Hi everyone,
I am working with a dimeric structure that has C2 symmetry. I am specifically interested in a short alpha hairpin on the surface of the structure which interacts with a small peptide.
Using global refinement, I was able to resolve my structure to 3.4 A, however the alpha helix of interest is not well resolved. I have performed symmetry expansion → local refinement → 3D classification with a mask around the monomer. I find that about 50% of the particles after 3D class have good density around this region, when I perform local refinement (with C1) on this subset of particles, I can better resolve the density of my helix and the bound peptide.
Is it possible to somehow generate a composite map of my full C2 dimer by applying symmetry to this volume and summing the volumes? or is this something that is frowned upon as I assume this would be considered a symmetry-breaking feature?