A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality

Structure. 2019 Feb 5;27(2):344-358.e3. doi: 10.1016/j.str.2018.10.003. Epub 2018 Nov 15.


There does not currently exist a standardized indicator of how well cryo-EM-derived models represent the density from which they were generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected deviation within a suite of models refined against EM maps reported to be at 5 Å resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.

Keywords: atomic modeling; cryo-EM; validation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cryoelectron Microscopy
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Software


  • Proteins