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

Dear Dorothee,

With squeeze, you remove solvent in order to make features visible lying 
underneath the noise density of the solvent. That's reminiscent to me as the 
cartoon on p.9 of the phenix_polder.pdf

In Platon, the structure factors are calculated from the density in the 
solvent region, Eq. (4) in the Platon paper. That appears to be the same as 
explained for phenix_polder on p. 4, except that phenix replaces 
rho(x_solvent) with 1 for the mask. The equation on p.2 of the PDF-file is 
identical to the line below Eq. 4 in the SQUEEZE paper, so it seems 
conceptually pretty much the same to me.

Since SQUEEZE was presented at the ACA in 1998 (based on a paper from 1990), I 
thought you may have been motivated by it. It is probably not much surprising 
that good ideas get invented at various places.

Best wishes,
Tim

On Wednesday, April 20, 2016 01:59:34 PM you wrote:
> 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  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:*[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
> > > > 
> > > > 
> > > > 
> > > > _______________________________________________
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> > > > http://phenix-online.org/mailman/listinfo/phenixbb
> > > > Unsubscribe: [email protected]
> > 
> > - --
> > - --
> > Paul Scherrer Institut
> > Tim Gruene
> > - - persoenlich -
> > OFLC/102
> > CH-5232 Villigen PSI
> > phone: +41 (0)56 310 5297
> > 
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Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

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