[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure
Nathaniel Echols
nechols at lbl.gov
Sun Sep 14 09:10:03 PDT 2014
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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