[cctbxbb] mean weighted phase error by resolution bin

Fri Dec 5 11:08:40 PST 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

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

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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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 <pafonine at lbl.gov>
To: cctbx mailing list <cctbxbb at phenix-online.org>,
        Blaine-Mooers at ouhsc.edu
Subject: Re: [cctbxbb] computing mean phase error between final
        refined model and experimental phases
Message-ID: <547E1BB0.3030103 at lbl.gov>
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:  blaine-mooers at ouhsc.edu
>
> Faculty webpage:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_department-2Dof-2Dbiochemistry-2Dand-2Dmolecular-2Dbiology_faculty_blaine-2Dmooers-2Dph-2Dd-2D&d=AAICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AH0SlXaLUI5-mryljMKz190LejYrsOzJYHpylspfeLY&s=rqaiZdx7q0FPgeqNSWoq7kwFM4tyeZxvBMfvxbRDYS4&e=
>
> Small Angle Scattering webpage:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_docs_default-2Dsource_ad-2Dbiochemistry-2Dworkfiles_small-2Dangle-2Dscattering-2Dlinks-2D27aug2014.html-3Fsfvrsn-3D0&d=AAICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AH0SlXaLUI5-mryljMKz190LejYrsOzJYHpylspfeLY&s=9XhXoxi5obT0IniNxBJh78HKJwRFzYJTH1dt4u4KXOw&e=
>
> X-ray lab webpage:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_department-2Dof-2Dbiochemistry-2Dand-2Dmolecular-2Dbiology_department-2Dfacilities_macromolecular-2Dcrystallography-2Dlaboratory&d=AAICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AH0SlXaLUI5-mryljMKz190LejYrsOzJYHpylspfeLY&s=EKobCa5YeL23c7JajiA5LYbpfBPGRSiMrp9pEX7ltr4&e=
>
>
>
>
> _______________________________________________
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