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<p class="MsoNormal">Nic,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We encountered this situation � see PDB ID 7MYB. We assigned the two stereoisomers to have unique residue names, unique residue numbers, and different alternate location identifiers (the A and B before the residue name below). They can
have the same chain ID. The A and B alternative location IDs prevent the molecules from clashing with each other. Here is how we set it up in our case:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><span class="s1">HETATM18364</span><span class="apple-converted-space">
</span><span class="s1">C02AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-4.302</span><span class="apple-converted-space"> </span>
<span class="s1">21.083 108.824</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 33.60 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18365</span><span class="apple-converted-space">
</span><span class="s1">C04AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-5.200</span><span class="apple-converted-space"> </span>
<span class="s1">19.877 108.429</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 32.58 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18366</span><span class="apple-converted-space">
</span><span class="s1">C06AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-5.027</span><span class="apple-converted-space"> </span>
<span class="s1">17.825 110.133</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 31.64 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18367</span><span class="apple-converted-space">
</span><span class="s1">C07AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-6.136</span><span class="apple-converted-space"> </span>
<span class="s1">18.797 110.502</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 32.44 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18368</span><span class="apple-converted-space">
</span><span class="s1">C08AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-6.405</span><span class="apple-converted-space"> </span>
<span class="s1">19.771 109.357</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 34.12 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18369</span><span class="apple-converted-space">
</span><span class="s1">O01AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-4.772</span><span class="apple-converted-space"> </span>
<span class="s1">22.201 108.497</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 30.85 </span><span class="apple-converted-space"> </span>
<span class="s1">O</span></p>
<p class="p1"><span class="s1">HETATM18370</span><span class="apple-converted-space">
</span><span class="s1">O03AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-3.216</span><span class="apple-converted-space"> </span>
<span class="s1">20.883 109.410</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 35.44 </span><span class="apple-converted-space"> </span>
<span class="s1">O1-</span></p>
<p class="p1"><span class="s1">HETATM18371</span><span class="apple-converted-space">
</span><span class="s1">S05AUJM B1301</span><span class="apple-converted-space">
</span><span class="s1">-4.377</span><span class="apple-converted-space"> </span>
<span class="s1">18.249 108.495</span><span class="apple-converted-space"> </span>
<span class="s1">0.50 29.52 </span><span class="apple-converted-space"> </span>
<span class="s1">S</span></p>
<p class="p1"><span class="s1">HETATM18372</span><span class="apple-converted-space">
</span><span class="s1">C02BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-4.324</span><span class="apple-converted-space"> </span>
<span class="s1">21.167 108.876</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 33.43 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18373</span><span class="apple-converted-space">
</span><span class="s1">C04BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-5.334</span><span class="apple-converted-space"> </span>
<span class="s1">20.003 108.712</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 32.97 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18374</span><span class="apple-converted-space">
</span><span class="s1">C06BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-5.399</span><span class="apple-converted-space"> </span>
<span class="s1">17.805 110.268</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 31.16 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18375</span><span class="apple-converted-space">
</span><span class="s1">C07BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-4.356</span><span class="apple-converted-space"> </span>
<span class="s1">17.742 109.183</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 32.66 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18376</span><span class="apple-converted-space">
</span><span class="s1">C08BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-4.618</span><span class="apple-converted-space"> </span>
<span class="s1">18.801 108.125</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 30.79 </span><span class="apple-converted-space"> </span>
<span class="s1">C</span></p>
<p class="p1"><span class="s1">HETATM18377</span><span class="apple-converted-space">
</span><span class="s1">O01BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-4.720</span><span class="apple-converted-space"> </span>
<span class="s1">22.265 108.413</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 30.37 </span><span class="apple-converted-space"> </span>
<span class="s1">O</span></p>
<p class="p1"><span class="s1">HETATM18378</span><span class="apple-converted-space">
</span><span class="s1">O03BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-3.227</span><span class="apple-converted-space"> </span>
<span class="s1">20.957 109.434</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 34.00 </span><span class="apple-converted-space"> </span>
<span class="s1">O1-</span></p>
<p class="p1"><span class="s1">HETATM18379</span><span class="apple-converted-space">
</span><span class="s1">S05BUJP B1302</span><span class="apple-converted-space">
</span><span class="s1">-6.135</span><span class="apple-converted-space"> </span>
<span class="s1">19.451 110.283</span><span class="apple-converted-space"> </span>
<span class="s1">0.31 35.84 </span><span class="apple-converted-space"> </span>
<span class="s1">S</span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-----------------------<o:p></o:p></p>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">John J. Tanner </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Professor of Biochemistry and Chemistry</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Associate Chair of Biochemistry</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Department of Biochemistry</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">University of Missouri<br>
117 Schweitzer Hall</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">503 S College Avenue<br>
Columbia, MO 65211<br>
Phone: 573-884-1280</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black"><a href="mailto:tannerjj@missouri.edu" target="_blank" title="mailto:tannerjj@missouri.edu"><span style="color:#0563C1">Email: tannerjj@missouri.edu</span></a><br>
<a href="https://cafnrfaculty.missouri.edu/tannerlab/" title="https://cafnrfaculty.missouri.edu/tannerlab/"><span style="color:#0563C1">https://cafnrfaculty.missouri.edu/tannerlab/</span></a></span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Lab: Schlundt Annex rooms 3,6,9, 203B, 203C</span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.5pt;font-family:Helvetica;color:black;background:white">Office: Schlundt Annex 203A</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Pavel Afonine <pafonine@lbl.gov><br>
<b>Date: </b>Thursday, September 14, 2023 at 10:47 PM<br>
<b>To: </b>Calvin N Steussy <csteussy@purdue.edu>, phenixbb@phenix-online.org <phenixbb@phenix-online.org><br>
<b>Subject: </b>Re: [phenixbb] racemic ligand refinement<o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:#FFC7CE"><b><span style="color:#9C0006">WARNING:</span></b><span style="color:black"> This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized
access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.</span><span style="font-size:10.0pt;color:black"><o:p></o:p></span></p>
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<p><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 9/14/23 21:09, Calvin N Steussy wrote:</p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">All,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">I need to refine a ligand that consists of two stereoisomers in my active site. I have decent density and have created models for the r and s forms of the guest with separate cif
files. They have been fit independently into the active site density. My questions are;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">How to show these in the pdb file. Separate chains? Separate amino acids in a given chain?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">How do I keep them from interacting with one another during refinement?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Creating an alt-position seems obvious but I'm not certain how to apply the different stereo restraints in that case.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">I'm sure someone has solved this before but I can't seem to find that information.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Nic Steussy<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Purdue University.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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