[phenixbb] exclude clashes for non-symmetry contacts

Edwin Pozharski pozharskibb at gmail.com
Thu Nov 1 11:15:15 PDT 2018

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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20181101/b3ecb677/attachment.htm>

More information about the phenixbb mailing list