On Sat, Sep 13, 2014 at 8:21 PM, Pavel Afonine <pafonine@lbl.gov> wrote:
2. "Restraining the zero-occupancy ligand (and perhaps adjacent residues) is strongly recommended, especially if it contains heavier elements.  (The newer versions of the phenix.refine GUI have a button in the Output tab to set this up.)  Without restraints, you run the risk of refining the surrounding model into the ligand density.  As always this is worse at lower resolution - at 2.8Å I'm not sure what to expect."

I am wondering how this could be done.

 I am not sure why you may want to do this at all. If you keep the ligand in PDB file and "omit" it by setting occupancies to zero then the omit map you will get is useless if you ask the program to not fill bulk solvent into ligand region. If you let the program to fill bulk-solvent into ligand region (= ask mask calculation to ignore zero occupancy atoms) then why don't you just remove the ligand from PDB file (then you don't need to worry about restraining it etc.)? In fact you can even keep it in file as you don't care (for map calculation purpose) where restraints will move it.

I think you're confusing what I wrote with the bulk solvent issue.  It is also sometimes necessary to prevent actual atoms from being refined into the omit region - this is the purpose of adding harmonic restraints on the omitted atoms.  (As far as I know this was first suggested in Hodel et al. 1992, although they don't go into a great deal of detail.)  It will have no effect on the bulk solvent mask, which will still be extended over the zero-occupancy atoms.  I'm sure there are plenty of cases where the restraints don't make a difference, but I just spent a great deal of time working with a structure where they were essential.

Wei: I've attached a slide showing how to set up the restraints.  But I agree with Pavel that changing the bulk solvent mask settings is dangerous.

-Nat