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Quantifying the local resolution of cryo-EM density maps


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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Figure 1: Local resolution.
Figure 2: ResMap-H2 results using experimental density maps.

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  1. Liao, H.Y. & Frank, J. Structure 18, 768–775 (2010).

    Article  CAS  Google Scholar 

  2. Leschziner, A.E. & Nogales, E. Annu. Rev. Biophys. 36, 43–62 (2007).

    Article  CAS  Google Scholar 

  3. Scheres, S.H. & Chen, S. Nat. Methods 9, 853–854 (2012).

    Article  CAS  Google Scholar 

  4. Unser, M. et al. J. Struct. Biol. 149, 243–255 (2005).

    Article  CAS  Google Scholar 

  5. Sousa, D. & Grigorieff, N. J. Struct. Biol. 157, 201–210 (2007).

    Article  CAS  Google Scholar 

  6. Lander, G.C. et al. Nature 482, 186–191 (2012).

    Article  CAS  Google Scholar 

  7. Hashem, Y. et al. Nature 494, 385–389 (2013).

    Article  CAS  Google Scholar 

  8. Heymann, J.B. & Belnap, D.M. J. Struct. Biol. 157, 3–18 (2007).

    Article  CAS  Google Scholar 

  9. Freeman, W.T. & Adelson, E.H. IEEE Trans. Pattern Anal. Mach. Intell. 13, 891–906 (1991).

    Article  Google Scholar 

  10. Derpanis, K.G. & Gryn, J.M. IEEE Int. Conf. Image Processing 3, 553–556 (2005).

    Google Scholar 

  11. Lehmann, E.L. & Romano, J.P. Testing Statistical Hypotheses 3rd edn. (Springer, New York, 2005).

  12. Benjamini, Y. & Yekutieli, D. Ann. Stat. 29, 1165–1188 (2001).

    Article  Google Scholar 

  13. Bai, X., Fernandez, I.S., McMullan, G. & Scheres, S.H. eLife 2, e00461 (2013).

    Article  Google Scholar 

  14. Yu, G. et al. PLoS ONE 8, e59817 (2013).

    Article  CAS  Google Scholar 

  15. Bartesaghi, A., Lecumberry, F., Sapiro, G. & Subramaniam, S. Structure 20, 2003–2013 (2012).

    Article  CAS  Google Scholar 

  16. Davies, K.M., Anselmi, C., Wittig, I., Faraldo-Gómez, J.D. & Kühlbrandt, W. Proc. Natl. Acad. Sci. USA 109, 13602–13607 (2012).

    Article  CAS  Google Scholar 

  17. Pettersen, E.F. et al. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  Google Scholar 

  18. Loader, C. Local Regression and Likelihood (Springer, New York, 1999).

  19. Farebrother, R.W. J. R. Stat. Soc. Ser. C Appl. Stat. 33, 332–339 (1984).

    Google Scholar 

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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.).

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Authors and Affiliations



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.

Corresponding author

Correspondence to Hemant D Tagare.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Notes 1–4 (PDF 4308 kb)

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 (ZIP 42 kb)

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. (MOV 11493 kb)

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Kucukelbir, A., Sigworth, F. & Tagare, H. Quantifying the local resolution of cryo-EM density maps. Nat Methods 11, 63–65 (2014).

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