Dear Edwin,

The alternative is probably to define the second orientation as an alternative conformation. Aside from aesthetic objections, I don't want to lose the ability to restrain NCS - I need two orientations to be identical structures, and I am not sure yet whether I can use NCS groups defined via alternative conformers.

I think this would be the easiest way forward and it looks like a very natural use of alternative conformations. You can definitely define NCS groups and even automatic search works. I'm attaching a small dummy example I experimented on. Two overlapping helices: chain A with altloc A and occupancy 0.5, chain B with altloc B and occupancy 0.5. Nothing prevents you from defining NCS groups using "altloc A" and it should work, but I imagine there should always be equivalent selection in terms of "chain A".

Best regards,

Oleg Sobolev.