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

Wed Apr 20 13:59:34 PDT 2016

Hi Tim,

I quickly looked over the SQUEEZE command in PLATON (are you referring to:
http://scripts.iucr.org/cgi-bin/paper?S2053229614024929 ?). To me, it does
not seem to be related to phenix.polder.

There is no complicated math involved in polder; slides 2-4 are a summary
of the flat bulk-solvent model (which is used in Phenix, and which is also
available in CNS and REFMAC).

The flat bulk-solvent model is described first here:
Phillips, S. E. (1980). *J. Mol. Biol.* *142*, 531–554.
I uses a similar concept than SQUEEZE, i.e. the total structure factor is
expressed as a sum of contributions from protein model and disordered
solvent.

More references can be found in this review about bulk solvent models in MX:
Weichenberger, C. X., Afonine, P. V, Kantardjieff, K. & Rupp, B. (2015). *Acta
Crystallogr. Sect. D Biol. Crystallogr.* *71*, 1023–1038.

The polder tool uses the bulk solvent mask (as it is generated for other
functionalities in phenix, such as phenix.refine), and then modifies the
mask locally. I am sorry if the presentation file is misleading, I should
maybe add some references to make clear what is summary and what is related
to the polder tool.

Best wishes,

Dorothee

PS:
I did not understand how the name "squeeze" relates to "polder"...

On Wed, Apr 20, 2016 at 12:07 PM, Tim Gruene <tim.gruene at psi.ch> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> 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 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
> > >
> > >
> > >
> > > _______________________________________________
> > > phenixbb mailing list
> > > phenixbb at phenix-online.org
> > > http://phenix-online.org/mailman/listinfo/phenixbb
> > > Unsubscribe: phenixbb-leave at phenix-online.org
> - --
> - --
> Paul Scherrer Institut
> Tim Gruene
> - - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v2
>
> iD8DBQFXF9NpUxlJ7aRr7hoRApIFAKCZ6gKgFMeeU4DSZfr5i/5Z3inC/ACeOmIh
> sjQCpCYG2CkH/N/RoIfhApQ=
> =t+dS
> -----END PGP SIGNATURE-----
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160420/da7f3f73/attachment.htm>