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.
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