But at higher resolution you would like to release the restraints and introduce more parameters in refinement, such as anisotropic Bs - ideally keeping the observation/parameter ration more or less constant...
On 3 Nov 2013, at 12:50, Edward Berry wrote: > Looking at it from the other side- suppose we say for a robust refinement we > need a certain number of reflections- say 4 times the number of atoms, maybe > less, I don't know. Any more than that is not really going to affect the > structure, So if you have high resolution you can afford to use a large > percentage of free reflections, and the cross-validation and maximum > liklihood will go really well, even with thin shells. On the other hand at > low resolution, well, sorry, you really can't spare any reflections for > cross-validation. (I have no idea whether this makes sense or not, but it > would be another way of looking at it). > > >>> Mark van Raaij <mjvanra...@cnb.csic.es> 11/01/13 7:39 PM >>> > the limit of 2000 reflections I guess is just because it would be a waste to > "throw away" more reflections for refinement, once the statistical minima for > calculating a reliable Rfree have been met. I.e. if you have 100.000 > reflections, it would be a waste to use 5 or 10% of the reflections instead > of just 2%. I'd rather use as many as possible reflections for refinement. > > On 31 Oct 2013, at 20:21, Pavel Afonine wrote: > > > Hi Joe, > > > > flags should be selected such that there is enough of them in each > > relatively thin resolution shell (thin enough so ML target parameters can > > be considered constant in each such shell). Lower end is about 50 > > reflections per shell. All in all this usually translates into about 10% > > overall. > > > > Yes, there is a limit parameter set to 2000 by default. I don't know what's > > the rationale for having it, may be someone can explain. > > > > Pavel > > > > On 10/31/13 12:10 PM, Joseph Noel wrote: > >> Hi All. I think I have asked this before but forgot. Old age. What is > >> the appropriate number / percentage of reflections to flag for a > >> statistically appropriate Free-R calculation? If I am correct, the > >> reflection file editor in Phenix chooses by default either 10% of the > >> measured reflections or 2000 whichever comes first. > >> ______________________________________________________________________________________ > >> Joseph P. Noel, Ph.D. > >> Arthur and Julie Woodrow Chair > >> Investigator, Howard Hughes Medical Institute > >> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics > >> The Salk Institute for Biological Studies > >> 10010 North Torrey Pines Road > >> La Jolla, CA 92037 USA > >> > >> Phone: (858) 453-4100 extension 1442 > >> Cell: (858) 349-4700 > >> Fax: (858) 597-0855 > >> E-mail: n...@salk.edu <mailto:n...@salk.edu> > >> > >> Publications & Citations: > >> http://scholar.google.com/citations?user=xiL1lscAAAAJ > >> > >> Homepage Salk: http://www.salk.edu/faculty/noel.html > >> Homepage HHMI: http://hhmi.org/research/investigators/noel.html > >> ______________________________________________________________________________________ > >> > >> > >> > >> _______________________________________________ > >> phenixbb mailing list > >> pheni...@phenix-online.org > >> http://phenix-online.org/mailman/listinfo/phenixbb > >> > > _______________________________________________ > > phenixbb mailing list > > pheni...@phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > phenixbb mailing list > pheni...@phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb
