[phenixbb] R free test set size

Nathaniel Echols nechols at lbl.gov
Wed Apr 20 15:24:32 PDT 2011

On Wed, Apr 20, 2011 at 3:14 PM, Yuri <yuri.pompeu at ufl.edu> wrote:
> I just noticed that the latest model I am working on has only 2% of
> reflections marked as free R after refinement!
> I usually give the GUI the .sca files out of HKL2000 that do not have an
> Rfree array pre-defined. The GUI lets you know about the lack of it and asks
> me if I want generate a test set of 10%. I say yes. However the pdb header
> shows the only 2.14% are chosen for free R.
> I see that some of my other models (lower resolution) have test arrays of
> around 7-10% as I would expect.

This is because Phenix has a default maximum of 2000 reflections in
the test set.  This is considered enough for all of the necessary
calculations to be robust, apparently (the maximum likelihood targets
depend on the test set somehow, but won't work properly if the
reflections are too sparse).

> How can I explicitly define the size I want?

In phenix.refine, click the "Options..." button in the section labeled
"X-ray data and experimental phases", look for a field labeled
"Maximum number of reflections in test set", and delete the value.
You can also do this from the reflection file editor, via the "R-free
flags generation" button.


More information about the phenixbb mailing list