribbon - shows ribbon
   ribrepr - changes ribbon style amongst flat/edged/round
   color - changes color
   colordef - defines a new color
   select - can be used to toggle activation status of a model  
(whether it can move or not; useful if you want to move a model  
around while another is held fixed)

Some of these are used in the example command file mentioned above.

Most commands, however, do not have frame arguments, so you cannot  
easily display/undisplay or color anything *gradually* using only  
Chimera commands (except for 2dlabels).  For example, to make a  
molecule increasingly transparent, it would be necessary to keep  
using "colordef" to define an increasingly transparent color.  Some  
of these fancier operations can be done with looping in python.  The  
python file can be called from the command file (e.g., "open  
myfile.py").  You can get the python translations of commands by  
using those commands, then opening the Command History (use black  
triangle to the right of the command line), highlighting the set of  
commands of interest, clicking "Record..."  and then choosing the  
option to record those commands as "Python commands".

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 5, 2005, at 9:49 AM, Pullan, Lee wrote:

> Hi,
> I am using the movie recorder in Chimera with the command line  
> file, as suggested in the tutorial.
> What do I enter into the command file in order to switch objects on  
> and off and also how do I change properties like transparencies/ 
> colors?
> Thanks
> Lee Pullan, PhD
> Center for Structural Biology
> Department of Biochemistry and Molecular Biology
> University of Texas - Houston Medical School
> Houston
> TX 77030
> Tel: 713 500 6121
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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