[phenixbb] lower Rfree in phenix.maps compared to phenix.refine and phenix.reciprocal_space_arrays

[Pavel Afonine]

Hi Gregers,

this is confusing I agree, thanks for pointing this out!

phenix.maps applies a correction to bulk-solvent mask to not fill 
bulk-solvent into internal "bulk-solvent free" voids in protein; it 
reports R-factors after this correction is done. Other tools also do 
this correction for the purpose of map calculation but they do not 
report corresponding R-factors (after such correction).

I will review this to make reported output clearer.

Pavel

On 7/31/14, 12:08 AM, Gregers Rom Andersen wrote:
>
> Dear bb
>
> I have encountered a quite significant difference between Rfree 
> reported by phenix.maps, refine and reciprocal_space_arrays. I have 
> used default values in the GUI, and don't find differences in 
> reflections statistics reported in the phenix.maps log that could 
> explain the difference. I have another example also, but with a 
> smaller difference between phenix.maps and phenix.refine. Both are 
> quite large structures with maximum resolution between 3.5 and 4. Any 
> explanation?
>
> phenix.maps
>
> -------------------------------------------------------------------------------
>
> Bulk solvent correction and anisotropic scaling:
>
> |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % 
> free)------------|
>
> | |
>
> | r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 
> 0.60 A |
>
> |                                                               |
>
> | x-ray target function (ml) for work reflections: 
> 6.433959                   |
>
> |-----------------------------------------------------------------------------|
>
> phenix.reciprocal_space_arrays
>
> |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % 
> free)------------|
>
> | |
>
> | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 
> 0.69 A |
>
> |                                                                |
>
> | x-ray target function (ml) for work reflections: 
> 6.492710                   |
>
> |-----------------------------------------------------------------------------|
>
> phenix.refine, strategy=none 1 macrocycle
>
> |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % 
> free)------------|
>
> | |
>
> | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 
> 0.69 A |
>
> | 
>                                                                            |
>
> | x-ray target function (ml) for work reflections: 
> 6.492702                   |
>
> |-----------------------------------------------------------------------------|
>
> gregers
>
> Professor Gregers Rom Andersen
>
> Department of Molecular Biology and Genetics
>
> Aarhus University
>
> Gustav Wiedsvej 10C DK8000 Aarhus C
>
> phone +45 871 55507 fax +45 861 23178
>
> email gra at mb.au.dk
>
>
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