<div dir="ltr">Jiang<div><br></div><div>I think the issue is that you "made a link" in Coot which is not honoured by Phenix. To "make a link" in Phenix you need to do one of three things. See the documentation here.</div><div><br></div><div><a href="https://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles">https://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles</a></div><div><br></div><div>Also, if you send me the model directly, I will take a look at it to see if it can be automated.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">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></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Aug 13, 2022 at 10:00 PM Jiang Xu <<a href="mailto:foxjuly@gmail.com">foxjuly@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello Guys,<div> I have a circular peptide structure solved from Xtal. The peptide is actually a circular peptide that has the N terminal and C terminal joined together by a peptide bond. When refining the structure, I had a problem getting the C-N terminal (between G34 and S2) joined together by the peptide bond. I even made a link between the C terminal carbon atom and N terminal N atom in coot and used this model as the input model to do the refinement using Phenix.refine. It seemed that the program didn't consider the link made in coot as a valid bond and intentionally avoid forming a bond between the C atom and the N atom. So, how can I solve this problem?</div><div>Thank you,</div><div>Best regards,</div><div>Jiang </div><div>Lin Chen Lab</div><div>University of Southern California</div><div><br></div><div><div>P.S.</div><div>coot manually made link between the C and N terminal</div></div><div><img src="cid:ii_l6suq6330" alt="unnamed.jpg" width="400" height="323"><br></div><div>After refinement<br></div><div><img src="cid:ii_l6suqxi51" alt="unnamed (1).jpg" width="400" height="377"><br></div></div>
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