Dear Rex, Bernie and Fred, The following paper bears on the question of generally slight, but not always, R factor differences between published and recalculated Rfactors. [The paper is open access.] Greetings, John
J. Appl. Cryst. (2010). 43, 669-676 [ doi:10.1107/S0021889810015608 ] phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams Abstract: phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed. Keywords: PHENIX; Protein Data Bank; data quality; model quality; structure validation; R factors. On Wed, Feb 16, 2011 at 1:43 PM, Vellieux Frederic <frederic.velli...@ibs.fr> wrote: > Hi Rex, > > There will be small differences in particular due to the different ways of > treating the solvent. How large of a difference are you talking about? > Normally the difference should not be very large... And if this related to > solvent effects, it will affect the low resolution reflections with a > decrease in the effect when you go to higher and higher resolutions (but > never completely disappear). > > Fred. > > REX PALMER wrote: >> >> Does anyone still use CNS ? >> Do we expect Rfree from CNS for example to be different from the value >> given by Refmac at the end of the refinement? >> Rex Palmer >> Birkbeck College >> > -- Professor John R Helliwell DSc
