Little known fact: The Ramachandran plot is really a PDB file with phi/psi/omega fractional coordinates rather than x/y/z coordinates. This means you can do all the selecting you usually do in Jmol on that plot.

display helix
display :A
display fx < 0 and fy < 0   # fx is phi, fy is psi for that plot.


I've added a new feature for Jmol 12.3.11 that would allow:

  display phi < 0 and psi < 0

for the Ramachandran plot as well, but for now you have to use fx and fy.

On Thu, Dec 29, 2011 at 12:12 AM, Jeffrey Cohlberg <> wrote:
There was a feature in Rasmol that allowed one to display a Ramachandran plot of the selected residues.  This was a great tool for teaching protein structure.  For example, you could separately display Ramachandran plots for all glycines in a protein, all prolines, or all non-glycine and non-proline residues.  Or you could choose a residue with a high helix potential or a high beta sheet potential.  Or you could select helix (or sheet or turn) and display the Ramachandran plot for those residues.  Doing this really helped the students learn what Ramachandran plots mean.

In Jmol it seems that the "plot Ramachandran" command constructs a plot for the entire protein, not the selected residues.

Is there any possibility of adding this function to Jmol?  Would others find this useful?

Jeff Cohlberg

Jeffrey A. Cohlberg, Professor
Department of Chemistry and Biochemistry
California State University, Long Beach
562-985-4944     FAX 775-248-1263

Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free!
Jmol-users mailing list

Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900