Dear Keitaro As far as I know different program behave differently. REFMAC by default replaces structure factors of the excluded reflections with their expected values (as a first approximation) that is equal to DFc, where D reflects errors in coordinates. It seems to be a balance between avoiding model bias in map calculations (due to use of FC) and bias in Rfree (due to use of free reflections in minimisation) and noise introduction due to missing reflections. As far as I recall coot uses map coefficients produced by the refinement programs. In case of refmac it uses FWT, PHWT (that has free reflection replaced with their expected values) and DELFWT PHDELWT (that does not have free reflections).
In refmac (I am sure in phenix also) there are keywords to turn this option on/off. I hope it helps. regards Garib On 24 May 2011, at 01:02, Keitaro Yamashita 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 <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 >> >>
