If you run coot with the FWT/PHWT columns from refmac, you are fine because refmac omits the observed F and substitutes a calculated F, giving a map which is rather less biased by omission of the free set while not contaminating the free set.
The buccaneer/refmac pipeline does the same. On Tue, 24 May 2011 09:02:20 +0900, Keitaro Yamashita <[email protected]> wrote: > 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 <[email protected]>: >> 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 <[email protected]> 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 >> >>
