Hi Nat,

it is all published. Below are the papers that I used in phenix.refine to code maximum-likelihood target, phase and coordinate errors estimates. The complete list of relevant papers will include those by Randy Read, G. Bricogne, and others.

Alpha/Beta and phase error estimation algorithms, ML target formula:
V.Yu., Lunin & T.P., Skovoroda. Acta Cryst. (1995). A51, 880-887. "R-free likelihood-based estimates of errors for phases calculated from atomic models"

Formula for coordinate error estimation:
V.Y., Lunin, P.V. Afonine & A.G., Urzhumtsev. Acta Cryst. (2002). A58, 270-282. "Likelihood-based refinement. I. Irremovable model errors"

P. Afonine, V.Y. Lunin & A. Urzhumtsev. J. Appl. Cryst. (2003). 36, 158-159. "MLMF: least-squares approximation of likelihood-based refinement criteria"

Paper suggesting to use TEST reflections in Alpha/Beta estimation:
A.G. Urzhumtsev, T.P. Skovoroda & V.Y. Lunin. J. Appl. Cryst. (1996). 29, 741-744. "A procedure compatible with X-PLOR for the calculation of electron-density maps weighted using an R-free-likelihood approach"

they will influence the  
final phases calculated in phenix.refine, but those will still be  
biased towards the refined model.

No, because the estimates are done using TEST reflections that are not supoosed to be used in any step of structure solution and refinement.

Pavel.


On 6/11/09 10:20 AM, Nathaniel Echols wrote: 
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
510-486-5136
[email protected]



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