Notes for running cryoSPARC

2D classification to clean up junk

  1. Import RELION extracted stack into cryoSPARC
  2. Perform 2D classification with 150-200 classes with these options added:
    • Preprocessing (advanced option): Window inner radius - use fraction of window that only includes particle
    • Preprocessing (advanced option): Window normalize - False
    • 2D classification: Number of 2D classes - 150-200
    • 2D classification (advanced option): Use clamp-solvent to solve 2D classes - True
    • 2D classification (advanced option): Use white noise model - False

3D initial model & sorting

  1. Run Ab Initio with a single model
  2. Select Ab Initio model x2 or x3 with particles to run heterogenous refinement
  3. Select model and class to run homogenous refinement