<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi,<br><br>It works well.</div><div>I appreciate it!</div><div><br></div><div>Wei</div><div><br>On Dec 12, 2013, at 11:52 AM, "Ryan Spencer" <<a href="mailto:rspencer@uci.edu">rspencer@uci.edu</a>> wrote:<br><br></div><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div class="WordSection1"><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Wei,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> I used Custom geometry restraints under the Refinement settings tab in phenix.refine. Select the bond you want to make, the angle and the plane you want to set. Should look something like this for the bond:<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">chain 'A' and resid ' 1 ' and name ' N ' and altloc ' '; chain 'A' and resid ' 16 ' and name ' C ' and altloc ' '. <o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">This will create a bond between the amine at position 1 and the carbonyl at position 16. Enter the appropriate distance (1.329) and sigma (0.06). <o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The same can be done for the angle and the plane.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ryan<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in"><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>] <b>On Behalf Of </b>wei xia<br><b>Sent:</b> Thursday, December 12, 2013 8:14 AM<br><b>To:</b> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><b>Subject:</b> [phenixbb] cyclic peptide refinement<o:p></o:p></span></p></div></div><p class="MsoNormal"><o:p> </o:p></p><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Hi, <o:p></o:p></span></p><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">I am trying to refine a structure with a cyclic peptide ligand.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic peptide during refinement.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">But there is obvious no bond formed between the two residues in the refined structure.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">I checked the geo file and found that there are only angle restraints but no bond restraints between the two residues<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Anyone can help me out?<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Thanks in advance!<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Wei<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">P.S. <o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">refinement.pdb_interpretation.apply_cif_link {<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""> data_link = TRANS<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""> residue_selection_1 = chain D and resname MVA and resid 5005<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""> residue_selection_2 = chain D and resname ARG and resid 5001<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""> }<o:p></o:p></span></p></div></div></div></div></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>phenixbb mailing list</span><br><span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></span><br><span><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br></div></blockquote></body></html>