Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps

Methods Enzymol. 2016;579:255-76. doi: 10.1016/bs.mie.2016.06.003. Epub 2016 Aug 12.


Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.

Keywords: CryoEM map-derived model; Model optimization; Model validation.

Publication types

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

MeSH terms

  • Algorithms*
  • Antigens, Viral / ultrastructure
  • Bacterial Proteins / ultrastructure
  • Bromovirus / ultrastructure
  • Capsid Proteins / ultrastructure
  • Cryoelectron Microscopy / instrumentation
  • Cryoelectron Microscopy / methods*
  • Image Processing, Computer-Assisted / methods
  • Image Processing, Computer-Assisted / statistics & numerical data*
  • Imaging, Three-Dimensional / instrumentation
  • Imaging, Three-Dimensional / methods
  • Models, Molecular
  • Protein Conformation
  • Software*
  • beta-Galactosidase / ultrastructure


  • Antigens, Viral
  • Bacterial Proteins
  • Capsid Proteins
  • VP6 protein, Rotavirus
  • beta-Galactosidase