I’ll also add for completeness, that (in Phenix at least) by default a total of 2000 reflections will be selected at most - meaning if you have a lot of reflections the total percentage selected will be substantially less than 10% or even 5%.
> On Jul 10, 2018, at 7:44 AM, Pavel Afonine <[email protected]> wrote: > > It's important to remember that free-R reflections are not only used to > calculate Rfree, but also are used in calculation of m and D scales in > 2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement targets. > The fact is that you need to have a sufficient amount of free-R reflections > in each relatively thin resolution bin. Some authors estimate this number as > at lest 50 reflections per bin. In Phenix binning is defined such that each > sufficiently thin bin gets no less than 150 reflections. Bernhard pointed out > about "precision or significance of Rfee". Also, I would add that too few > free-R reflections can affect refinement progress (not only robustness of > Rfree value) (I've done relevant tests to convince myself more than a decade > ago)! Thus I favor having 10% just to be on a safer side. > > Pavel > > > On Tue, Jul 10, 2018 at 1:02 AM, 张士军 <[email protected]> wrote: > Dear all > > I am confusing the choose of free R-flags recently. Rfactor means calculatted > from reflection not used in refinement,so what's big the difference between > different percentage of R-flags,like it's about 5% in ccp4 -refmac, while it > is 10% in phenix-refinement,what's the difference between them and how they > affect the Rwork and Rfree values when do refinement. Thanks a lot ! > > best regards > > shijun > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] -- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
