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

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:

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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:

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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:

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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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- -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297

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