This protocol wraps e2refine2d_bispec.py EMAN2 program.
This program is used to produce reference-free class averages from a population of mixed, unaligned particle images. These averages can be used to generate initial models or assess the structural variability of the data. They are not normally themselves used as part of the single particle reconstruction refinement process, which uses the raw particles in a reference-based classification approach. However, with a good structure, projections of the final 3-D model should be consistent with the results of this reference-free analysis.
This variant of the program uses rotational/translational invariants derived from the bispectrum of each particle.
Run the EMAN program to refine 2d.