[phenixbb] Average B-factor and ML error - P.S.
PAfonine at lbl.gov
Wed Jul 15 11:19:12 PDT 2009
One more option to get the average B-factor:
phenix.model_vs_data model.pdb data.hkl
will give you pretty complete statistics about your data, model and
On 7/15/09 10:58 AM, Leo Sazanov wrote:
> 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 and
> would it be possible to output there also the average B-factor of all
> the atoms in the structure?
> Also, deposition into PDB requires only Luzzati coordinate errors, while
> phenix produces only ML based ones. Presumably ML estimate is better
> than Luzzati?, but it looks like often people just ignore PDB input for
> errors. It seems that it would it be useful in future to have ML option
> in the PDB submission process? Or should Phenix produce Luzzati errors
> as well?
> (I know that one can calculate av. B-fac in other programs or ask PDB to
> add some data to the deposition, but if the idea is to streamline the
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