Re: [phenixbb] Maximum-likelihood score calculation

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 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 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