Dear Jane,
I just found out that we (Proteopedia's SAT) is the responsible for Jmol
displaying element information instead of the default phi,psi and omega values
on a Ramachandran plot.
Please hover points on
http://proteopedia.org/wiki/index.php/User:Jaime_Prilusky/Ramachandran_plot for
a correct behavior.
Sorry for the confusion. I will try to fix this ASAP.
Jaim
On Jun 14, 2012, at 7:14 PM, Robert Hanson wrote:
Dear Jane,
That would be me! Thanks for your feedback on this. I've actually been meaning
to talk with you for a long time, just not gotten around to it....
What version of Jmol are you using?
-- When you click on a point on the 3D Ramachandran plot you should see three
numbers: phi, psi, and what I will call omega', and when you hover over a point
you should see those as well. Earlier versions of Jmol behaved as you describe,
and I agree those are not very helpful.
omega' is the difference between omega and +/-180, which ever is closer to
zero. (I don't know a simple way of saying that.) The reason we use omega', is
that, unlike traditional Ramachandran plots, we have that third dimension. It
makes no sense to use omega itself, because values close to ideal such as 179
and -179 would be in totally different places. The way we do it, the Z axis can
be read as "difference from ideal" and cis-prolines show up as outliers, which
is convenient.
I would love to show contours. It might be a trick to do that in 3D, but maybe
not too bad. I think I could manage it. If you send me the coordinates of the
contours, I'll look into that.
The Ramachandran plot is interesting, of course, but also note that you have
full access to the phi, psi, and omega values themselves for any specific
residue or group of residues for any sort of analysis or tabulation you would
like.
Note also that there is a subtle distinction between "helix" and
"within(helix)" in case you start being interested in comparing Ramachandran
angles between structures. "within(helix)" cuts out the first and last residue
of each helix structure.
Aside from that, not sure you know that Jmol can now read and display Kinemage
files created by MolProbity.
Also, while I'm at it -- are you aware the MolProbity reverses the placement of
the hydrogen atoms on CH2 groups when it calculates H atoms? Probably not
something anyone but me cares about. But that's one of the things I've been
meaning to talk with you about.
Bob Hanson
On Wed, Jun 13, 2012 at 8:22 PM, Eric Martz
<[email protected]<mailto:[email protected]>> wrote:
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 -- [email protected]<mailto:[email protected]> -- 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
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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