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

New software tools in EMAN2 inspired by EMDatabank map challenge.

Author information

1
Graduate Program in Quantitative and Computational Biology, Baylor College of Medicine, United States.
2
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, United States.
3
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, United States. Electronic address: sludtke@bcm.edu.

Abstract

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

PMID:
30189321
PMCID:
PMC6163079
[Available on 2019-11-01]
DOI:
10.1016/j.jsb.2018.09.002

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