Job: Homogeneous Reconstruction Only

Homogeneous reconstruction only (no alignment).


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).

    • Break Symmetry: Break Symmetry can be used to generate an asymmetric reference from particles that were previously refined with symmetry enforced. If activated, will randomize each particles' pose to one of its symmetry-related orientations. Note this assumes particles have previously been aligned to a symmetric reference. Must specify either the symmetry group, or the helical symmetry parameters (including helical symmetry order). Refer to the for an example of using this feature.

    • 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 being 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.

  • Ewald Sphere Correction:

    • Do EWS correction: This can be activated to reconstruct the volume using Ewald Sphere correction.

    • EWS curvature sign: Reconstruction with Ewald Sphere correction enabled requires knowledge of the curvature sign, which can either be negative or positive. Currently, this must be determined by running the job with both curvature signs and comparing the resolutions. For more information, refer to the Ewald Sphere correction tutorial for a detailed walkthrough.


  • Reconstructed half-maps

  • Particles

  • Gold-standard FSC curve

Common Next Steps

  • Download and inspect map

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