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

Hi Bjarte, I am glad that the polder tool was useful for you! As Pavel said, there is no citation yet. I agree that you could use the official Phenix citation and add maybe a reference to the presentation file on the web: Phenix: Acta Cryst. D66, 213-221 (2010) Phenix.polder: http://www.phenix-online.org/presentations/phenix_polder.pdf Best wishes, Dorothee On Wed, Apr 20, 2016 at 4:18 AM, Lund Bjarte Aarmo wrote:

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:* [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