mean weighted phase error by resolution bin

5 Dec 2014

      Thanks to Pavel's suggestion,
I was able to calculate the overall mean weighted phase error
between to sets of phases in miller_arrays 2 and 5. I am stumped on how to
retrieve the mean weighted phase error by resolution bin.

#! /usr/bin/env cctbx.python
import sys
import iotbx
mtz_filename = sys.argv[1] 
mtz_file = mtz.object(mtz_filename)
miller_arrays = mtz_file.as_miller_arrays()
binner=miller_array.setup_binner_d_star_sq_step(d_star_sq_step=0.01)
mwpe = miller_arrays[2].mean_weighted_phase_error(miller_arrays[5])

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

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Today's Topics:

   1. Re: computing mean phase error between final refined model
      and experimental phases (Pavel Afonine)

----------------------------------------------------------------------

Message: 1
Date: Tue, 02 Dec 2014 12:06:08 -0800
From: Pavel Afonine 
To: cctbx mailing list ,
        [email protected]
Subject: Re: [cctbxbb] computing mean phase error between final
        refined model and experimental phases
Message-ID: <[email protected]>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

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]
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Mooers, Blaine H.M. (HSC)

Pavel Afonine

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