Hi Wei,

Yes, I think it's true that "if ligand density is strong enough it may not be masked by the bulk-solvent completely".

indeed. You can verify it yourself by taking a few examples of protein-ligand complexes with ligand occupancy (or mobility or both) varying in some range.

Hi Nat, you mentioned that

1. "I thought phenix.refine ignores zero-occupancy atoms when calculating the bulk solvent mask?  In fact there is an option specifically to toggle this option, and I've noticed very different results with and without it."

Yes, results are expected to be very different for reasons I explained in previous email.

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.

Pavel

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