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<p class="MsoNormal"><span style="font-size:11.0pt">Dear Nick, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you very much for your quick reply. Indeed, “or” worked very nicely!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">phenix.polder model.pdb sf.mtz selection="resseq 111 or resseq 222"
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">However, it escapes my understanding why
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">phenix.polder model.pdb sf.mtz selection="resseq 111 and resseq 222</span><span style="font-size:11.0pt">"
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">does not work equally well. <o:p>
</o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Nevertheless, “or” does the trick!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Many thanks, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Eike<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><b><span style="color:black">From:
</span></b><span style="color:black">"Pearce, N.M. (Nick)" <n.m.pearce@uu.nl><br>
<b>Date: </b>Wednesday, 28. March 2018 at 09:49<br>
<b>To: </b>"Schulz, Eike-Christian" <eike.schulz@mpsd.mpg.de><br>
<b>Cc: </b>"phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>
<b>Subject: </b>Re: [phenixbb] non-consecutive residue selection in phenix.polder</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Times New Roman""><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Hi, <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Assuming it uses the standard phenix syntax you should be able to string together a series of residue selections connected by “or”. <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">See: <a href="https://www.phenix-online.org/documentation/reference/atom_selections.html">https://www.phenix-online.org/documentation/reference/atom_selections.html</a><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt">
It should also be noted that any type of OMIT map will only show “unambiguous” density for full occupancy ligands. If your ligands are partial occupancy (which you generally can’t determine a priori), be aware that you’ll be looking at a superposition of ligand
density and the other (unknown) state of the crystal. <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Thanks, <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Nick<o:p></o:p></p>
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<br>
On 28 Mar 2018, at 09:42, Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de">eike.schulz@mpsd.mpg.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear all,
</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">To generate unambiguous ligand density in a number of structures we would like to omit the surrounding active site residues in the polder-map calculation. However, so far we were
unable to figure out how <i>non-consecutive</i> residues can be selected for phenix.polder.
</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><a href="https://www.phenix-online.org/documentation/reference/atom_selections.html">https://www.phenix-online.org/documentation/reference/atom_selections.html</a>
</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">The documentation only explains how to select ranges of residues but not how to select say 5 individual residues.
</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Is there a syntax to achieve this ?</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Thanks for your advice,
</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Eike</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Times New Roman";mso-fareast-language:EN-GB">_______________________________________________<br>
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