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.