Is there some way to make phenix.refine to ignore clashes for specific pair(s) of chains? I am dealing with a rare case of twinning where same protein molecule exists in two orientations in the same unit cell. I tried just to duplicate the molecule and set initial occupancy to 0.5, but refinement fails (as I expected) saying that there are too many close contacts. Ideally, I would like to proceed with ignoring close contacts between, say, chains A/B.

I am aware that one can exclude groups of residues from symmetry clashes, but these two copies are in the same cell. I guess I could try shifting one into the next unit cell and then excluding symmetry clashes, but even assuming that will work it is a rather ugly hack.

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.

Cheers,

Ed.