Bob + other Lords of Jmol—I'm looking for some clarification of the "plot
ramachandran r" specification from the Interactive Script Docs; particularly
the definition of theta. It makes sense to me that theta is approximately
the sum of delta phi and delta psi. I get lost with two points:
- How theta relates to dq[i]/dq[i-1] (and what exactly is represented by
this quantity...does it have something to do with the rotation of residues
[i] and [i-1] w.r.t. one another? I'm thinking about the definition of
quaternion division described in your wonderful post about quaternions,
which I happened to come across today, as describing the relationship
between two rotational states)
- The distinction between "C" and "P" straightness, and how the "P"
straightness approximation for theta was derived
Related to point 1, I can't see how this is a second derivative. It looks
like a derivative of the quaternion of residue [i] w.r.t. residue [i-1].
What am I missing here? I'm trying to dumb down a description of the 3-D
Rama plot as much as possible, to add it to a tooltip in an interface. With
just a tooltip I don't have enough space to launch into a full-blown
mathematical derivation, but if that's what it's going to take to really get
at theta, I'll probably just leave it out :-)
Cheers and thanks as always, Mike
--
Mike Evans
Organic Chemistry Graduate Student
Moore Group
University of Illinois, Urbana-Champaign
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