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 partic..., , # CryoSPARC scripts for oligomer classification and extraction of (pseudo)symmetric biomacromolecules

Dataset DOI: [10.5061/dryad.8kprr4z12](10.5061/dryad.8kprr4z12)

## Description of the data and file structure

### Files and variables

#### File: sym_class_build230719.zip

**Description:** This is a Python3 script pack designed to integrate monomer classification results generated from [CryoSPARC](https://cryosparc.com/) symmetry expansion and 3D classification jobs into (pseudo)symmetric protein oligomer classes, as well as re-extract selected classes of aligned oligomers for further refinement and reconstruction in CryoSPARC. Primarily validated and tested on pentameric ligand-gated ion channel (pLGIC) datasets. Proteins with other symmetry types (C3, C4, etc.) should also be supported.

To run the integration job, both symmetry-expanded particle files (the split output option MUST be checked in CryoSPARC) and monomer-classified particle files should be prepared. Annotations for n...,