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

Dorothee Liebschner dcliebschner at lbl.gov
Wed Apr 20 10:18:39 PDT 2016


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 <bjarte.lund at uit.no>
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:* 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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