Hello,

A question for Tristan, since I know you read this list. :-)

I have a cryoEM map that was produced with C7 symmetry enforced. I can fit the alphafold prediction of one protomer, and am pretty confident in this initial rigid fit because the map is good. Now with Tom's help I know how to generate the C7 symmetric assembly and store the symmetry info in a cif file with a single protomer, so I can regenerate the heptamer as needed (and this seems like the correct way to deposit the end result). But this model still needs proper refinement: the rigid fit shows that the conformation predicted by alphafold deviates from the map at several locations.

What is a sensible refinement strategy for something like this?

Because symmetry was enforced for the map, I am inclined to refine only a single protomer and add the correct symmetry info that will regenerate the heptamer. But don't I need the neighboring protomers during refinement, for the interface residues to behave correctly during MDFF? I would think so.

Not sure what to do, some advice would be very helpful.

Thank you in advance,