[Chimera-users] Flipping between alternate conformations (depiction/movie)

[Elaine Meng]

Hi Dave,
The Morph Conformations tool (under Tools... Structure Comparison)  
generates interpolated intermediate structures and then opens the  
result as a trajectory in the MD Movie tool.  With MD Movie you can  
interactively play the trajectory but also save a movie file.

These are not in command form, however.  Take a look and see if these  
tools allow you to do what you want...

Morph Conformations:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html 
 >

MD Movie:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html 
 >

Tutorials with morphing examples:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html 
 >

Tutorial that includes saving a movie with MD Movie:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1 
 >

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

On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:

> Dear Chimera team,
>
> Is there a movie command that can easily depict the interconversion
> between two alternate conformations in a nucleic acid or protein
> residue (designated conformation a and b) within a pdb file. I am
> really trying to illustrate with a movie how the phosphates flip
> between two well defined states in an ultra-high resolution DNA
> crystal structure using a chimera movie.
>
> Thanks in advance,
> Dave Chenoweth