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

Pavel Afonine 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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