C2 symmetry with symmetry breaking features

@Bassem people often ask questions like this - “do you think X might work given these caveats?” My answer is almost always that I don’t know, but that trying will only cost you a few hours of GPU time. Just go for it!

Of course, I have lots of opinions about what parameters to use, like in the post above.

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To add: in relion 4 under optimization you can select to run the initial model in C1 and then ask relion to align to C2 so that the upcoming step is more straight forward in symmetry relaxation. Earlier version of relion you will need to use command line relion commands to set the structure to C2 symmetry.

I gave the masking a go on cryosparc but it did not help. Here is the plan, I will mask both mickey mouse ears of my structure and try that combined with the symmetry relaxation in relion.

Cool, let us know how it goes! The structures need to be aligned with the (pseudo) C2 axis as the Z axis of the box - like the output of a C2 imposed refinement.