[Chimera-users] comparing angles in 28 structures

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 25 16:08:36 PST 2013


Hi Paola,
Other than measuring the angle in each one, the only other idea I have is to open the 28 structures as a single trajectory in the MD Movie tool.  You can only do that if each file has the same atoms with the same names.  Then you can plot the angle across the 28 "frames" in the trajectory.   However, if the structures do not have the exactly the same atoms, I don't know any other method than opening and measuring each one individually.

There are several trajectory input options including multiple PDB files, although in that case you would need to give the files names including numbers and ending in ".pdb".  The MD Movie tool including input options is described here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

 After you open the trajectory, you can use the MD Movie controller to "play" through the 28 frames.  You can plot values such as the angle of interest, see the MD Movie menu:  Analysis.... Plot
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>

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

P.S. this is a "user" question,  so chimera-users at cgl.ucsf.edu (CC'd here) is a better place to send it than chimera-dev, which is for programming questions

On Feb 21, 2013, at 12:30 PM, Paola Peshkepija wrote:

> Good afternoon,
> I am a new chimera user. I am using Chimera to look at the backbone dihedral angle variations for 28 GFP structures. I was wondering if there is a way I can look at the changes in dihedral angles using the 28 structures altogether rather than looking at each structure individually. Please, let me know. 
> Thank you in advance for your help!
> Paola




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