[phenixbb] phenix.polder - tool for calculating omit maps by excluding bulk solvent

Dorothee Liebschner dcliebschner at lbl.gov
Tue Mar 22 13:46:27 PDT 2016

Dear phenix users,

Starting from the nightly build dev-2356, a new tool for calculating ligand
omit-maps, called 'polder', is included in phenix.


phenix.polder   model.pdb    data.mtz    selection='chain A and resseq 123’

Phenix.polder calculates omit maps for atom selections by preventing the
bulk solvent mask to flood into the atom selection area and its vicinity.
The tool can be useful in cases where the density of the selected atoms is
weak and possibly obscured by bulk solvent.

Polder produces less biased maps compared to procedures where the atom
selection occupancy is set to zero, and the atoms are included in the
solvent mask calculation (in that case, the resulting difference density
can have similar shape than the selected atoms). Phenix.polder excludes a
larger volume from the bulk solvent and therefore prevents misinterpreting
bulk solvent density as omit density.

If you want to know more about how the tool is working and to see some
examples, have a look at the presentation file:

The documentation page can be found here:


Best wishes,

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