Re: [Jmol-users] Ramachandran plot of selected residues?

[Robert H. <ha...@st...>]

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.

etc.

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 <
Jef...@cs...> 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
> coh...@cs...
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
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