[phenixbb] Ramachandran maps

Nathaniel Echols nechols at lbl.gov
Tue Dec 9 10:39:36 PST 2014

On Tue, Dec 9, 2014 at 6:47 AM, PC <patrick.cossins at 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

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.

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