On Fri, Aug 12, 2011 at 6:15 AM, David Goldstone
I am by no means an expert in such things and I am sure that you will get a comprehensive answer at some point. My understanding is that differences in weightings, and the treatment of the solvent correction means reproducing R-factors across different programs is not really possible.
Correct, although we can usually come close. See Pavel's paper on phenix.model_vs_data for more details: http://www.ncbi.nlm.nih.gov/pubmed/20648263 I'm not sure if the use of total vs. residual B-factors in Phenix and Refmac will also contribute - although if model_vs_data detects that a PDB file was refined with Refmac, it will automatically adjust its treatment of B-factors to compensate. In general, the R-factors from Refmac and Phenix recalculated in the other program will be fairly similar - this discrepancy is on the upper end of the range, but it's not unheard of. -Nat