Confidence maps: statistical inference of cryo-EM maps
Open Access
- 1 April 2020
- journal article
- research article
- Published by International Union of Crystallography (IUCr) in Acta Crystallographica Section D-Structural Biology
- Vol. 76 (4), 332-339
- https://doi.org/10.1107/S2059798320002995
Abstract
Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.This publication has 27 references indexed in Scilit:
- Quantifying the local resolution of cryo-EM density mapsNature Methods, 2013
- RELION: Implementation of a Bayesian approach to cryo-EM structure determinationJournal of Structural Biology, 2012
- Bsoft: Image processing and molecular modeling for electron microscopyJournal of Structural Biology, 2007
- SPARX, a new environment for Cryo-EM image processingJournal of Structural Biology, 2007
- Estimation of variance in single-particle reconstruction using the bootstrap techniqueJournal of Structural Biology, 2006
- Coot: model-building tools for molecular graphicsActa crystallographica. Section D, Structural biology, 2004
- UCSF Chimera?A visualization system for exploratory research and analysisJournal of Computational Chemistry, 2004
- Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery RateNeuroImage, 2002
- The control of the false discovery rate in multiple testing under dependencyThe Annals of Statistics, 2001
- Assembly and Stability of the Tobacco Mosaic Virus ParticleAdvances in protein chemistry, 1964