[phenixbb] Occupancy Refinement of substrate and product occupying the same coordinates.

[Ralf W. Grosse-Kunstleve]

Hi Joe,

> the .cif file created by "phenix.elbow modified.pdb" were all
> accepted by phenix.refine, however the two molecules were still driven
> away from each other =(

The main way of controlling nonbonded interactions (the only forces
that will drive molecules away from each other) is the "altloc" identifier
in column 17. The rules are:

  blank pushes blank
  X pushes blank
  Y pushes blank
  X has no nonbonded interactions with Y

These rules are independent of the covalent connectivity.
Could you double-check your altloc assignments?
I'll be happy to look at your files.

Ralf