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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