Single particle tutorial

• Introduction
• Preprocessing
  • Getting organised
  • Beam-induced motion correction
  • CTF estimation
  • Manual particle picking
• Particle picking
  • Select a subset of the micrographs
  • LoG-based auto-picking
  • Particle extraction
  • 2D class averaging to select good particles
  • Selecting good 2D classes for Topaz training
  • Re-training the TOPAZ neural network
  • Pick all micrographs with the re-trained TOPAZ neural network
  • Particle extraction
• Reference-free 2D class averaging
  • Running the job
  • Selecting good particles for further processing
  • Analysing the Class2D results in more detail
  • Making groups
• De novo 3D model generation
  • Running the job
  • Analysing the results
• Unsupervised 3D classification
  • Running the job
  • Selecting good particles for further processing
  • Analysing the results in more detail
• High-resolution 3D refinement
  • Running the auto-refine job
  • Analysing the results
• Mask creation & Postprocessing
  • Making a mask
  • Post-processing
• CTF and aberration refinement
  • Higher-order aberrations
  • Anisotropic magnification
  • Per-particle defocus values
• Bayesian polishing
  • Running in training mode
  • Running in polishing mode
  • Re-running refinement and post-processing
  • When and how to run CTF refinement and Bayesian polishing
• Local-resolution estimation
  • Running the job
  • Analysing the results
• Checking the handedness
• Wrapping up
  • Making a flowchart
  • Cleaning up your directories
  • Asking questions and citing us
  • Further reading