[phenixbb] R factor

Pavel Afonine pafonine at lbl.gov
Tue Sep 7 14:32:56 PDT 2010

  Hi Hailiang,

> I want to calculate Fc based on the PDB file and reproduce the R factor in
> it.

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
> phenix.fmodel.

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 
R-factor formula.

Good luck!

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