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

Pavel Afonine pafonine at lbl.gov
Wed Apr 20 07:28:16 PDT 2016


it's good to know it was useful for you, thanks for feedback! I afraid 
it's too new so that we don't have a publication to cite yet. We are 
working on a manuscript but it may take a little while before it appears 
somewhere. For now I guess you can use this link (unless Dorothee has a 
better idea)


and use official Phenix citation:

Acta Cryst. D66, 213-221 (2010).

That's all we have at the moment anyway.

All the best,

On 4/20/16 04:18, Lund Bjarte Aarmo wrote:
> DearDorothee 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.
> Usage:
> 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:
> www.phenix-online.org/version_docs/dev-2356/reference/polder.html
> Best wishes,
> Dorothee
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