The ManifoldEM method for conformational heterogeneity analysis in single-particle cryo-EM was first presented nearly a decade ago; however, its accessibility to a wide audience has been limited. Here, we describe a step-by-step breakdown accompanied by a modern Python implementation with increased usability, enhanced performance and improved accessibility to future feature additions.

Roodmus is a toolkit sourcing conformational heterogeneity of biomacromolecules from molecular dynamics simulations to generate high-quality synthetic data for the development and benchmarking of heterogeneous reconstruction algorithms.