Re: [cctbxbb] mean weighted phase error by resolution bin

5 Dec 2014

      Hi Blaine,

hope this helps...

from cctbx.array_family import flex
from cctbx.sgtbx import space_group_info
from cctbx.development import random_structure

def run():
   xray_structure = random_structure.xray_structure(
     space_group_info = space_group_info("P 1"),
     elements = ('C', 'N', 'O', 'H')*10)
   f_calc = abs(xray_structure.structure_factors(d_min=1.5).f_calc())
   f_calc.setup_binner(reflections_per_bin = 50)
   for i_bin in f_calc.binner().range_used():
     d_range = f_calc.binner().bin_legend(
       i_bin=i_bin, show_bin_number=False, show_counts=False)
     selection = f_calc.binner().selection(i_bin)
     f_calc_data_bin = f_calc.data().select(selection)
     print d_range, f_calc_data_bin.min_max_mean().as_tuple(), \
       flex.mean(f_calc_data_bin)

if (__name__ == "__main__"):
   run()

...please let me know if not!

All the best,
Pavel

On 12/5/14 11:08 AM, Mooers, Blaine H.M. (HSC) wrote:
...
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@ouhsc.edu
Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/f...
Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/smal...
X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/d...
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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 ,
         Blaine-Mooers@ouhsc.edu
Subject: Re: [cctbxbb] computing mean phase error between final
         refined model and experimental phases
Message-ID: <547E1BB0.3030103@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@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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