[Chimera-users] image showing the trajectory of a domain rotation

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 27 10:33:58 PDT 2013

Hi Andy,
It sounds like you made a morph trajectory that is being displayed with the MD Movie tool.  You can save the whole trajectory to a single PDB file (using main menu: File... Save PDB, and choosing only the morph model and other appropriate settings including saving "all frames" instead of "current frame").  Then maybe save the session so you won't lose your work, but then close session.  Open the new single PDB file to see all the different steps at the same time.  Then you can color, change display style, etc.  For example, commands:

rainbow models
ribscale licorice

... to rainbow-color the different steps, make ribbon into a thin tube, and hide atoms.  

There is also a nice "ViewMotions" web server from the Kantrowitz group that does basically all of this stuff including the morphing, and includes a Chimera session in the output so you can change the orientation etc. as desired before saving an image:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 26, 2013, at 8:10 PM, Anindito Sen wrote:

> Dear All,
> I have generated a movie that shows the rotation of a domain of the protein molecule in Chimera. I want to prepare a figure which shows that trajectory of the domain movement between the 2 states (probably using lines instead of the ribbons). How can I do that in Chimera.
> Thanks.
> Andy

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