[phenixbb] Maximum-likelihood score calculation

Jouko Virtanen jouko at umich.edu
Sat Jul 12 13:00:12 PDT 2014

I got this working.  Thanks for also explaining the difference between this
score and the one used in phenix.phaser.

On Fri, Jul 11, 2014 at 8:54 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  ML used in phenix.refine does not contain a constant term (to save
> computation time; perhaps there is no huge gain!) and is normalized by the
> number of reflections so the value is between 0 and ~10 most of the time
> (that makes it predictable and so it can be calibrated to use for various
> purposes).
> Pavel
> On 7/11/14, 5:07 PM, Nathaniel Echols wrote:
> On Fri, Jul 11, 2014 at 4:57 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> 1) ML targets used in phenix.refine and Phaser are essentially the same
>> but parametrized differently (alpha/beta vs sigmaA).
>  ... but they are not reported the same way - phenix.refine shows a raw
> target value (normalized?), while Phaser outputs TFZ and LLG.  Presumably
> these are related somehow but it is not obvious to me.
>  -Nat
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