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Adaptive FDR thresholding of Fourier shell correlation for resolution estimation of cryo-EM maps

View ORCID ProfileMaximilian Beckers, View ORCID ProfileCarsten Sachse
doi: https://doi.org/10.1101/2020.03.13.990705
Maximilian Beckers
1European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
2Candidate for Joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences
3Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
4JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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  • For correspondence: maximilian.beckers@embl.de c.sachse@fz-juelich.de
Carsten Sachse
1European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
3Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
4JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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  • For correspondence: maximilian.beckers@embl.de c.sachse@fz-juelich.de
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Abstract

Fourier shell correlation (FSC) has become a standard quantity for resolution estimation in electron cryo-microscopy. However, the resolution determination step is still subjective and not fully automated as it involves a series of map interventions before FSC computation and includes the selection of a common threshold. Here, we apply the statistical methods of permutation sampling and false discovery rate (FDR) control to the resolution-dependent correlation measure. The approach allows fully automated and mask-free resolution determination based on adaptive thresholding of FSC curves. We demonstrate the applicability for global, local and directional resolution estimation and show that the developed criterion termed FDR-FSC gives realistic resolution estimates based on a statistical significance criterion while eliminating the need of any map manipulations. The algorithms are implemented in a user-friendly GUI based software tool termed SPoC (https://github.com/MaximilianBeckers/SPOC).

Footnotes

  • Highlights We introduce a robust cryo-EM map resolution estimation tool that adaptively thresholds the Fourier Shell correlation curve by statistical methods of false discovery rate control. The procedure accepts untreated half-maps and does not require any masking. We compare the results with reported resolution values determined by common fixed threshold routines. We further demonstrate the utility of the approach by applying it to demanding cases of estimating local and directional resolution.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 14, 2020.
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Adaptive FDR thresholding of Fourier shell correlation for resolution estimation of cryo-EM maps
Maximilian Beckers, Carsten Sachse
bioRxiv 2020.03.13.990705; doi: https://doi.org/10.1101/2020.03.13.990705
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Adaptive FDR thresholding of Fourier shell correlation for resolution estimation of cryo-EM maps
Maximilian Beckers, Carsten Sachse
bioRxiv 2020.03.13.990705; doi: https://doi.org/10.1101/2020.03.13.990705

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