C2 symmetry with symmetry breaking features

I had a similar problem for three of my reconstructions in this manuscript.
https://www.nature.com/articles/s41586-021-03680-3

Symmetry relaxation in Relion was useful to get better results for pseudo symmetry for one of the reconstruction and symmetry expansion + 3d classification without alignment for another. However, your reconstructions should be in correct symmetry axis otherwise it wont work. Basically when you open the map on chimera you should be looking through the sym axis. We requested cryosparc to implement symmetry relaxation, it may be helpful to endorse it so cryosparc scientist may prioritize it.

Good luck.

Alpay

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