CryoSPARC scripts for oligomer classification and extraction of (pseudo)symmetric biomacromolecules

Ligand-gated ion channels with multiple ligand binding sites, such as
nicotinic acetylcholine receptors, could be important therapeutic targets
for various diseases. Single-particle cryo-EM has proved to be a powerful
approach to help understand the molecular mechanics of these channels in
recent years; however, the (pseudo-)symmetric feature of the channels
largely troubles precise determination of channel structures in some
situations, especially when partial breaking down of the symmetry occurs
(caused by insufficient ligand binding, asymmetric conformational change,
etc). Local variability analysis combined with symmetry expansion may
provide valuable insights into a single monomer of the channel, but up to
now, there lacks an easy-accessible method to restore the featured
monomers to the whole oligomeric channels. Here, I provide a simple pack
of Python3 scripts, based on outputs of CryoSPARC single-particle
cryoEM workflows, to classify, align, and extract the oligomer particles
with different monomer features. The re-extracted particle stacks could be
imported back into CryoSPARC manually, in which further refinement jobs
would be available for providing detailed structures of the channel.