[phenixbb] Average B-factor and ML error
Pavel Afonine
PAfonine at lbl.gov
Wed Jul 15 11:16:04 PDT 2009
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.
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