When you chose the option “Do not use the Free R flag”, then you were telling Refmac not to use cross-validation and therefore to use all reflections as the working set.
My experience (doubtless very limited compared to the ARP/wARP developers) is that it’s significantly better to use the Rfree flag, which makes sense since you need cross-validation data in order for likelihood targets to be calibrated properly. But maybe the developers have some set of test cases that led them to choose the opposite as the default. Best wishes, Randy Read On 20 Oct 2014, at 14:24, luzuok <luzuo...@126.com> wrote: > > Dear Colin and Tim, > But ARPwARP uses REFMAC5 for refinement, does this means that REFMAC5 > uses all reflections as working set? > How to validate that the refinement is not over fit? > > Best wishes! > > Lu Zuokun > > > > -- > 卢作焜 > 南开大学新生物站A202 > > > At 2014-10-20 17:38:58, "Tim Gruene" <t...@shelx.uni-ac.gwdg.de> wrote: > >Dear Lu Zuokun, > > > >since you can use the output mtz-file from ArpWarp for model building, > >but not for refinement, there is no need to include the Rfree flag in > >its output file. Maybe the omission is a deliberate caveat to the users > >to pay attention to this. > > > >Best regards, > >Tim > > > > >On 10/20/2014 04:41 AM, luzuok wrote: > >> Dear all, > >> I was using ARP/wARP in ccp4i, the input mtz file certainly has free R > >> flag, but the output mzt file doesn't have the free R flag label? > >> I chose " do not use the Free R flag" in the ARP/wARP GUI. Can anyone tell > >> me what's wrong with this? > >> > >> > >> best reagrds! > >> Lu Zuokun > >> > >> > >> > >> -- > >> 卢作焜 > >> 南开大学新生物站A202 > >> > > > >-- > >Dr Tim Gruene > >Institut fuer anorganische Chemie > >Tammannstr. 4 > >D-37077 Goettingen > > > >GPG Key ID = A46BEE1A > > > > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
