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Title: Decision-Making in Structure Solution using Bayesian Estimates of Map Quality: The PHENIX AutoSol Wizard

Abstract

Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the map calculated based on a final refined model. Here we examine 10 different measures of experimental map quality using a set of 1359 maps calculated by reanalysis of 246 solved MAD, SAD, and MIR datasets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. We find that a Bayesian estimator based on the skew of histograms of electron density is the most accurate of the 10 individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skew of electron density with the local correlation of rms density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol Wizard carries out automated structure solution based on any combination of SAD, MAD, SIR, or MIR datasets. The Wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest-quality solutions after experimental phasing.

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Physical Biosciences Division
OSTI Identifier:
961603
Report Number(s):
LBNL-1970E
Journal ID: 0907-4449; TRN: US200923%%210
DOE Contract Number:  
DE-AC02-05CH11231; 1P01 GM063210
Resource Type:
Journal Article
Journal Name:
Acta Crystallographica D
Additional Journal Information:
Journal Name: Acta Crystallographica D
Country of Publication:
United States
Language:
English
Subject:
59; DECISION MAKING; ELECTRON DENSITY; LAWRENCE BERKELEY LABORATORY

Citation Formats

Terwilliger, T C, Adams, P D, Read, R J, McCoy, A J, Moriarty, Nigel W, Grosse-Kunstleve, R W, Afonine, P V, Zwart, P H, and Hung, L -W. Decision-Making in Structure Solution using Bayesian Estimates of Map Quality: The PHENIX AutoSol Wizard. United States: N. p., 2009. Web. doi:10.1107/S0907444909012098.
Terwilliger, T C, Adams, P D, Read, R J, McCoy, A J, Moriarty, Nigel W, Grosse-Kunstleve, R W, Afonine, P V, Zwart, P H, & Hung, L -W. Decision-Making in Structure Solution using Bayesian Estimates of Map Quality: The PHENIX AutoSol Wizard. United States. https://doi.org/10.1107/S0907444909012098
Terwilliger, T C, Adams, P D, Read, R J, McCoy, A J, Moriarty, Nigel W, Grosse-Kunstleve, R W, Afonine, P V, Zwart, P H, and Hung, L -W. 2009. "Decision-Making in Structure Solution using Bayesian Estimates of Map Quality: The PHENIX AutoSol Wizard". United States. https://doi.org/10.1107/S0907444909012098. https://www.osti.gov/servlets/purl/961603.
@article{osti_961603,
title = {Decision-Making in Structure Solution using Bayesian Estimates of Map Quality: The PHENIX AutoSol Wizard},
author = {Terwilliger, T C and Adams, P D and Read, R J and McCoy, A J and Moriarty, Nigel W and Grosse-Kunstleve, R W and Afonine, P V and Zwart, P H and Hung, L -W},
abstractNote = {Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the map calculated based on a final refined model. Here we examine 10 different measures of experimental map quality using a set of 1359 maps calculated by reanalysis of 246 solved MAD, SAD, and MIR datasets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. We find that a Bayesian estimator based on the skew of histograms of electron density is the most accurate of the 10 individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skew of electron density with the local correlation of rms density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol Wizard carries out automated structure solution based on any combination of SAD, MAD, SIR, or MIR datasets. The Wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest-quality solutions after experimental phasing.},
doi = {10.1107/S0907444909012098},
url = {https://www.osti.gov/biblio/961603}, journal = {Acta Crystallographica D},
number = ,
volume = ,
place = {United States},
year = {Sun Mar 01 00:00:00 EST 2009},
month = {Sun Mar 01 00:00:00 EST 2009}
}