[phenixbb] R factor

[zhangh1 at umbc.edu]

Hi Pavel:

Thanks for the python script in the previous thread. It is basically same
as mine, so I think the reason for the R-factor discrepancy should be that
I can't simply read in ksol/bsol/b_cart from model_vs_data output and do a
fmodel calculation followed by merging into experimental files. Then, do
you think phenix cand o the similar thing as model_vs_data (hope can be
somehow faster:), but generate Fc-containing mtz file?

Thanks!

Hailiang

> Hi,
>
> 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:)
>
> Thanks!
>
> Best Regards, Hailiang
>
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