[phenixbb] MolProbity C-beta outliers
christopher.sci.williams at gmail.com
Mon Jul 18 10:35:52 PDT 2016
MolProbity developer here. You have asked a very reasonable question.
The "angle" reported in the C-beta position outliers is a dihedral defined
by the residue's N-CA-idealCB-modeledCB positions. If you are looking at
the markup kinemage, that's N-CA-purple sphere-modeled CB. This dihedral
indicates the direction of the CB deviation relative to the ideal CB
position and the geometry of the residue. You can imagine the CB deviation
in a radial coordinate space, with the ideal position at 0, and the modeled
position at some distance and angle.
Generally speaking, the deviation distance is the most intuitive and
interpretable measure, but the angle - the angular position of the modeled
atom in radial space - may be useful in some applications. On the
MolProbity website, after validating a structure, you can find a "Cbeta
deviation scatter plot" that uses this radial representation of CB geometry.
Thanks for the questions, and hope that helps,
---Richardson Lab, Duke University
On Mon, Jul 18, 2016 at 9:35 AM, Yufan Wu <y.wu at bioc.uzh.ch> wrote:
> Dear all,
> Anyone knows the definition of “angle” shown in the report of "MolProbity
> C-beta position outliers” after refinement ?
> It means the bond angle or dihedral angle? Between which atoms or planers?
> I am just wondering the definition of it.
> Thank you in advance!
> Yufan Wu
> Yufan Wu
> The Plueckthun Lab
> Phone: +41 44 635 5574
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> phenixbb at phenix-online.org
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