[phenixbb] R factor
zhangh1 at umbc.edu
zhangh1 at umbc.edu
Sat Sep 18 23:13:45 PDT 2010
Just want to make sure, by doing:
phenix.model_vs_data model.pdb data.mtz --map=fc
will 0Fobs+Fmodel/P0Fobs+Fmodel in the output mtz file
(fo_0Fobs+Fmodel_map_coeffs.mtz) be the calculated results from model.pdb,
which is independent (eg NO sigmaa weighting) from the experemental Fo in
Best Regards, Hailiang
> Hi Hailiang,
>> I want to calculate Fc based on the PDB file and reproduce the R factor
> then phenix.model_vs_data is the right tool to accomplish this.
>> I first tried phenix.model_vs_data. It optimized ksol bsol and b_cart,
>> and the output R factor (0.2143) is close enough to that in PDB (0.215).
> The difference between the R-factors is very small. See
> J. Appl. Cryst. (2010). 43, 669-676.
> phenix.model_vs_data: a high-level tool for the calculation of
> crystallographic model and data statistics
> P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W.
> Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart
> and P. D. Adams
> for explanations of possible differences between published and
> re-computed R-factors.
>> However, it didn't generate mtz files containing the calculated Fc.
> Yes, it's not supped to do that. Actually, phenix.model_vs_data can
> output the map defined as:
> Examples: 2mFo-DFc, 3.2Fo-2.3Fc, Fc, anom, fo-fc_kick.
> So, if you say
> phenix.model_vs_data model.pdb data.mtz --map=fc
> you will get an MTZ file with desired structure factors. So, yes, you
> can get what you want out of phenix.model_vs_data !
>> Then, I take the optimized ksol bsol and b_cart as the input and tried
> This should (to some accuracy) reproduce the R-factor reported by
>> I wrote my own code to calcuate the R factor. However, I
>> got a lower R factor (0.2078).
> Any bugs ?
>> I think the reason might be my R calculation formula
>> (sigma(fo-fc)/sigma(fo)) is wrong; or model_vs_data did more than just
>> flat solvent correction and anisotropic scaling.
> Yup, you are missing the scale factor (unless you applied it to your fc
> already). See previous email for details - the script there shows the
> R-factor formula.
> Good luck!
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