[phenixbb] Average B-factor and ML error

Leo Sazanov sazanov at mrc-mbu.cam.ac.uk
Wed Jul 15 10:58:07 PDT 2009


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,

-- 
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




-- 
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




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