Brief Communication | Published:

Quantifying the local resolution of cryo-EM density maps

Nature Methods volume 11, pages 6365 (2014) | Download Citation

Abstract

We propose a definition of local resolution for three-dimensional electron cryo-microscopy (cryo-EM) density maps that uses local sinusoidal features. Our algorithm has no free parameters and is applicable to other imaging modalities, including tomography. By evaluating the local resolution of single-particle reconstructions and subtomogram averages for four example data sets, we report variable resolution across a 4- to 40-Å range.

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Acknowledgements

We are grateful to S. Scheres, G. Lander, A. Bartesaghi and K. Davies for stimulating discussions and sharing their density maps for this study. This work was supported by Natural Sciences and Engineering Research Council of Canada award PGS-D3 (A.K.) and US National Institutes of Health grants R01LM010142 (H.D.T.), R01GM095658 (A.K. and H.D.T.) and R01NS021501 (F.J.S.).

Author information

Affiliations

  1. Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA.

    • Alp Kucukelbir
    • , Fred J Sigworth
    •  & Hemant D Tagare
  2. Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA.

    • Fred J Sigworth
  3. Department of Diagnostic Radiology, Yale University, New Haven, Connecticut, USA.

    • Hemant D Tagare

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Contributions

A.K. and H.D.T. conceived of the theory. A.K. developed the algorithm and performed experiments. A.K., F.J.S. and H.D.T. designed the experiments and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hemant D Tagare.

Supplementary information

PDF files

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    Supplementary Text and Figures

    Supplementary Figures 1–5 and Supplementary Notes 1–4

Zip files

  1. 1.

    Supplementary Software

    The Python source code of our software package ResMap. You may find the latest Mac, Linux, and Windows binaries and the user manual at http://resmap.sourceforge.net

Videos

  1. 1.

    A close-up visualization of ResMap-H2 results under varying surface

    A close-up visualization of the sub-tomogram reconstruction of GroEL (EMD-2221). The surface is colored using ResMap-H2 results and its threshold is being varied between values 1 and 1.8 (arbitrary units). A docked atomic model is visible through the surface for ease of interpretation. ResMap results point to parts of the alpha helix being resolved to different levels, which is visually corroborated as the surface threshold is varied.

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DOI

https://doi.org/10.1038/nmeth.2727

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