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<p>Dear Andrew, also look into here<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12">https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12</a><br>
<br>
</p>
<p>If you need something like example 5 (pdbcode 1EJG)( crambin:
crambin displays amino acid heterogeneity at <br>
position 22(Pro or Ser) and 25 (Leu or Ile)).<br>
<br>
This crashes Coot until you add*<br>
<br>
allow_duplicate_sequence_numbers()<br>
<br>
to $HOME/.coot.py in OSX or the appropriate place on Windows. For
<br>
Windows, as there is no $HOME, Coot uses .coot.py or
.coot-preferences/ <br>
directory for configuration - these can be found (added to) the <br>
directory in which Coot was installed (e.g. C:\WinCoot).<br>
<br>
Best regards, Georg.<br>
</p>
<div class="moz-cite-prefix">On 31.01.19 05:27, Schnicker, Nicholas
J wrote:<br>
</div>
<blockquote type="cite"
cite="mid:DBFF9FAB-26BC-4A8E-ADDB-856F83B2B48D@uiowa.edu">
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<p class="MsoNormal">Hi Andrew,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">You should use group constrained refinement
to link the occupancies of each isomer. You can see the
documentation for how to implement it.<o:p></o:p></p>
<p class="MsoNormal"><a
href="https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement"
moz-do-not-send="true">https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal">Nick<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span
style="font-size:12.0pt;color:black">From: </span></b><span
style="font-size:12.0pt;color:black"><a class="moz-txt-link-rfc2396E" href="mailto:phenixbb-bounces@phenix-online.org"><phenixbb-bounces@phenix-online.org></a>
on behalf of Andrew Philip Thompson
<a class="moz-txt-link-rfc2396E" href="mailto:andrew.thompson@adelaide.edu.au"><andrew.thompson@adelaide.edu.au></a><br>
<b>Date: </b>Wednesday, January 30, 2019 at 10:18 PM<br>
<b>To: </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>[phenixbb] Occupancy larger than 1<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">Hi Phenix BB, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">We discovered that a fragment had
degraded in our crystallography condition and the product
was observed bound in the resulting crystal structure.
Unfortunately we have been unable to separate certain
stereoisomers of this compound or its analogues, and so are
looking to simultaneously model two of the isomers into the
crystal structure. I have made a .cif file corresponding to
each isomer and modelled them into my crystal structures
with altloc tags A & B, however after refinement, the
occupancy of the two adds up to more than 1 in some
instances (ie. 0.51 and 0.53). I’ve never had this before
when trying to model dual conformations of the
stereoisomers. I tried to make the ligands the same residue
number as discussed in a previous thread (<a
href="http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html"
moz-do-not-send="true">http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html</a>),
however neither coot or pymol will open the pdb file after
refinement if I do this. Unfortunately I am unable to share
the pdb file as we do not want to disclose the compound
structure. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Does anyone have any suggestions as to
how to proceed?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks in advance,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Andrew<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<div>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:Helvetica;color:black">Andrew
Thompson<br>
PhD Candidate<br>
Molecular and Cellular Biology<br>
School of Biological Sciences<br>
The University of Adelaide, Australia<o:p></o:p></span></p>
</div>
</div>
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<br>
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