Hi, I am fairly new at cryoEM reconstructions (and structural biology). I have obtained a map of my protein at 5.9A FSC and I see several distinct secondary structural (alpha helical) features. When I try to fit the structure (pdb) of a known homolog to map on chimera, the fit is terrible but when I zflip the obtained map, the structure of the known homolog fits well into the zflipped map. Is this sufficient evidence to suggest that the original map that I obtained is opposite in handedness?
Yes, if the overall fold or quaternary arrangement is itself chiral, then handedness can be determined at lower resolutions.
Is there a need to redo refinement job right away with the map with correct handedness or is it okay to wait until later and zflip only the map that I finally obtain as the final result?
It’s annoying to constantly have to flip your new maps, so I would flip it at some point. Datasets sometimes prefer one hand over the other, though, so it might revert to the wrong hand again.