[phenixbb] phasine error

Nathaniel Echols NEchols at lbl.gov
Thu Jun 11 10:20:52 PDT 2009

On Jun 10, 2009, at 9:18 PM, Pavel Afonine wrote:
> you can get it using phenix.refine. Just type from the command line:
> phenix.refine model.pdb data.mtz strategy=none  
> main.number_of_macro_cycles=1
> and hit Enter. Look for the numbers towards the end of log file or  
> output to the screen (after bulk solvent correction and scaling is  
> reported done).

I've never been able to understand the math involved, but isn't the  
phase error calculated by phenix.refine is based on the estimates of  
model error (and incompleteness) used for maximum likelihood  
calculations, not an evaluation of the original experimental phases?   
If experimental phase restraints were used (which is the default for  
phenix.refine, and I assume AutoBuild too), they will influence the  
final phases calculated in phenix.refine, but those will still be  
biased towards the refined model.

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

More information about the phenixbb mailing list