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<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dear</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dorothee and phenixbb,<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I found this software very useful for protein-fragment complexes with weak electron density. I was wondering how the software should be
cited?</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Bjarte Aarmo Lund<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">PhD candidate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">UiT – The arctic university of Norway<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Dorothee Liebschner<br>
<b>Sent:</b> 22. mars 2016 21:46<br>
<b>To:</b> PHENIX user mailing list <phenixbb@phenix-online.org><br>
<b>Subject:</b> [phenixbb] phenix.polder - tool for calculating omit maps by excluding bulk solvent<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dear phenix users,<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Starting from the nightly build dev-2356, a new tool for calculating ligand omit-maps, called 'polder', is included in phenix.<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Usage:<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">phenix.polder model.pdb data.mtz selection='chain A and resseq 123’<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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.
<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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.<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">If you want to know more about how the tool is working and to see some examples, have a look at the presentation file:
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="https://www.phenix-online.org/presentations/phenix_polder.pdf">https://www.phenix-online.org/presentations/phenix_polder.pdf</a><span style="color:black">.</span><o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> <o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">The documentation page can be found here:<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="www.phenix-online.org/version_docs/dev-2356/reference/polder.html">www.phenix-online.org/version_docs/dev-2356/reference/polder.html</a><o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Best wishes,<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dorothee<o:p></o:p></span></p>
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