New software tools in EMAN2 inspired by EMDatabank map challenge

J Struct Biol. 2018 Nov;204(2):283-290. doi: 10.1016/j.jsb.2018.09.002. Epub 2018 Sep 4.


EMAN2 is an extensible software suite with complete workflows for performing high-resolution single particle analysis, 2-D and 3-D heterogeneity analysis, and subtomogram averaging, among other tasks. Participation in the recent CryoEM Map Challenge sponsored by the EMDatabank led to a number of significant improvements to the single particle analysis process in EMAN2. A new convolutional neural network particle picker was developed, which dramatically improves particle picking accuracy for difficult data sets. A new particle quality metric capable of accurately identifying "bad" particles with a high degree of accuracy, no human input, and a negligible amount of additional computation, has been introduced, and this now serves as a replacement for earlier human-biased methods. The way 3-D single particle reconstructions are filtered has been altered to be more comparable to the filter applied in several other popular software packages, dramatically improving the appearance of sidechains in high-resolution structures. Finally, an option has been added to perform local resolution-based iterative filtration, resulting in local resolution improvements in many maps.

Keywords: 3-D reconstruction; CryoEM; EMDatabank map challenge; Image processing; Single particle analysis; Structural biology.

Publication types

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

MeSH terms

  • Algorithms
  • Cryoelectron Microscopy / methods*
  • Neural Networks, Computer
  • Software*