[phenixbb] exclude clashes for non-symmetry contacts

[Oleg Sobolev]

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.
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