Hi Nate,

I was taught to set aside 10% for the free R set, only going lower
if setting aside the full 10% compromised completeness.  I'm just
wondering what is the rationale for the numeric cap?  Am I making
any error(s) with my methodology?


For the alpha/beta (or sigmaa) calculation you need a certain number
of reflections per resolution bin to get reasonable estimates. Say
you have 10 bins, 2000/10 = 200 is a sufficiently large sample per
bin.

I have to admit I'm uncertain about the pros and cons of setting
aside a larger number of reflections.

Test reflections are not used in map calculation. So obviously, more reflections you exclude as free reflections, less reflections will be used in map calculation. Personally, I've never seen this being a trouble but the rumor is that this may worsen the maps.

I think the way PHENIX generates free-flags for you is totally fine (unless you prove otherwise).

Pavel.