Q: What paper should I cite if I use EMAN2 for a reconstruction ?
A: While we plan to publish something a bit more up to date documenting newer procedures in EMAN2, for now this the main reference to cite:
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.
The most impressive structure published to date with EMAN2 alone (in case you want to document it's reliability) is this one:
Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW (2011) Structure of the Drosophila apoptosome at 6.9 å resolution. Structure 19: 128-140