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<p>watch also the video tutorial under
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/documentation/reference/atom_selections.html">https://www.phenix-online.org/documentation/reference/atom_selections.html</a></p>
<p>around min 3.</p>
<p>Best, Georg.<br>
</p>
<br>
<div class="moz-cite-prefix">Am 28.03.2018 um 12:02 schrieb Pearce,
N.M. (Nick):<br>
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That�s the difference between human logic and computer (Boolean)
logic.�
<div><br>
</div>
<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>
<div><br>
<div id="AppleMailSignature">Thanks,
<div>Nick</div>
</div>
<div><br>
On 28 Mar 2018, at 09:59, Schulz, Eike-Christian <<a
href="mailto:eike.schulz@mpsd.mpg.de" moz-do-not-send="true">eike.schulz@mpsd.mpg.de</a>>
wrote:<br>
<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>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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"
moz-do-not-send="true">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"
moz-do-not-send="true">eike.schulz@mpsd.mpg.de</a>><br>
<b>Cc: </b>"<a
href="mailto:phenixbb@phenix-online.org"
moz-do-not-send="true">phenixbb@phenix-online.org</a>"
<<a href="mailto:phenixbb@phenix-online.org"
moz-do-not-send="true">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>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span
style="font-family:"Times New Roman""><o:p>�</o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:36.0pt">Hi, <o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p>�</o:p></p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p>�</o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">See:�<a
href="https://www.phenix-online.org/documentation/reference/atom_selections.html"
moz-do-not-send="true">https://www.phenix-online.org/documentation/reference/atom_selections.html</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p>�</o:p></p>
</div>
<div>
<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>
<div id="AppleMailSignature">
<p class="MsoNormal" style="margin-left:36.0pt">Thanks,
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Nick<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"><br>
On 28 Mar 2018, at 09:42, Schulz, Eike-Christian
<<a href="mailto:eike.schulz@mpsd.mpg.de"
moz-do-not-send="true">eike.schulz@mpsd.mpg.de</a>>
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<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"
moz-do-not-send="true">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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