Single-Particle Refinement and Variability Analysis in EMAN2.1

Methods Enzymol. 2016;579:159-89. doi: 10.1016/bs.mie.2016.05.001. Epub 2016 Jul 1.


CryoEM single-particle reconstruction has been growing rapidly over the last 3 years largely due to the development of direct electron detectors, which have provided data with dramatic improvements in image quality. It is now possible in many cases to produce near-atomic resolution structures, and yet 2/3 of published structures remain at substantially lower resolutions. One important cause for this is compositional and conformational heterogeneity, which is both a resolution-limiting factor and presenting a unique opportunity to better relate structure to function. This manuscript discusses the canonical methods for high-resolution refinement in EMAN2.12, and then considers the wide range of available methods within this package for resolving structural variability, targeting both improved resolution and additional knowledge about particle dynamics.

Keywords: 3-D reconstruction; CryoEM; EMAN; Heterogeneity; Image processing; Motion; Single-particle analysis; Structural biology; Structural variability.

Publication types

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

MeSH terms

  • Algorithms*
  • Analysis of Variance
  • Artifacts
  • Bacterial Proteins / ultrastructure
  • Chaperonin 60 / ultrastructure
  • Cryoelectron Microscopy / methods*
  • Image Processing, Computer-Assisted / methods*
  • Image Processing, Computer-Assisted / statistics & numerical data
  • Imaging, Three-Dimensional / instrumentation
  • Imaging, Three-Dimensional / methods
  • Motion
  • Ribosomes / ultrastructure
  • Software*


  • Bacterial Proteins
  • Chaperonin 60