[cctbxbb] computing mean phase error between final refined model and experimental phases

[Pavel Afonine]

Hi Blaine,

key functionality for this is the method of Miller array class called 
mean_phase_error, see:

cctbx/miller/__init__.py .

Unit and regression tests are best usage examples most of the time. In 
this case see:

cctbx/regression/tst_miller.py .

Let me know if you have any questions.

I don't have a good grasp of phase error value as a quality measure. For 
example, I do not know what number is good, what is poor, etc. I think 
to some extent what you are trying to do can be converted to Fourier map 
comparison: just compute two maps, each one using identical amplitudes 
and two different sets of phases, and then compare maps. To me at least 
the map CC is a more telling metric.

However, map comparison is tricky too (usual map CC may be misleading!) 
and you need to use proper metrics, as explained in details here:

Acta Cryst. (2014). D70, 2593-2606.
Metrics for comparison of crystallographic maps
A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams

Pavel

On 12/2/14 9:20 AM, Mooers, Blaine H.M. (HSC) wrote:
> Dear CCTBXBB,
>
> I want to compare the phases from the final refined model and a set of 
> experimental phases
> to calculate the weighted mean phase error.
>
> How do I this using python?
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Assistant Professor
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
>
> Shipping address:
>
>
> office: (405) 271-8300   lab: (405) 271-8313 fax:  (405) 271-3910
> e-mail:  blaine-mooers at ouhsc.edu
>
> Faculty webpage: 
> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
>
> Small Angle Scattering webpage: 
> http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0
>
> X-ray lab webpage: 
> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
>
>
>
>
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