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That’s the difference between human logic and computer (Boolean) logic.
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<div>“And” in the way you used it only selects atoms that are in BOTH residue 111 AND residue 222 (which is impossible as an atom can only be part of one residue). “Or” selects atoms that are in one OR the other. </div>
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<div id="AppleMailSignature">Thanks,
<div>Nick</div>
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On 28 Mar 2018, at 09:59, Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de">eike.schulz@mpsd.mpg.de</a>> wrote:<br>
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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)" <<a href="mailto:n.m.pearce@uu.nl">n.m.pearce@uu.nl</a>><br>
<b>Date: </b>Wednesday, 28. March 2018 at 09:49<br>
<b>To: </b>"Schulz, Eike-Christian" <<a href="mailto:eike.schulz@mpsd.mpg.de">eike.schulz@mpsd.mpg.de</a>><br>
<b>Cc: </b>"<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>" <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><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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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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