[Chimera-users] morphing movie

[Elaine Meng]

>  Actually I would like to do some movie with chimera but I never used  
> before. I have two crystal structure of two different conformation of  
> the protein that I work with. I would like to see the trajectory from  
> conformation 1 to 2. I just downloaded the chimera but I don't know  
> how to start.
>
> Could you tell me how to make the movie? I would appreciate you help.
> Is that possible to load molecule 1 and 2 and see how the trajectory  
> is ?

Begin forwarded message:

From: Elaine Meng <meng at cgl.ucsf.edu>
Date: November 30, 2007 10:29:41 AM PST

It sounds like you want to use the Morph Conformations tool (under  
Tools... Structure Comparison).  If you have two structures, it will  
"make up" a series of in-between structures to create a trajectory. You  
have to match (superimpose) the two structures yourself first.  There  
are different options of how to make the in-between structures and how  
many to make.  The trajectory-viewing tool, MD Movie, is automatically  
started to show the trajectory.  From MD Movie you can record the  
trajectory as a movie file (Quicktime or other formats) or just save it  
as a PDB file for later viewing in Chimera.

Probably you will need to learn a little bit about using Chimera so  
that you can set the display (ribbons, background color, displaying  
important sidechains) how you want for the movie.

Chimera comes with a User's Guide. You can open it directly or search  
it from the Chimera Help menu.  Also clicking the Help buttons on  
dialogs will automatically open the corresponding man pages.  I will  
give some links to our Web site, but most of the same pages are  
included with your download.

Tutorial on matching structures and making nice images:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
frameimages.html

Manual page for Morph Conformations:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ 
morph.html

for MD Movie:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ 
framemovie.html
(see the "Recording a Movie" section)

For basic Chimera use, there is "Getting Started" tutorial:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html

and a more detailed version of that at our web site (not in the User's  
Guide):
http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html

but if you get stuck or have trouble finding something, you can ask me  
about it.
Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html