[phenixbb] exclude clashes for non-symmetry contacts

[Edwin Pozharski]

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.
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