[Jmol-users] Ramachandran issues in Jmol

[Eric M. <em...@mi...>]

At 6/13/12, Jane Richardson wrote:
>      For the Rama plots, do you know who wrote the script for that 
> in JMol and might be able to make a couple of changes that would 
> improve it enormously?  At present, it's nearly useless because the 
> -180 to +180 range is compressed into the center, there are no 
> numbers on the axes, and when you click on a point you get its 
> residue name and number but not the phi,psi values.  It would be 
> good, altho not essential, to show contours for the favored and 
> outlier divisions;  we'd be glad to provide those either for 
> current MolProbity general-case or for the new version that will be 
> adopted soon for PDB use.  Also, the documentation for the Rama 
> feature (as well as the whole Ramachandran plot page, before I 
> fixed it) always refers to "psi,phi".  It's not just non-standard 
> to reverse the sequence order, it's actually wrong, because a 
> psi,phi plot is occasionally used and looks very different, since 
> it shows psi(i-1), phi(i) rather than the real Rama plot which is 
> phi(i), psi(i).

Dear Jane,

The code within Jmol for Jmol's built-in Ramachandran capability was 
probably written by Bob Hanson -- ha...@st... -- he is the 
primary developer of Jmol. I am copying this to jmol-users, where 
most of the issues in Jmol are discussed and then remedied by Bob.

-Eric