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You can practice atom selection by using this command line utility<br>
<br>
phenix.pdb_atom_selection model.pdb "(chain A and resseq 123:321) or
(chain A and resid 345)"<br>
<br>
that will show selected atoms on the screen.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/28/18 01:59, Schulz,
Eike-Christian wrote:<br>
</div>
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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 class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-rfc2396E" href="mailto:eike.schulz@mpsd.mpg.de"><eike.schulz@mpsd.mpg.de></a><br>
<b>Cc: </b><a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org">"phenixbb@phenix-online.org"</a>
<a class="moz-txt-link-rfc2396E" 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>
</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>
</div>
</blockquote>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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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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