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

Lund Bjarte Aarmo bjarte.lund at uit.no
Wed Apr 20 04:18:05 PDT 2016

Dear Dorothee and phenixbb,

I found this software very useful for protein-fragment complexes with weak electron density. I was wondering how the software should be cited?

Kind regards,

Bjarte Aarmo Lund
PhD candidate
UiT – The arctic university of Norway

From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Dorothee Liebschner
Sent: 22. mars 2016 21:46
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: [phenixbb] phenix.polder - tool for calculating omit maps by excluding bulk solvent

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:  https://www.phenix-online.org/presentations/phenix_polder.pdf.

The documentation page can be found here:


Best wishes,

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