Dear all, I'm very interested in this topic. I have a question about the default behaviors in output reflection files of each refinement softwares. Are test set reflections excluded from the columns for calculating electron density maps?
I found in phenix.refine documentation the option electron_density_maps.exclude_free_r_reflections was equal to False by default. (Does this option affect real space refinement in phenix.refine?) And I don't think Coot excludes test set reflections when opening MTZ file... because there's no option to specify the flag number, right? Thanks in advance, Keitaro 2011/5/24 Pavel Afonine <pafon...@gmail.com>: > Hailiang, > r-free reflections should not participate in refinement, regardless whether > it is real or reciprocal space one, done with machine driven minimizers or > your hands moving atoms in Coot. Period. The issue of correcting the > map appearance for missing data (resolution or completeness) is relevant but > different. Removing the data is noticeable, but most of the time putting > aside test set is not critical for map appearance (given that reflections > are selected randomly and do not exceed a reasonable fraction of available > data); and when it is critical, the cross validation should be done > differently anyway. > So the answer to your question is: every time you compute a map not just to > enjoy its appearance but to use it to improve your model, do not include > test flagged reflections into it. > Pavel. > > On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang <zhan...@umbc.edu> wrote: >> >> Hi, >> >> I have a preliminary question. I understand Rfree reflection sets are >> never used during automatic refinement, but, when generating the real >> space density maps, do we have to exclude Rfree columns? Any references >> will also be greatly appreciated! >> >> Best Regards, Hailiang > >
