[phenixbb] phenix.polder - tool for calculating omit maps by excluding bulk solvent
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
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
> *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:
> The documentation page can be found here:
> Best wishes,
> phenixbb mailing list
> phenixbb at phenix-online.org
> Unsubscribe: phenixbb-leave at phenix-online.org
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