<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Oliver,<div class=""><br class=""></div><div class="">your suggestion works nicely. Thank you!</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Wei-Chun<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 28. Jul 2021, at 16:04, Oliver Smart <<a href="mailto:oliver.s.smart@GMAIL.COM" class="">oliver.s.smart@GMAIL.COM</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Wei-Chun,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><ul type="disc" style="margin-bottom: 0cm;" class=""><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Start from the PDB file produced by Grade (for instance<span class="Apple-converted-space"> </span><span style="font-size: 10pt; font-family: "Courier New";" class="">grade-XXX.pdb</span>)<o:p class=""></o:p></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Load this into CSD Mercury.<span class="Apple-converted-space"> </span><o:p class=""></o:p></li><ul type="circle" style="margin-bottom: 0cm;" class=""><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">select the Mercury option "Edit" -> "Auto Edit"<o:p class=""></o:p></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">accept the default options in the popup window:<o:p class=""></o:p></li></ul></ul><div style="margin: 0cm 0cm 0cm 72pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="https://gitlab.com/gphl/grade2/uploads/e7c05313e70bdb24b6b25faa02455773/Screenshot_2021-07-26_at_15.58.42.png" target="_blank" style="color: blue; text-decoration: underline;" class=""><span style="text-decoration: none;" class=""><span id="cid:image001.png@01D783C1.E253F9C0"><image001.png></span></span></a><o:p class=""></o:p></div><ul type="disc" style="margin-bottom: 0cm;" class=""><ul type="circle" style="margin-bottom: 0cm;" class=""><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">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 class=""></o:p></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">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: 10pt; font-family: "Courier New";" class="">.mol2</span><span class="Apple-converted-space"> </span>file.<o:p class=""></o:p></li></ul><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Use the<span class="Apple-converted-space"> </span><span style="font-size: 10pt; font-family: "Courier New";" class="">.mol2</span><span class="Apple-converted-space"> </span>file as the input to<span class="Apple-converted-space"> </span><span style="font-size: 10pt; font-family: "Courier New";" class="">grade2 --in</span>.<o:p class=""></o:p></li></ul><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hope this answer is useful. Please let us know if anything is unclear.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best regards,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Oliver (for BUSTER developers)<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 11pt; font-family: Calibri, sans-serif;"><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">buster-discuss <<a href="mailto:buster-discuss-bounces@globalphasing.com" class="">buster-discuss-bounces@globalphasing.com</a>> on behalf of Wei-Chun Kao <<a href="mailto:wei-chun.kao@biochemie.uni-freiburg.de" class="">wei-chun.kao@biochemie.uni-freiburg.de</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Monday, 26 July 2021 at 12:55<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b><a href="mailto:buster-discuss@globalphasing.com" class="">buster-discuss@globalphasing.com</a> <<a href="mailto:buster-discuss@globalphasing.com" class="">buster-discuss@globalphasing.com</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>[buster-discuss] Grade2 atom naming<o:p class=""></o:p></span></p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello,<o:p class=""></o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Is there any way to get the same atom naming “conventions” as in the original Grade?<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">*My system is CentOS7. CCP4-7.1 and CCDC 2021 were installed with the latest updates.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best regards,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Wei-Chun Kao<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">—<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">Dr. rer. nat. Wei-Chun Kao<o:p class=""></o:p></span></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class=""><a href="mailto:wei-chun.kao@biochemie.uni-freiburg.de" style="color: blue; text-decoration: underline;" class="">wei-chun.kao@biochemie.uni-freiburg.de</a></span><span style="" class=""><o:p class=""></o:p></span></div></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">TEL: </span><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(18, 85, 204);" class=""><a href="tel:%2B49-761-203-5277" style="color: blue; text-decoration: underline;" class="">+49-761-203-5277</a><o:p class=""></o:p></span></div></div><div class=""><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 12pt; font-family: "Proxima Nova Soft", serif; color: rgb(145, 145, 145);" class=""><a href="http://orcid.org/0000-0001-8687-6334" style="color: blue; text-decoration: underline;" class="">orcid.org/0000-0001-8687-6334</a><span class="apple-tab-span"></span></span><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(18, 85, 204);" class=""><o:p class=""></o:p></span></div></div></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">Institute for Biochemistry and Molecular Biology<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">AG Carola Hunte<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">Albert-Ludwigs-Universitaet Freiburg<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">Stefan-Meier-Str. 17<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">D-79104 Freiburg im Breisgau<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: "Proxima Nova Soft", serif; color: rgb(136, 136, 136);" class="">Germany</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div><br class=""></div></body></html>