A big thanks to the developers for all the new features of Cryosparc 4.4! We are working on a filamentous protein and have got to a 2.5Å map using helical reconstruction. We are now trying to figure out how to do symmetry relaxation in case of helical symmetry. After performing homogeneous reconstruction while breaking the symmetry we tried to (a) run non-uniform refinement with symmetry relaxation (while keeping the GS split from the previous helical reconstruction to prevent particle duplication-related overfitting) but we could not find a way to input the helical symmetry parameter and (b) run helical reconstruction but here we could not find an option for symmetry relaxation. Perhaps I am missing something obvious? Any advice will really help us out.
Doesn’t exist in cryosparc yet I’m afraid
CryoSPARC currently does not implement symmetry relaxation for helical symmetry, as Oli noted. We have recorded this request.
To better understand the utility of symmetry relaxation in helical refinement, would you be willing to share information about the expected pseudosymmetry in your sample? For example, do you expect the presence of a binding partner to the filament?
Dear Oli and Michael
Many thanks for your response. I am new to helical refinement but based on the literature I am aware that it might be relatively easy to end up in a symmetry trap with helical maps. Here is a presentation from a recent Faraday conference describing the situation Escaping the symmetry trap in helical reconstruction - Faraday Discussions (RSC Publishing) DOI:10.1039/D2FD00051B.
Now, we have really good density in the periphery and we have refined with and without imposing helical symmetry and now I am refining the symmetry parameter search as well. So, perhaps this should be enough to figure out in there is a higher order symmetry present.
Another reason why I was hoping to run symmetry relaxation was to better resolve a small loop in our map. It seems to adopt different configurations based on the position of the monomer in the helical filament. I was hoping to run symmetry relaxation followed by classification without alignment with a mask around the loop. But I guess I can do similar things using symmetry expansion.
Thank you very much for the information; this use case makes sense as an addition to symmetry relaxation. Currently, it may be a useful workflow to experiment with Symmetry Expansion over the helical symmetry, followed by 3D Classification and Local Refinement.