<div dir="ltr">Hi Tim,<div><br></div><div>I quickly looked over the SQUEEZE command in PLATON (are you referring to: <a href="http://scripts.iucr.org/cgi-bin/paper?S2053229614024929" target="_blank">http://scripts.iucr.org/cgi-bin/paper?S2053229614024929</a> ?). To me, it does not seem to be related to phenix.polder.</div><div><br></div><div>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). </div><div><br></div><div>The flat bulk-solvent model is described first here:</div><div>Phillips, S. E. (1980). <i>J. Mol. Biol.</i> <b>142</b>, 531–554.</div><div>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.</div><div><br></div><div>More references can be found in this review about bulk solvent models in MX:</div><div>Weichenberger, C. X.,
Afonine, P. V, Kantardjieff, K. & Rupp, B. (2015). <i>Acta Crystallogr.
Sect. D Biol. Crystallogr.</i> <b>71</b>, 1023–1038.</div><div><br></div><div>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. </div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div><div><br></div><div>PS:</div><div>I did not understand how the name "squeeze" relates to "polder"...</div><div><p class="MsoNormal" style="margin-left:24pt"><span><br></span></p>
</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 20, 2016 at 12:07 PM, Tim Gruene <span dir="ltr"><<a href="mailto:tim.gruene@psi.ch" target="_blank">tim.gruene@psi.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">-----BEGIN PGP SIGNED MESSAGE-----<br>
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Hi Pavel,<br>
<br>
this is an interesting concept. It seems related to the SQUEEZE command in<br>
platon - even the name appears to suggest a relationship. I did not understand<br>
the maths entirely: Are they similar concept, or do I misinterprete?<br>
<br>
Best,<br>
Tim<br>
<span class=""><br>
On Wednesday, April 20, 2016 07:28:16 AM Pavel Afonine wrote:<br>
> Hello,<br>
><br>
> it's good to know it was useful for you, thanks for feedback! I afraid<br>
> it's too new so that we don't have a publication to cite yet. We are<br>
> working on a manuscript but it may take a little while before it appears<br>
> somewhere. For now I guess you can use this link (unless Dorothee has a<br>
> better idea)<br>
><br>
> <a href="http://www.phenix-online.org/presentations/phenix_polder.pdf" rel="noreferrer" target="_blank">http://www.phenix-online.org/presentations/phenix_polder.pdf</a><br>
><br>
> and use official Phenix citation:<br>
><br>
> Acta Cryst. D66, 213-221 (2010).<br>
><br>
> That's all we have at the moment anyway.<br>
><br>
> All the best,<br>
> Pavel<br>
><br>
> On 4/20/16 04:18, Lund Bjarte Aarmo wrote:<br>
</span>> > DearDorothee and phenixbb,<br>
<span class="">> ><br>
> > I found this software very useful for protein-fragment complexes with<br>
> > weak electron density. I was wondering how the software should be cited?<br>
> ><br>
> > Kind regards,<br>
> ><br>
> > Bjarte Aarmo Lund<br>
> ><br>
> > PhD candidate<br>
> ><br>
> > UiT – The arctic university of Norway<br>
> ><br>
</span>> > *From:*<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a><br>
> > [mailto:<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>] *On Behalf Of *Dorothee<br>
> > Liebschner<br>
> > *Sent:* 22. mars 2016 21:46<br>
> > *To:* PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
> > *Subject:* [phenixbb] phenix.polder - tool for calculating omit maps<br>
<div><div class="h5">> > by excluding bulk solvent<br>
> ><br>
> > Dear phenix users,<br>
> ><br>
> > Starting from the nightly build dev-2356, a new tool for calculating<br>
> > ligand omit-maps, called 'polder', is included in phenix.<br>
> ><br>
> > Usage:<br>
> ><br>
> > phenix.polder model.pdb data.mtz selection='chain A and resseq 123’<br>
> ><br>
> > Phenix.polder calculates omit maps for atom selections by preventing<br>
> > the bulk solvent mask to flood into the atom selection area and its<br>
> > vicinity. The tool can be useful in cases where the density of the<br>
> > selected atoms is weak and possibly obscured by bulk solvent.<br>
> ><br>
> > Polder produces less biased maps compared to procedures where the atom<br>
> > selection occupancy is set to zero, and the atoms are included in the<br>
> > solvent mask calculation (in that case, the resulting difference<br>
> > density can have similar shape than the selected atoms). Phenix.polder<br>
> > excludes a larger volume from the bulk solvent and therefore prevents<br>
> > misinterpreting bulk solvent density as omit density.<br>
> ><br>
> > If you want to know more about how the tool is working and to see some<br>
> > examples, have a look at the presentation file:<br>
> > <a href="https://www.phenix-online.org/presentations/phenix_polder.pdf" rel="noreferrer" target="_blank">https://www.phenix-online.org/presentations/phenix_polder.pdf</a>.<br>
> ><br>
> > The documentation page can be found here:<br>
> ><br>
> > <a href="http://www.phenix-online.org/version_docs/dev-2356/reference/polder.html" rel="noreferrer" target="_blank">www.phenix-online.org/version_docs/dev-2356/reference/polder.html</a><br>
> ><br>
> > Best wishes,<br>
> ><br>
> > Dorothee<br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > phenixbb mailing list<br>
> > <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
> > <a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
> > Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><br>
</div></div>- --<br>
- --<br>
Paul Scherrer Institut<br>
Tim Gruene<br>
- - persoenlich -<br>
OFLC/102<br>
CH-5232 Villigen PSI<br>
phone: <a href="tel:%2B41%20%280%2956%20310%205297" value="+41563105297">+41 (0)56 310 5297</a><br>
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