After homogenous refine I end up with a nice map at 4A which shows the wrong handedness. I flip the handedness, and use that as input for a NU refine job. The output from the NU refine job now has it’s handedness flipped back to what it was after the homogenous refine job. In other words, NU refine seems to have flipped the volume handedness.
What resolution did you start NU at? If you start at very low res, and your molecule doesn’t have distinct asymmetric features at low res, then this can happen
yes, of course! thanks Oli.
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@orangeboomerang, are you refining into the volume that is in the correct hand ? Volume tools to flip the hand, only does the volume. If you do homogeneous reconstruction with flip hand enabled, all of the meta data, volume, and particles should be correct. I often run both just to compare, especially for medium resolution data.