<div dir="ltr">Damian<div><br></div><div>Peptide bonds are usually automatic, however, because only bond restraints are permitted across symmetry mates it can sometimes be "interesting". Have you try refining and checking the .geo file for the bond restraints?</div><div><br></div><div>Please feel free to send the model file directly to me for testing purposes.</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><img src="https://monitor-mailtracker.com/pixel/DVDu2DM0kMl1o9oQ3WAM?rid=DVDu2DM0kMl1o9oQ3WAM" width="1" height="1" border="0"></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 23, 2021 at 7:19 AM Damian Ekiert <<a href="mailto:damian.ekiert@ekiertlab.org">damian.ekiert@ekiertlab.org</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">Hi All,<br>
<br>
We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers.<br>
<br>
Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond.<br>
<br>
Thanks for your help!<br>
<br>
Best,<br>
<br>
Damian<br>
<br>
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -<br>
Damian Ekiert<br>
Assistant Professor<br>
Skirball Institute | NYU School of Medicine<br>
Depts. Cell Biology and Microbiology<br>
<a href="mailto:damian.ekiert@ekiertlab.org" target="_blank">damian.ekiert@ekiertlab.org</a><br>
<a href="http://www.bhabhaekiertlab.org" rel="noreferrer" target="_blank">www.bhabhaekiertlab.org</a><br>
<br>
<br>
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