Hi Ed, On Tue, Oct 11, 2011 at 11:47 AM, Ed Pozharski <epozh...@umaryland.edu>wrote:
> On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote: > > better, but not always. What about say 80% or so complete dataset? > > Filling in 20% of Fcalc (or DFcalc or bin-averaged <Fobs> or else - it > > doesn't matter, since the phase will dominate anyway) will highly bias > > the map towards the model. > > DFc, if properly calculated, is the maximum likelihood estimate of the > observed amplitude. I'd say that 0 is by far the worst possible > estimate, as Fobs are really never exactly zero. Not sure what the > situation would be when it's better to use Fo=0, perhaps if the model is > grossly incorrect? But in that case the completeness may be the least > of my worries. > Yes, that's all true about what is DFc. In terms of missing-Fobs-filling it's not too important (as map appearance concerned) which values you take, DFc, <Fobs> , etc. I spent a few days playing with this some years ago. > Indeed, phases drive most of the model bias, not amplitudes. If model > is good and phases are good then the DFc will be a much better estimate > than zero. If model is bad and phases are bad then filling in missing > reflections will not increase bias too much. But replacing them with > zeros will introduce extra noise. In particular, the ice rings may mess > things up and cause ripples. > Yep, that was the point - sometimes it is good to do, and sometimes it is not, and ... > On a practical side, one can always compare the maps with and without > missing reflections. > ... this is why phenix.refine outputs both maps -:) All the best, Pavel
