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Hello,<br>
<br>
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)<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/phenix_polder.pdf">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>
<div class="moz-cite-prefix">On 4/20/16 04:18, Lund Bjarte Aarmo
wrote:<br>
</div>
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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">
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Dorothee Liebschner<br>
<b>Sent:</b> 22. mars 2016 21:46<br>
<b>To:</b> PHENIX user mailing list
<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a><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>
<div>
<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
moz-do-not-send="true"
href="https://www.phenix-online.org/presentations/phenix_polder.pdf"><a class="moz-txt-link-freetext" href="https://www.phenix-online.org/presentations/phenix_polder.pdf">https://www.phenix-online.org/presentations/phenix_polder.pdf</a></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
moz-do-not-send="true"
href="www.phenix-online.org/version_docs/dev-2356/reference/polder.html"><a class="moz-txt-link-abbreviated" href="http://www.phenix-online.org/version_docs/dev-2356/reference/polder.html">www.phenix-online.org/version_docs/dev-2356/reference/polder.html</a></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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