[phenixbb] Validation question: R-factor (all) and # of unique reflections (all)

Pavel Afonine pafonine at lbl.gov
Tue Jul 5 13:04:52 PDT 2011

Hi Young-Jin,

>  I feel like I should calculate R(all). As mtz file is usually big, 
> how can I extract Fobs and Fmodel from phenix generated mtz file?

If you feel you want it, then go ahead, and this command might be of 
help here:

phenix.mtz.dump data.mtz --column-data-format=spreadsheet -c

Yet another (easier) alternative is to run a dummy phenix.refine run 
like this:

phenix.refine data.mtz model.pdb 
xray_data.r_free_flags.ignore_r_free_flags=true main.number_of_mac=1 
strategy=none output.prefix=junk

then take the reported R-factor (Rwork will be equal to Rfree, so take 
any of them), and discard the files.

All the best!

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