Dear Pavel, Thanks for comprehensive reply - since refinement itself was done some time ago, I forgot to look now into "REMARK stage"... Leonid Pavel Afonine wrote:
Hi Leo,
Hi, phenix.refine outputs "WILSON B" value into PDB header after refinement, which is not the same as average B-factor of all the atoms in the structure, and not exactly the same as Wilson B-factor from SCALA scaling. How exactly is Wilson B-factor for phenix header calculated
Wilson B is computed using Peter's procedure as described in:
Zwart, P.H., Grosse-Kunstleve, R.W. & Adams, P.D. (2005). CCP4 newsletter. No. 42.
or in one of there references in this paper. Peter may comment on this some more.
and would it be possible to output there also the average B-factor of all the atoms in the structure?
It is reported by phenix.refine many times in many different places:
- in PDB file header:
REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 100.80 7.48 28.20 100.80 7.48 27.43 78.39 12.05 40.43 REMARK 1_bss: 101.17 7.85 28.57 101.17 7.85 27.80 78.76 12.42 40.80 REMARK 1_xyz: 101.17 7.85 28.18 101.17 7.85 27.80 58.46 14.33 35.27 REMARK 1_adp: 113.33 11.63 27.68 113.33 11.63 27.44 55.19 16.55 32.10 REMARK 2_bss: 113.47 11.78 27.82 113.47 11.78 27.58 55.33 16.70 32.24 REMARK 2_xyz: 113.47 11.78 27.93 113.47 11.78 27.58 55.28 14.61 34.43 REMARK 2_adp: 114.56 11.66 27.71 114.56 11.66 27.46 52.95 16.40 32.23 REMARK 3_bss: 114.64 11.73 27.79 114.64 11.73 27.54 53.03 16.48 32.30 REMARK 3_xyz: 114.64 11.73 27.86 114.64 11.73 27.54 57.12 13.65 33.94 REMARK 3_adp: 115.09 11.32 27.64 115.09 11.32 27.42 53.24 16.30 31.94 REMARK 3_bss: 115.15 11.38 27.68 115.15 11.38 27.48 53.31 16.37 31.63
- in log file:
|-ADP statistics--------------------------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 3549 0 11.38 115.15 27.68 None None None | | all(noH): 3549 0 11.38 115.15 27.68 None None None | | Sol. : 169 0 16.37 53.31 31.63 None None None | | Mac. : 3380 0 11.38 115.15 27.48 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 11.384 - 21.760: 1339 | 5: 63.266 - 73.643: 30 | | 1: 21.760 - 32.137: 1407 | 6: 73.643 - 84.019: 24 | | 2: 32.137 - 42.513: 442 | 7: 84.019 - 94.396: 18 | | 3: 42.513 - 52.890: 200 | 8: 94.396 - 104.772: 18 | | 4: 52.890 - 63.266: 68 | 9: 104.772 - 115.149: 3 | | =>continue=> | |-----------------------------------------------------------------------------|
- finally, you can type:
phenix.pdbtools model.pdb --show-adp-statistics [optionally, give a CIF file]
Also, deposition into PDB requires only Luzzati coordinate errors, while phenix produces only ML based ones. Presumably ML estimate is better than Luzzati?,
ML error estimate is better than Luzzati one, indeed. That's exactly why phenix.refine outputs ML error estimate. And even ML error estimate has it's own known problems (not just in phenix, but in general), so it shouldn't be taken too literally.
phenix.refine outputs PDB file almost ready for PDB deposition, and "almost" means here that you have to remove the upper part of the header till where the REMARK 3 section starts.
Pavel.
-- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915