Single‐particle cryo‐EM—Improved ab initio 3D reconstruction with SIMPLE/PRIME

Cryogenic electron microscopy (cryo‐EM) and single‐particle analysis now enables the determination of high‐resolution structures of macromolecular assemblies that have resisted X‐ray crystallography and other approaches. We developed the SIMPLE open‐source image‐processing suite for analysing cryo‐EM images of single‐particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single‐particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over‐the‐counter laptops and CPU workstations is demonstrated.