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Hi Pavel,
this is an interesting concept. It seems related to the SQUEEZE command in
platon - even the name appears to suggest a relationship. I did not understand
the maths entirely: Are they similar concept, or do I misinterprete?
Best,
Tim
On Wednesday, April 20, 2016 07:28:16 AM Pavel Afonine wrote:
> 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:*phenixbb-bounces@phenix-online.org
> > [mailto:phenixbb-bounces@phenix-online.org] *On Behalf Of *Dorothee
> > Liebschner
> > *Sent:* 22. mars 2016 21:46
> > *To:* PHENIX user mailing list <phenixbb@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
> >
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb@phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: phenixbb-leave@phenix-online.org
- --
Paul Scherrer Institut
Tim Gruene
- - persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
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