[phenixbb] R factor
pafonine at lbl.gov
Tue Sep 7 14:32:56 PDT 2010
> I want to calculate Fc based on the PDB file and reproduce the R factor in
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
> 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 did
> 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
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