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]