Hi all,
Just confirming that dihedral symmetry in cryoSPARC uses y as the dyad axis, rather than x as done in the Heymann reference and in RELION. Thus, as of now, one would need to run symmetry alignment for any Dn structures to re-align any imported volumes from RELION, or use the command from pyem that @thomaspv kindly provided.
For anyone curious, I believe this inconsistency happened sometime in 2018, when we changed the definition of the x and y axes in terms of how we computed actual 3D array indices. In v0 (and perhaps very early versions of v2), y was the “fast” axis of our 3D arrays, whereas x was the second-fastest axis, and z was the slowest index. In v2, we made x the fastest index, y second fastest, and z slowest… but that had the effect of swapping the x and y axes for the previously defined dihedral symmetry operator.
Best,
Michael