Hello,
When running a helical refinement with real-space symmetrization enforced, what are the differences between the volume.map_sharp and the volume.map_sym_sharp outputs?
Thank you,
Sarah
Hi @SarahN,
Apologies for the delayed reply. The map_sharp output is the sharpened reconstruction after applying helical symmetry in Fourier space. Applying helical symmetry in Fourier space results in the protein density being strongest near the central z slice, and decaying out toward the top and bottom of the box. This is because of the wrap-around effect when applying phase shifts in fourier space. The map_sym_sharp output is the same map, but with symmetry applied again in real space – this is done to ensure that the protein density in the box is constant over the central column (which could possibly be helpful when it comes to atomic modelling – but that’s just my speculation). In either case, the raw half maps could be used for further density modification procedures, including sharpening with different b-factors, applying real space symmetry, etc., to use downstream for atomic modelling.
Hope this helps,
Michael
1 Like