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

Hello, 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) http://www.phenix-online.org/presentations/phenix_polder.pdf and use official Phenix citation: Acta Cryst. D66, 213-221 (2010). That's all we have at the moment anyway. All the best, Pavel 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:*[email protected] [mailto:[email protected]] *On Behalf Of *Dorothee Liebschner *Sent:* 22. mars 2016 21:46 *To:* PHENIX user mailing list *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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