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(a)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
Elaine and co,
I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this:
select #6:.a-p #8 #9
write selected relative 0 #6,8,9 /path/to/file.pdb
~select
The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number.
Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher.
Thank you for your excellent program and support.
Ed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Edward Brignole
NIH Kirschstein Postdoctoral Fellow
Francisco Asturias Lab, CB227
Center for Integrative Molecular Biosciences
The Scripps Research Institute
www.scripps.edu/~brignole
brignole(a)scripps.edu
443-653-2070 (cell)
858-784-8598 (lab)
