On 9/13/14 5:57 PM, Nathaniel Echols wrote:
On Sat, Sep 13, 2014 at 3:03 PM, Pavel Afonine <[email protected]> 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.

Pavel