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.
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
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.