Thanks for all the advices. The REFMAC PDB didn't provide ksol and bsol in the author's refinement, otherwise I would fix them in my refinement.
Best Regards, Hailiang > Hi Hailiang, > >> I want to reproduce the R factor provided by PDB file. The structure was >> refined by REFMAC, and so I think if I try a REFMAC refinement based on >> the pdb file and reflection data, the initial R factor given by REFMAC >> should be it. >> >> The pdb file provides residual B factors with TLS given by the header. I >> therefore generated the PDB with the total anisotropic B, based on which >> I >> tried REFMAC. However, the initial R_free was higher than provide by PDB >> (0.226 vs 0.216). >> >> Not sure why I can't reproduce R based on the same program. Thanks for >> any >> advice. > > 1. Unless something isn't right (with the data, model or your scripts or > all of them), (normally) you don't have to do the refinement to > reproduce the R-factor reported in PDB file header of a deposited > structure. > > 2. For particular structure you mentioned in this thread (1ss8) the > R-factor is easily reproducible with phenix.model_vs_data (*): > > phenix.model_vs_data pdb1ss8.ent 1ss8.mtz gives me: > > (...) > Model_vs_Data: > r_work(re-computed) : 0.214 > r_free(re-computed) : 0.243 > (...) > Information extracted from PDB file header: > program_name : REFMAC > year : 4 > r_work : 0.215 > r_free : 0.249 > (...) > > which is close given the diffeernces in how the bulk-solvent and > anisotropic scaling is done and loss of accuracy due to back-and-forth > conversions of ADPs (from total to partial+TLS matrices and from > partial+TLS matrices to total). > > Pavel. > > (*) > Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, > Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: > phenix.model_vs_data: a high-level tool for the calculation of > crystallographic model and data statistics. J. Appl. Cryst. 2010, > 43:677-685. > > >
