[phenixbb] phenix and weak data

[Douglas Theobald]

On Dec 12, 2012, at 1:46 AM, Ed Pozharski <epozh001 at UMARYLAND.EDU> wrote:

> On Tue, 2012-12-11 at 11:27 -0500, Douglas Theobald wrote:
> 
>> What is the evidence, if any, that the exptl sigmas are actually negligible compared to fit beta (is it alluded to in Lunin 2002)?  Is there somewhere in phenix output I can verify this myself?
> 
> Essentially, equation 4 in Lunin (2002) is the same as equation 14 in
> Murshudov (1997) or equation 1 in Cowtan (2005) or 12-79 in Rupp (2010).
> The difference is that instead of combination of sigf^2 and sigma_wc you
> have a single parameter, beta.  One can do that assuming that
> sigf<<sqrt(beta).  Phenix log files list optimized beta parameter in
> each resolution shell.  

From the log file: 

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 44.4859 -  3.0705 14086   154  0.93  12.12   1.00     0.98     118346.13|
|  2:  3.0705 -  2.4372 13777   149  0.91  15.26   1.00     0.99      58331.77|
|  3:  2.4372 -  2.1291 13644   148  0.94  11.42   1.00     0.99      23216.31|

it appears that phenix estimates alpha and beta from the R-free set rather than from the working set (I might be misreading that).  Is that correct?