CryoSPARC Guide
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Job: Ab-Initio Reconstruction

Ab-Initio reconstruction.

Description

  • Reconstruct a single (homogeneous) or multiple (heterogeneous) 3D maps from a set of particles, without any initial models or starting structures required.

Input

  • Particles
  • Initial model (optional)

Common Parameters

  • Number of classes: The default number of classes is 1. Increase this value if you expect to find multiple conformations/states in your data, or if you are trying ab-initio reconstruction to identify junk particles.
  • Number particles to use: The number of particles to use in optimization. Only this many particles are read and classified, selected randomly from the particle stack. Unused particles are added to the particles_unused output group.

Output

  • 3D map(s)
  • Plots, including orientation distributions
  • Classified particles

Notes

  • Use ab-initio reconstruction to reconstruct one or more 3D maps from a set of particles, without any initial model required. You can also use this job to identify junk particles from the raw particle stack or following 2D classification.
  • When performing an ab-initio reconstruction on a symmetric structure, enforcing symmetry is not recommended.
  • For large particle sets run with only one 3D class in ab-initio reconstruction, not every particle may be classified and used for reconstruction. Unused particles are added to the particles_unused output group.
  • For more information on ab-initio reconstruction, please see Nature Methods.

Limitations

Ab-initio reconstruction can fail when data quality is poor or when viewing directions are missing or strongly biased. For strongly biased viewing directions, subsequent rounds of 2D classification and rebalancing of 2D classes may help equalize views. Highly symmetric structures can also pose challenges. It is not recommended to enforce symmetry during ab-initio reconstruction but can be helpful when symmetry is known in advance.

Common Next Steps

  • Homogeneous or Heterogeneous Refinement