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 <
[email protected]> 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
> [email protected]
>
>
>
>
>
>
>
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--
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Professor of Chemistry
St. Olaf College
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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
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