[Chimera-users] Can I use Chimera to report psi-phi angles

[Elaine Meng]

Hi Sumitro,
As soon as you open a protein structure, the angle values are  
available as the residue attributes named "phi" and "psi".  Chimera  
doesn't make a Ramachandran plot, but you can write out the values to  
a file or show them as labels (or as colors etc. just like any other  
numerical attributes).

To save the values to a file or show them with colors etc., you would  
use Render by Attribute (under Tools... Structure Analysis) as  
documented here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render 
 >

How to save to a file is described at the very bottom of that page.

To show the values as labels you could use "Actions... Label...  
residue... custom" and substitute phi or psi for name or number, but  
the values are not rounded and not easy to view all at once.  It is  
reasonable if you only select and label a few residues at a time,  
however.

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

On Mar 23, 2010, at 4:00 AM, Sumitro Harjanto wrote:

> Hi ,
> Is it possible to use chimera to report the psi-phi angle of pdb  
> protein
> models..?
> Cheers,
> Sumitro