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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 corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skewness of electron density with the local correlation of r.m.s. 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 data sets. 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.

SUBMITTER: Terwilliger TC

PROVIDER: S-EPMC2685735 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

Terwilliger Thomas C TC Adams Paul D PD Read Randy J RJ McCoy Airlie J AJ Moriarty Nigel W NW Grosse-Kunstleve Ralf W RW Afonine Pavel V PV Zwart Peter H PH Hung Li Wei LW

Acta crystallographica. Section D, Biological crystallography 20090515 Pt 6

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 corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more mea ...[more]

PMID: 19465773

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Dataset Information

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

Publications

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

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