Job: Homogeneous Reconstruction Only


Create a 3D reconstruction from input particles that already have alignments in 3D. Two reconstructions are created based on the split of particles into half-maps either from the input, or by resplitting (as an option). The half-maps are reconstructed the same way as they would be in a refinement job, but no alignment iterations are performed.

The input mask (which is required) is used for computing FSC between the reconstructed half-maps.

The output of this job can be used with the FSC Validation job, or with the sharpening job, or any other that requires volumes and half-maps.


  • Particles (with alignments3D)

  • Mask

Common Parameters

  • Symmetry Parameters:

    • Note: if particles were previously symmetry expanded, all symmetry parameters should be left to their default values. As well, for reconstruction with helical symmetry, particles must be from a source Helical Refinement job to ensure they are properly aligned with the helical symmetry axis

    • Symmetry: Point group symmetry string (e.g. C6, D7, I, O, T).

    • 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".

  • Flip the reconstruction hand: Whether or not to flip the particles' alignments along the z-axis to flip the hand of the reconstruction. Note that this is done before applying symmetry, so if the hand is being flipped and helical symmetry is beling applied, the sign of the helical twist should be inverted.

  • Ignore tilt/trefoil/tetra: Whether or not higher order CTF aberrations should be ignored during reconstruction (if they are already fit).

  • Optimize FSC mask: Whether or not the FSC mask tightness should be optimized to find the best mask; this is similar to the FSC mask optimization done in the final iteration of a refinement job.


  • Reconstructed half-maps

  • Particles

  • Gold-standard FSC curve

Common Next Steps

  • Download and inspect map