[phenixbb] R factor

zhangh1 at umbc.edu zhangh1 at umbc.edu
Tue Sep 7 14:12:39 PDT 2010


I want to calculate Fc based on the PDB file and reproduce the R factor in
it. 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).
However, it didn't generate mtz files containing the calculated Fc.

Then, I take the optimized ksol bsol and b_cart as the input and tried
phenix.fmodel. I wrote my own code to calcuate the R factor. However, I
got a lower R factor (0.2078).

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. So, I am wondering
whether phenix can:

(1) Do the similar thing as model_vs_data (hope can be somehow faster:),
but generate Fc-containing mtz file;
(2) Do a simple R factor calculate to see whether my code is wrong (maybe
answered already:)


Best Regards, Hailiang

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