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.
