<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="">Thanks Jack! Although I’m finding that Coot isn’t writing the refinement info in the output file either… (this is for deposition, so I need the refinement data). Maybe I need to try a newer version.<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 15 Oct 2023, at 3:36 PM, Tanner, John J. <<a href="mailto:TannerJJ@missouri.edu" class="">TannerJJ@missouri.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><table width="100%" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; letter-spacing: normal; orphans: auto; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><tbody class=""><tr class=""><td style="border-left-width: 4px; border-left-style: solid; border-left-color: goldenrod; background-color: cornsilk; padding: 0px 3pt; background-position: initial initial; background-repeat: initial initial;" class=""><p style="font-style: normal; font-variant-caps: small-caps; font-weight: bold; font-stretch: normal; font-size: 14px; line-height: normal; font-family: sans-serif;" class="">External.</p></td></tr></tbody></table><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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;" class=""><div class="WordSection1" style="page: WordSection1;"><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Hi Pat,<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Coot has a tool to shift the residue numbers by a positive or negative increment. See Edit…Renumber Residues.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Best Regards,<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Jack<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div id="mail-editor-reference-message-container" class=""><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><p class="MsoNormal" style="margin: 0in 0in 12pt; font-size: 10pt; 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=""><a href="mailto:phenixbb-bounces@phenix-online.org" style="color: blue; text-decoration: underline;" class="">phenixbb-bounces@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb-bounces@phenix-online.org" style="color: blue; text-decoration: underline;" class="">phenixbb-bounces@phenix-online.org</a>> on behalf of Patrick Loll <<a href="mailto:pjloll@gmail.com" style="color: blue; text-decoration: underline;" class="">pjloll@gmail.com</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Sunday, October 15, 2023 at 1:22 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" style="color: blue; text-decoration: underline;" class="">phenixbb@phenix-online.org</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>[phenixbb] Renumbering while retaining refinement info<o:p class=""></o:p></span></p></div><div style="border: 1pt solid rgb(156, 0, 6); padding: 2pt; margin-bottom: 2pt;" class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif; line-height: 12pt; background-color: rgb(255, 199, 206);" class=""><b class=""><span style="color: rgb(156, 0, 6);" class="">WARNING:</span></b><span style="" class=""><span class="Apple-converted-space"> </span>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.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Hello all,<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">I've finished refining a handful of related structures, but now I need to renumber the residues to reflect the fact that I’m working with a truncated construct (like a dope I didn’t do this at the outset). However, when I run PDB Tools, it does not write the refinement information into the output CIF. <o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Is there a way to get around this, other than re-running the final cycle of refinement with the renumbered coordinates (or entering the refinement info by hand? This would be easy in the PDB format, but not so much in mmCIF). <o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Cheers,<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Pat<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">__________________________________<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">Patrick J. Loll, PhD (he, him, his)<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">Professor of Biochemistry & Molecular Biology<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">Drexel University College of Medicine<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">Room 10-102 New College Building<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">245 N. 15th St.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">Philadelphia, PA 19102-1192 USA<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class="">(267) 359-2653<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt;" class=""><a href="mailto:pjl28@drexel.edu" style="color: blue; text-decoration: underline;" class="">pjl28@drexel.edu</a><o:p class=""></o:p></span></div></div><div style="margin: 0in; font-size: 10pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div></div></div></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; float: none; display: inline !important;" class="">phenixbb mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; float: none; display: inline !important;" class=""><a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; float: none; display: inline !important;" class=""><a href="http://phenix-online.org/mailman/listinfo/phenixbb" class="">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; float: none; display: inline !important;" class="">Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" class="">phenixbb-leave@phenix-online.org</a></span></div></blockquote></div><br class=""><div class="">
<div>Patrick Loll</div><div><a href="mailto:pjloll@gmail.com" class="">pjloll@gmail.com</a></div><div class=""><br class=""></div><br class="Apple-interchange-newline">
</div>
<br class=""></body></html>