On Tue, Dec 9, 2014 at 6:47 AM, PC <patrick.cossins@inbox.com> wrote:

I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my coordinates phi and psi?

Something like what appears in COOT->Validate->Ramachandran Plot.

We do the same thing in the Phenix GUI using the matplotlib library, and the same code can be used to generate images independently of the GUI. If you run this command:

phenix.ramalyze --plot model.pdb

it will generate PNG images of the plots for each residue type. Since all of the code is available you are welcome to tinker with it if you want to adjust the appearance (or extract the core routines and use them differently). FYI, the actual contours are generated by using the contour() function in matplotlib, and the smooth gradients generated using imshow().

How does one generate such images for publications?

The PNG might be good enough, but you can also output postscript or PDF from matplotlib - this isn't directly exposed in phenix.ramalyze, however.

-Nat