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<p class="MsoNormal">Hi Nigel,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for pointing me to this info!</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The code for NADH seems to be NAI. I was initially not sure about using it since the kink in the C4 and C6 atoms of its nicotinamide ring (which occurs with the conversion of NAD to NADH) didn�t seem to be very drastic when looking at it
on COOT with the NAI .cif file. However, upon closer inspection it doesn�t seem very different from published density. Perhaps, these changes are only subtle!</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,</p>
<p class="MsoNormal">Vatsal </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p style="margin:0cm;background:white"><span style="font-size:10.0pt;color:black">PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University</span><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"><o:p></o:p></span></p>
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<span style="font-size:10.0pt;color:black">PULSe-Biophysics and Structural Biology training group</span><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"><o:p></o:p></span></p>
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<span style="font-size:10.0pt;color:black"><a href="mailto:prakashp@purdue.edu" target="_blank"><span style="color:#1155CC">vpurohi@purdue.edu</span></a> | 346-719-9409</span><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"><o:p></o:p></span></p>
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<p class="MsoNormal" style="border:none;padding:0cm"><b>From: </b><a href="mailto:nwmoriarty@lbl.gov">Nigel Moriarty</a><br>
<b>Sent: </b>01 January 2021 16:23<br>
<b>To: </b><a href="mailto:vpurohi@purdue.edu">Vatsal Purohit</a><br>
<b>Cc: </b><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject: </b>Re: [phenixbb] Variation in bonds after loading restraints</p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Vastal<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">To see bond order in REEL is optional so you need to set it under viewing.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Also, NADH is a well known ligand (NDP, I think) so you can start with that code. You should confirm what is the exact code you need and use it thus:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">phenix.elbow --chemical_comp=NDP<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Nigel<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">---<o:p></o:p></p>
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<p class="MsoNormal">Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<o:p></o:p></p>
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<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><o:p></o:p></p>
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<p class="MsoNormal"><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 Fri, Jan 1, 2021 at 12:20 PM Vatsal Purohit <<a href="mailto:vpurohi@purdue.edu">vpurohi@purdue.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I�ve been having issues with obtaining consistent number of bonds after generating .cif files using eLBOW. To generate the .cif file for an NADH molecule on eLBOW, I�ve been using
a SMILE string generated using Chemdraw and a template .pdb file that was generated after using LigFit with a ligand .pdb model (also initially generated using a SMILE string).
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">However, I find that when I load the restraints the bonds in the molecule only show correctly on the older version of coot (0.8.9.2). The double bonds on the adenine ring don�t
appear in the latest version of coot (0.9.3) and the double bonds on the molecule don�t show up at all when I load the .cif file on REEL.
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Is there a reason why they could be inconsistent? Could I be viewing them incorrectly on REEL?
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Any thoughts on this would be appreciated! I�ve attached the SMILE string, template .pdb file and final .cif file in this email for your reference.
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Regards,</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Vatsal</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p style="margin:0cm;background:white"><span style="font-size:10.0pt;color:black">PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University</span></p>
<p style="margin:0cm;background:white"><span style="font-size:10.0pt;color:black">PULSe-Biophysics and Structural Biology training group</span></p>
<p style="margin:0cm;background:white"><span style="color:black"><a href="mailto:prakashp@purdue.edu" target="_blank"><span style="font-size:10.0pt;color:#1155CC">vpurohi@purdue.edu</span></a></span><span style="font-size:10.0pt;color:black"> | 346-719-9409</span></p>
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