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: [email protected]

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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