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FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation

In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done local...

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Autores principales: Ramírez-Aportela, Erney, Maluenda, David, Fonseca, Yunior C., Conesa, Pablo, Marabini, Roberto, Heymann, J. Bernard, Carazo, Jose Maria, Sorzano, Carlos Oscar S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782520/
https://www.ncbi.nlm.nih.gov/pubmed/33397925
http://dx.doi.org/10.1038/s41467-020-20295-w
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author Ramírez-Aportela, Erney
Maluenda, David
Fonseca, Yunior C.
Conesa, Pablo
Marabini, Roberto
Heymann, J. Bernard
Carazo, Jose Maria
Sorzano, Carlos Oscar S.
author_facet Ramírez-Aportela, Erney
Maluenda, David
Fonseca, Yunior C.
Conesa, Pablo
Marabini, Roberto
Heymann, J. Bernard
Carazo, Jose Maria
Sorzano, Carlos Oscar S.
author_sort Ramírez-Aportela, Erney
collection PubMed
description In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the quality measure “FSC-Q”, and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to detect overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atoms.
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spelling pubmed-77825202021-01-11 FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation Ramírez-Aportela, Erney Maluenda, David Fonseca, Yunior C. Conesa, Pablo Marabini, Roberto Heymann, J. Bernard Carazo, Jose Maria Sorzano, Carlos Oscar S. Nat Commun Article In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the quality measure “FSC-Q”, and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to detect overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atoms. Nature Publishing Group UK 2021-01-04 /pmc/articles/PMC7782520/ /pubmed/33397925 http://dx.doi.org/10.1038/s41467-020-20295-w Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Ramírez-Aportela, Erney
Maluenda, David
Fonseca, Yunior C.
Conesa, Pablo
Marabini, Roberto
Heymann, J. Bernard
Carazo, Jose Maria
Sorzano, Carlos Oscar S.
FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
title FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
title_full FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
title_fullStr FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
title_full_unstemmed FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
title_short FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
title_sort fsc-q: a cryoem map-to-atomic model quality validation based on the local fourier shell correlation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782520/
https://www.ncbi.nlm.nih.gov/pubmed/33397925
http://dx.doi.org/10.1038/s41467-020-20295-w
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