Align 3D maps - test z-flip? [feature request]


I really like the (I think new?) utility “Align 3D maps”, which allows automatic alignment of multiple maps to a reference map (and calculation of difference maps).

I like it for aligning maps after multi-class ab initio reconstruction, for subsequent heterogeneous refinement. For this purpose, it would be really useful if it had an option to test alignment of both the original and z-flipped maps - this would allow easy combination of classes that differ only in whether they are the correct or inverted hands, and easy alignment/flipping of classes to match a correctly oriented/flipped reference.

Also, being able to easily use the output maps for subsequent jobs (without using the low level results interface) would be handy too. It would also be helpful to be allow users to select which of the input maps is used as a reference (I believe it is the last one by default, but it would be clearer I think if it was given as a different input group).