[phenixbb] phenix and weak data

Randy Read rjr27 at cam.ac.uk
Wed Dec 12 07:47:19 PST 2012

On 12 Dec 2012, at 15:36, Douglas Theobald wrote:

> 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?

Yes, using the cross-validation data was a key step in getting maximum likelihood refinement to work.  A long time ago (a few years before our first paper on ML refinement) I implemented a first version of the MLF target we put into CNS, but the sigmaA values were estimated from the working data.  What happened was that the data would be over-fit, then the sigmaA estimates would go up (with part of the increase being a result of the overfitting), then in the next cycle the pressure to fit the data compared to the restraints would be higher, and so on.  The best I could claim for this at the time was that the resulting models were at least as good as the ones from least-squares refinement, but the R-factors were higher (indicating that there was still less over-fitting).  It would have been hard to sell the advantage of higher R-factors to the protein crystallography community so it was good that, when we started using cross-validated sigmaA values, the convergence radius improved and we could get significantly better models with lower R-factors.  I think you'll find that all the programs use just the cross-validation data to estimate the variance parameters for the likelihood target, not just phenix.refine.


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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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