[Chimera-users] write selected command

[Elaine Meng]

Hi Ed,
Are there conformational changes in this process, or do chains simply  
move as rigid bodies?  I had thought there were conformational  
changes within chains, but now looking at your movie again, I'm not  
sure.

If each rigid body is a separate model, you would simply save the  
different configurations of the entire set as named positions with  
the command "savepos".  Then you can reset to successive named over a  
specified number of frames with "reset" or smoothly interpolate over  
multiple saved positions with "fly".  There have been recent  
improvements including addition of "fly" so I'd recommend a recent  
daily build if it sounds like this approach is doable.

The process would then be scripted in a Chimera command file rather  
than appearing as playback in MD Movie.  Once the command file  
generates the desired movie content, you could put a "movie record"  
command at the top and "movie stop" and "movie encode" commands at  
the bottom.

example command files:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html