Q: What paper should I cite if I use EMAN2 for a reconstruction ?

A: This is the original EMAN2 reference:

• Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I. & Ludtke, S.J., 2007, EMAN2: an extensible image processing suite for electron microscopy, Journal of structural biology, 157(1), pp. 38-46.

For specific methods/concepts:

• Fluty AC, Ludtke SJ. Precision requirements and data compression in CryoEM/CryoET. J Struct Biol. 2022; 214(3) 107875. PMID: 35724904. PMC9645247.

• Chen M, Ludtke SJ. Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM. Nat Methods. 2021; 18(8) 930-936. PMID: 34326541. PMC8363932.

• Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. A complete data processing workflow for cryo-ET and subtomogram averaging. Nat Methods. 2019; 16(11) 1161-1168. PMID: 31611690. PMC6858567.

• Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. New software tools in EMAN2 inspired by EMDatabank map challenge. J Struct Biol. 2018; 204(2) 283-290. PMID: 30189321. PMC6163079.

• Chen M, Dai W, Sun SY et al. Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat Methods. 2017; 14(10) 983-985. PMID: 28846087. PMC5623144.

• Ludtke SJ. Single-Particle Refinement and Variability Analysis in EMAN2.1. Methods Enzymol. 2016; 579 159-189. PMID: 27572727. PMC5101015.