[phenixbb] r-work and r-free for specific resolution range(s)

Pavel Afonine pafonine at lbl.gov
Wed Aug 4 14:12:39 PDT 2010

  Hi Kay,

0) I guess by FC you actually mean Fmodel, see page #6 here

you can ask phenix.refine to output Fcalc, Fmodel, Fbulk, FOM, alpha, 
beta, TestFlags, Fobs  etc...

Example that does just this (after bulk solvent correction and 
anisotropic scaling):

phenix.refine model.pdb data.mtz strategy=none 
main.number_of_macro_cycles=1 export_final_f_model=mtz


phenix.refine model.pdb data.mtz strategy=none 
main.number_of_macro_cycles=1 export_final_f_model=mtz

2) I will add detailed R-factor statistics output as part of 
phenix.model_vs_data tool.

3) phenix.refine chooses the amount of resolution bins based on 
availability of free-R flags (so each relatively thin resolution shell 
receives not less then ~150 test reflections). By the way, "150" or so 
is the parameter that you can change. Apart from cosmetics (the amount 
of output bins) this will influence the refinement too.

Let me know what exactly you are trying to achieve and I will think how 
we can accommodate it in available tools.


On 8/4/10 10:22 AM, Kay Diederichs wrote:
> Hi,
> is there a way to get the R-factor statistics from phenix.refine, for 
> a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that 
> I would like to specify the same resolution range as the data 
> reduction program does.
> I tried with
> phenix.reflection_statistics x_map_coeffs.mtz x_data.mtz 
> --low-resolution=2.6 --resolution=2.5
> but with the default settings, phenix.refine writes 2FOFCWT and 
> FOFCWT, but not FC . So it looks like I have to re-run phenix.refine 
> and make it write out FC? Or is it easier to run phenix.xmanip for 
> that purpose?
> thanks,
> Kay
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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