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 [email protected]