Hi, On Sun, Oct 16, 2011 at 7:48 PM, Ed Pozharski <epozh...@umaryland.edu>wrote:
> On Sat, 2011-10-15 at 11:48 +0300, Nicholas M Glykos wrote: > > > > For structures with a small number of reflections, the > > statistical > > > > noise in the 5% sets can be very significant indeed. We have seen > > > > differences between Rfree values obtained from different sets > > reaching > > > > up to 4%. > this is in line with my observations too. Not surprising at all, though (see my previous post on this subject): a small seemingly insignificant change somewhere may result in refinement taking a different pathway leading to a different local minimum. There is even way of making practical use of this (Rice, Shamoo & Brunger, 1998; Korostelev, Laurberg & Noller, 2009; ...). This "seemingly insignificant change somewhere" may be: - what Ed mentioned (different noise level in free reflections or simply different strength of reflections in free set between sets); - slightly different staring conditions (starting parameter value); - random seed used in Xray/restraints target weight calculation (applies to phenix.refine), - I can go on for 10+ possibilities. I do not know whether choosing the result with the lowest Rfree is a good idea or not (after reading Ed's post I am slightly puzzled now), but what's definitely a good idea in my opinion is to know the range of possible R-factor values in your specific case, so you know which difference between two R-factors obtained in two refinement runs is significant and which one is not. Pavel
