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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Wei-Chun,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">If you hit another case where you want to generate a Grade2 restraint dictionary with atom names consistent with an<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Existing Grade dictionary then it normally obabel can be used.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Please see:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><a href="https://gphl.gitlab.io/grade2_docs/faqs.html#how-can-i-use-grade2-to-generate-a-restraint-dictionary-with-atom-names-consistent-with-an-existing-grade-dictionary">https://gphl.gitlab.io/grade2_docs/faqs.html#how-can-i-use-grade2-to-generate-a-restraint-dictionary-with-atom-names-consistent-with-an-existing-grade-dictionary</a>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">The procedure using Mercury is a bit more involved but will work for more complex cases.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">The next Grade2 release will make this easier.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Oliver<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></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">Wei-Chun Kao <wei-chun.kao@biochemie.uni-freiburg.de><br>
<b>Date: </b>Thursday, 29 July 2021 at 17:12<br>
<b>To: </b>Oliver Smart <oliver.s.smart@GMAIL.COM><br>
<b>Cc: </b>buster-discuss@globalphasing.com <buster-discuss@globalphasing.com><br>
<b>Subject: </b>Re: [buster-discuss] Grade2 atom naming<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Oliver,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">your suggestion works nicely. Thank you!<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Wei-Chun<o:p></o:p></p>
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<p class="MsoNormal">On 28. Jul 2021, at 16:04, Oliver Smart <<a href="mailto:oliver.s.smart@GMAIL.COM">oliver.s.smart@GMAIL.COM</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">Hi Wei-Chun,<o:p></o:p></p>
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<p class="MsoNormal">Thanks for the positive feedback about Grade2. Currently, the recommended best way to produce a Grade2 restraint dictionary that is consistent with a previously produced Grade restraint dictionary is to:<o:p></o:p></p>
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<li class="MsoNormal" style="mso-list:l1 level1 lfo1">Start from the PDB file produced by Grade (for instance<span class="apple-converted-space"> </span><span style="font-size:10.0pt;font-family:"Courier New"">grade-XXX.pdb</span>)<o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo1">Load this into CSD Mercury.<span class="apple-converted-space"> </span><o:p></o:p></li></ul>
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<li class="MsoNormal" style="mso-list:l1 level2 lfo1">select the Mercury option "Edit" -> "Auto Edit"<o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level2 lfo1">accept the default options in the popup window:<o:p></o:p></li></ul>
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<p class="MsoNormal"><a href="https://gitlab.com/gphl/grade2/uploads/e7c05313e70bdb24b6b25faa02455773/Screenshot_2021-07-26_at_15.58.42.png" target="_blank"><span style="text-decoration:none"><image001.png></span></a><o:p></o:p></p>
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<li class="MsoNormal" style="mso-list:l0 level2 lfo2">Mercury will show you the bonds in its main window. Check that the bonding applied corresponds to the molecule wanted. If not use Mercury to manually edit the bond definitions.<o:p></o:p></li><li class="MsoNormal" style="mso-list:l0 level2 lfo2">select the Mercury option "File" -> "Save As" and the option "Mol2 files". Save to a<span class="apple-converted-space"> </span><span style="font-size:10.0pt;font-family:"Courier New"">.mol2</span><span class="apple-converted-space"> </span>file.<o:p></o:p></li></ul>
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<li class="MsoNormal" style="mso-list:l0 level1 lfo2">Use the<span class="apple-converted-space"> </span><span style="font-size:10.0pt;font-family:"Courier New"">.mol2</span><span class="apple-converted-space"> </span>file as the input to<span class="apple-converted-space"> </span><span style="font-size:10.0pt;font-family:"Courier New"">grade2
--in</span>.<o:p></o:p></li></ul>
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<p class="MsoNormal">Apologies this is rather laborious! In a future release, it is intended to produce an easier process where the Grade output CIF restraint dictionary can be directly used as input to Grade2. (It is already possible to use Acedrg and Grade2
restraint dictionaries as an input to Grade2).<o:p></o:p></p>
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<p class="MsoNormal">Hope this answer is useful. Please let us know if anything is unclear.<o:p></o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal">Oliver (for BUSTER developers)<o:p></o:p></p>
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<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">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">buster-discuss <<a href="mailto:buster-discuss-bounces@globalphasing.com">buster-discuss-bounces@globalphasing.com</a>>
on behalf of Wei-Chun Kao <<a href="mailto:wei-chun.kao@biochemie.uni-freiburg.de">wei-chun.kao@biochemie.uni-freiburg.de</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Monday, 26 July 2021 at 12:55<br>
<b>To:<span class="apple-converted-space"> </span></b><a href="mailto:buster-discuss@globalphasing.com">buster-discuss@globalphasing.com</a> <<a href="mailto:buster-discuss@globalphasing.com">buster-discuss@globalphasing.com</a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>[buster-discuss] Grade2 atom naming</span><o:p></o:p></p>
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<p class="MsoNormal">Hello,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I just started using Grade2 with the latest BUSTER release. For a phospholipid input from SMILES Grade 2 took only 13 second as compared 266 seconds required by the original Grade on the same computer*. The performance of Grade2 is astonishing!<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">However the atom naming of the output coordinates from Grade2 are different than what produced from Grade, which means that I cannot just re-refine the structure directly using BUSTER for which I would just need to change the restraint
paths in my existing refinement /job submission script. Instead the ligand molecules have to be re-modelled from scratch using the new restraints in Coot. <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Is there any way to get the same atom naming “conventions” as in the original Grade?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">*My system is CentOS7. CCP4-7.1 and CCDC 2021 were installed with the latest updates.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Wei-Chun Kao<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">—</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">Dr. rer. nat. Wei-Chun Kao</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888"><a href="mailto:wei-chun.kao@biochemie.uni-freiburg.de">wei-chun.kao@biochemie.uni-freiburg.de</a></span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">TEL: </span><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#1255CC"><a href="tel:%2B49-761-203-5277">+49-761-203-5277</a></span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:#919191"><a href="http://orcid.org/0000-0001-8687-6334">orcid.org/0000-0001-8687-6334</a></span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">Institute for Biochemistry and Molecular Biology</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">AG Carola Hunte</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">Albert-Ludwigs-Universitaet Freiburg</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">Stefan-Meier-Str. 17</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">D-79104 Freiburg im Breisgau</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:#888888">Germany</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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