[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure

[Nathaniel Echols]

On Sat, Sep 13, 2014 at 8:21 PM, Pavel Afonine <pafonine at 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
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