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

Eric Pettersen pett at cgl.ucsf.edu
Tue Aug 19 11:59:34 PDT 2008

Actually, Morph Conformations has a bug right now in showing altlocs.   
You need to make two copies of your PDB and in one strip the B  
locations of that residue and the replace the 'A' indicator letters  
with blanks, and in the other do the converse.  If you open those two  
files you should be able to morph between them as Elaine describes.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Aug 19, 2008, at 11:26 AM, Elaine Meng wrote:

> 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
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> Chimera-users at cgl.ucsf.edu
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