[phenixbb] Rw/Rf -phenix - wwPDB Validation Server

Pavel Afonine pafonine at lbl.gov
Sun Jan 11 08:24:37 PST 2015

> 1- after getting structure refined with phenix.refine to  0.145 , 
> 0.164 Rw/Rf. and then you feel happy with that.
> then after using validation server from PDB you get 0.158 , 0.181 
> Rw/Rf. why this big jump for R free. why phenix.refine giving us low R 
> free where in reality is not?

I would guess something happened to the model file.
Can you reproduce R-factors yourself? Take data file and model that you 
sent to PDB, and use either of availbale tools in Phenix to compute 

phenix.model_vs_data model.pdb data.mtz
phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1

Do you get the same R-factors?

> 2- if i want to show kick map for metal binding site for publication, 
> which map and how could i generate it.

Use FEM instead:

phenix.fem model.pdb data.mtz

There is option in the GUI too. More information

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