New tools for automated high-resolution cryo-EM structure determination in RELION-3

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Cryo-electron microscopy (cryo-EM) is a powerful technique for determining 3D structures of biomolecules.
• Software for image processing and 3D reconstruction is crucial for achieving high-resolution results in cryo-EM.
• Previous versions of RELION have been widely adopted for cryo-EM data processing.

Purpose of the Study:

• To introduce the third major release of RELION (REgularised LIkelihood OptimisatioN).
• To detail new features enhancing computational efficiency and data processing capabilities.
• To demonstrate resolution improvements achieved with the updated software.

Main Methods:

• Implementation of CPU-based vector acceleration alongside existing GPU support.
• Development of reference-free autopicking using Laplacian-of-Gaussian filtering.
• Integration of Python scripting for non-interactive processing and job execution.
• Introduction of per-particle CTF parameter refinement and beam tilt correction.
• Application of Ewald sphere curvature correction for large particles.
• Utilisation of a Bayesian approach for beam-induced motion correction.

Main Results:

• Enhanced computational flexibility and resource utilization through combined CPU and GPU acceleration.
• Streamlined, non-interactive data processing pipelines, including 2D classification, *de novo* model generation, and 3D classification.
• Improved resolution in 3D reconstructions by correcting for variations in CTF parameters and beam tilt.
• Further resolution gains for large particles via Ewald sphere curvature correction.
• Achieved resolution improvements of 0.2-0.7 Å compared to previous RELION versions on publicly available datasets.

Conclusions:

• The latest RELION release offers significant advancements in cryo-EM data processing efficiency and resolution.
• New features provide greater flexibility in hardware utilization and enable automated, high-throughput analysis.
• The demonstrated resolution enhancements underscore the software's utility for cutting-edge structural biology research.