[Chimera-users] comparing angles in 28 structures

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 25 16:55:06 PST 2013

A few more options:

You can see the range of phi/psi/chi angles for a set of selected residues by bringing up the selection inspector (magnifying glass icon in lower right corner of Chimera window) and changing its "Inspect" menu to "Residue".  You could easily select residue 20 in each structure (for example) with the command "sel :20".  You could then select only those residues whose phi/psi angles are in a certain range by using the Render by Attribute tool, changing to its "Select" tab, and adjusting the vertical bars on the displayed histogram to the range you want and clicking OK.  This will select such residues across the entire structure, but you can then restrict them back to just residue 20 with "sel sel & :20".

You can also write selected residues to a file or the reply log with the Actions->Write List... menu item.

If you want to write some kind of program for getting the angles, it is not too hard since the phi/psi/chi angles are properties of the Residue object (e.g. r.phi, r.chi2, etc.).  The "Atomic Measurements" programmer's example covers this:



                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Feb 25, 2013, at 4:08 PM, Elaine Meng wrote:

> 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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