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Limitations of the iterative electron density reconstruction algorithm from solution scattering data

Nature Methods volume 18, pages 244–245 (2021)Cite this article

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Matters Arising to this article was published on 01 March 2021

The Original Article was published on 29 January 2018

arising from T. D. Grant Nature Methods https://doi.org/10.1038/nmeth.4581 (2018)

Small-angle X-ray scattering (SAXS) is widely utilized to study biological macromolecules in solution, and methods are established to recover ab initio low-resolution shapes from the scattering data. In a recent publication by Grant1, an iterative algorithm named DENSS (DENsity from Solution Scattering) is described, which it is claimed reconstructs ab initio inhomogeneous electron density maps from SAXS data. We are concerned that this approach is not capable of reconstructing internal structure and that it yields models that do not fit the experimental data. We therefore urge users to be cautious when interpreting DENSS results.

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Fig. 1: DENSS reconstructions from theoretical scattering data computed up to a nominal resolution of 12 Å.

Data availability

All models, computed scattering curves and reconstructions presented in this manuscript are available in Supplementary Data 1.

Code availability

The program DENSS is available open source at https://github.com/tdgrant1/denss. EMAN2 software is available at https://hpc.nih.gov/apps/EMAN2.html. The programs DAMMIN, MONSA, CRYSOL and SUPALM are included in the ATSAS software, which is freely available to academic users at https://www.embl-hamburg.de/biosaxs/software.html.

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Acknowledgements

P.V.K. acknowledges support from the Ministry of Science and Higher Education of the Russian Federation within the State assignment FSRC ‘Crystallography and Photonics’ of the Russian Academy of Sciences. D.I.S. acknowledges support from the German Federal Ministry of Education and Research (grant SAS-BSOFT (16QK10A)).

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Authors and Affiliations

  1. A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’, Russian Academy of Sciences, Moscow, Russia

    Petr V. Konarev

  2. European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany

    Dmitri I. Svergun

Authors
  1. Petr V. Konarev
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  2. Dmitri I. Svergun
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Contributions

D.I.S. drafted the manuscript with primary editing and revision support from P.V.K. P.V.K. carried out calculations from the SAXS data and built the models. D.I.S. and P.V.K. read and approved the final manuscript.

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Correspondence to Dmitri I. Svergun.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–3.

Reporting Summary

Supplementary Data 1

Models, scattering curves and reconstructions.

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Konarev, P.V., Svergun, D.I. Limitations of the iterative electron density reconstruction algorithm from solution scattering data. Nat Methods 18, 244–245 (2021). https://doi.org/10.1038/s41592-021-01082-x

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