Hi Mahesh, They will be close but not the same. RMSDs should be very close normally, but different treatment of hetero compounds (ligands and such), outliers and LINKs added during annotation may cause small deviations. The deviations in R-factors can be much larger for all sorts of reasons. The data that is used now can be (slightly) different from what was used before due to different scaling, merging of I+ and I-, conversion from F to I, outlier rejection, R-free set annotation, deposition errors (i.e. missing data), or deposition of all measured data, not just the data used in the final refinement (this is actually a good thing). Different programs have different treatment of bulk solvent. There can be rounding errors is the conversion from TLS to anisotropic B-factors. The use of riding hydrogens can also make a big difference. There are several papers that discuss the sources of these R-factor deviations, e.g. papers about EDS, PDB_REDO and phenix.model_vs_data.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Mahesh Lingaraju > Sent: Friday, October 11, 2013 21:59 > To: [email protected] > Subject: [ccp4bb] R and R free from CIF file deposited in PDB > > Hello Experts, > > I was wondering if the R, Rfree, RMSD for bonds and angles calculated by > polygon plug in in PHENIX GUI using the cif file & pdb file deposited in protein > structure database would be the same as reported in database/publication ? > > I apologize in advance if this is a PHENIX specific question. > > Many thanks > > Mahesh
