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<p class="MsoNormal"><span style="color:#1F497D">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Just an update on the solution (which was to use the altloc). I needed to use a different residue numbers as well as different names all with an altloc flag<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">e.g. AABA B 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> BABB B 2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> CABC B 3 etc<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">This way they were all recognised and were all maintained as different molecules with differing stereochemistry<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks to all who gave help<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">J<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="mso-fareast-language:EN-NZ">From:</span></b><span lang="EN-US" style="mso-fareast-language:EN-NZ"> Phan, Jason [mailto:jason.phan@Vanderbilt.Edu]
<br>
<b>Sent:</b> Friday, 11 September 2015 8:05 a.m.<br>
<b>To:</b> Joel Tyndall <joel.tyndall@otago.ac.nz><br>
<b>Subject:</b> Re: [phenixbb] refining different enantiomers<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">J, I’d give it the same res num and chain id so the program won’t treat them as different residues. Don’t for get the altloc (AS3L and BS3L in my case).
<span style="font-size:12.0pt;mso-fareast-language:EN-NZ"><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">HETATM 1467 S19AS3L A 204 -5.833 10.423 7.671 0.62 23.15 S<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1468 N20AS3L A 204 -3.414 9.416 7.552 0.62 24.27 N<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1469 C21AS3L A 204 -3.040 10.374 10.388 0.62 29.37 C<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1470 N22AS3L A 204 -2.138 10.275 11.024 0.62 30.28 N<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1471 N01BS3L A 204 -4.128 11.351 13.823 0.38 32.89 N<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1472 C02BS3L A 204 -4.731 10.188 13.418 0.38 32.83 C<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1473 O03BS3L A 204 -4.635 9.141 14.001 0.38 34.60 O<o:p></o:p></p>
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<p class="MsoNormal">HETATM 1474 O04BS3L A 204 -5.450 10.323 12.316 0.38 28.92 O<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Jason<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Sep 10, 2015, at 12:02 AM, Joel Tyndall <<a href="mailto:joel.tyndall@otago.ac.nz">joel.tyndall@otago.ac.nz</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Hi all,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">I have a case where we have crystallised a ligand in our protein and the ligand purchased is a mixture of 4 structural isomers (enantiomers and diastereomers). There is no way of telling
if one over the other is bound in the active site so we have assumed all 4 are binding. I have generated 4 separate ligands with 4 separate cifs and the all fit the density. I am refining the complex with all 4 ligands at 0.25 occupancy (occupancy refinement
is switched off, I have changed the clash guard non-bonded distance threshold is set to 0.0 (as an initial error message came up with nonbonded interactions < 0.5).</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">My refinement ran to completion, but something is definitely not right. The pdb file won’t load in Coot and in pymol the ligands have imploded/exploded. I am just wondering if this is the
best way to refine this structure (or I have missed something) and probably more to the point what have I missed with the ligands. To me it is almost identical to alternate conformations, but I have obviously missed something</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">I have just install phenix 1.10 on a windows machine.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Thanks</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">J</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif">_________________________________</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif">Joel Tyndall, PhD<br>
<br>
Associate Professor in Medicinal Chemistry<br>
National School of Pharmacy<br>
University of Otago<br>
PO Box 56 Dunedin 9054<br>
New Zealand </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif">Skype: jtyndall</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif">Ph: +64 3 479 7293</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-NZ">_______________________________________________<br>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-NZ"><o:p> </o:p></span></p>
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