[phenixbb] the Ming dial

Nathaniel Echols nechols at lbl.gov
Sat Dec 3 18:25:48 PST 2011

On Sat, Dec 3, 2011 at 2:10 PM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> Dear All and Nat,
> The Ming webpage is following, which I am also in the learning process.
> http://kinemage.biochem.duke.edu/teaching/workshop/MolProbity/

Oh, did you mean "KiNG"?

> Will you please also introduce  me a webpage based on which I can reduce my
> rotamer outlier (currently 8% by Phenix evaluation).

The tutorials at that URL are the best introduction I know of.

> The outlier here (for rotamer) analyzed by Phenix evalutation is defined by
> that the outlier rotamer conformaton does not comply with the statstics of
> the rotamer conformation of that residue in the published PDB, or it is
> because the so-called rotamer outlier is caused by its the outlier rotamer
> conformation does not comply with the electronic density map?

They're purely statistical - the fifth citation on that page ("The
penultimate rotamer library") gives details.  The validation in PHENIX
does calculate fit to the electron density, but this is done


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