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]>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] -- 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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