[phenixbb] Average B-factor and ML error - P.S.

Pavel Afonine 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 
> process...)
> Thanks,

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