Question: What paper should I cite if I use EMAN1 in published results ?
Answer: This one: Ludtke, S.J., Baldwin, P.R., and Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128, 82-97.
Question: What about the support for icosahedral viruses?
Answer: EMAN supports icosahedral symmetry similarly to other symmetries. Basically you will follow the same procedures as for particles of other symmetries. Of course, you need to specify sym=icos for the refine command. To build initial model, you can use starticos program. If you still have questions specific to icosahedral viruses, please contact Dr. Wen Jiang <jiang12 at purdue.edu> who made most of the changes in EMAN to support icosahedral symmetry well.