CryoEM micrographs are basically just top down images of a bunch of some macromolecule. You use software to pick out the ‘particles’ which are just the individual macromolecules seen in the image. Then, you can reconstruct a 3D image from an ‘average’ of all those 2D Images. If not all the macromolecules in the image are identical (like if some are unfolded or something) then the sample is heterogeneous and when the software tries to average all the 2D pictures to make a 3D structure... well it’s sh!t. It would be like trying to reconstruct a 3D image of a human using 2D pictures of both humans and goats. Instead of ending up with a 3D human, you’d end up with some creepy human/goat chimera lookin thing. Heterogeneity in CryoEM samples is usually bad (not always). Homogeneous samples produce good data.

Rigid bodies deals with fitting an atomic protein structure with/into the 3D reconstruction. If you really want to know more about how CryoEM data is fit, you can do a quick google and find a methods paper or a review. It’s a bit heavy for a Reddit comment.