Job: Symmetry Expansion

Description

Symmetry expansion enables the creation of a new particle dataset that duplicates the original particles' poses around a point group symmetry. The primary use of symmetry expansion is in generating a new particle stack to be used by a Local Refinement or a 3D Variability job, with the goal of resolving symmetry-breaking features. The original particle dataset must have been aligned previously to a reference, meaning one of the global refinement jobs (e.g., Homogeneous or Non-uniform Refinement) must have previously been run with the input particle stack. The new particle dataset refers back to the image data of the original particle dataset, meaning no new images are written to disk by this job.
Note that reconstructions and refinements with global pose searches (e.g., Ab-Initio Reconstruction, and Homogeneous, Heterogeneous, Non-uniform, and Helical refinements) should not be run with the output dataset, as it will cause particle duplication and hence mis-estimation of Fourier Shell Correlation curves. Only Local Refinement and 3D Variability Jobs should be used after a symmetry expansion.

Input

  • Particles (alignments3D are required).

Parameters

  • Symmetry group
    • The desired point group symmetry string (e.g., D7, C4, T, O, I).
  • Helical symmetry parameters:
    • Helical twist (degrees): The helical twist in degrees, if helical symmetry is present in the particle stack.
    • Helical rise (Angstroms): The helical rise in Angstroms, if helical symmetry is present in the particle stack.
    • Helical symmetry order (integer): The helical symmetry order. This can be found at the end of the streamlog from the source Helical Refinement job, underneath "Final Helical Parameters".
    • Note: for symmetry expansion with helical symmetry, particles must be from a source Helical Refinement job to ensure they are properly aligned with the helical symmetry axis.
    • Before running symmetry expansion with helical symmetry, it is strongly recommended to run the source Helical Refinement with the "Limit shifts along the helical axis" parameter activated. This ensures that the particles are aligned such that the shifts along the helical axis are minimized.

Output

  • Particles (expanded stack)
    • The size of the output particle stack will be equal to the size of the input particle stack, multiplied by the symmetry order. For example, for a particle stack of size 10,000 symmetry expanded with D7 symmetry, the output particle stack will have size 140,000.

Common Next Steps

After symmetry expansion, the next steps usually involve running a 3D Variability Analysis job, or a Local Refinement job. Both can help resolve symmetry-breaking features, such as inter-subunit flexibility. For more information on 3D Variability Analysis, including this use case of the symmetry expansion job, refer to the 3D Variability Analysis tutorial (both part 1 and part 2). For more information about Local Refinements, refer to the guide page for a detailed job description and case study. Homogeneous Reconstruction jobs (with specified symmetry of C1) can also be run with the symmetry expanded particle stack, to ensure that the symmetry expansion was successful.