Measurement of atom resolvability in cryo-EM maps with Q-scores

Nat Methods. 2020 Mar;17(3):328-334. doi: 10.1038/s41592-020-0731-1. Epub 2020 Feb 10.


Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Animals
  • Apoferritins / chemistry*
  • Cryoelectron Microscopy*
  • Fourier Analysis
  • Humans
  • Hydrogen Bonding
  • Ligands
  • Macromolecular Substances / chemistry
  • Mice
  • Microscopy, Electron
  • Models, Molecular
  • Normal Distribution
  • Protein Structure, Secondary
  • RNA / chemistry
  • Solvents / chemistry


  • Ligands
  • Macromolecular Substances
  • Solvents
  • RNA
  • Apoferritins