[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure
pafonine at lbl.gov
Sat Sep 13 18:13:16 PDT 2014
On 9/13/14 5:57 PM, Nathaniel Echols wrote:
> On Sat, Sep 13, 2014 at 3:03 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> wrote:
> In the first case the bulk-solvent mask will be set in the ligand
> region and therefore it will mask ligand density (bulk-solvent
> will be filled into the ligand region). Depending on the strength
> of ligand density it may be masked completely or deteriorated.
> If you follow the second option you will always get positive
> density in ligand area. This density may correspond to
> bulk-solvent, ligand or mixture of both. That is there will be no
> simple way to differentiate whether this density arises from the
> ligand or bulk-solvent.
> 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.
It is bad both ways:
1) If you ignore zero occupancy atoms then you fill bulk-solvent into
ligand region and therefore mask the ligand;
2) If you do not ignore zero occupancy atoms then what you compute is
bulk-solvent-omit map in region around atoms with zero occupancy. This
means that the "green" density you are going to see may be ligand or may
be bulk-solvent or may be the mixture of the two.
In fact, #1 above is better than #2 because if ligand density is strong
enough it may not be masked by the bulk-solvent completely.
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