Hi Nigel,<br><br>Beautiful -- those new restraints did the trick. Thank you!<br><div><br></div><div>~Daniel</div><br><div class="gmail_quote">On Mon Dec 01 2014 at 1:54:12 PM Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dan<div><br></div><div>The problem is that NLE restraints file is a legacy from the v2 PDB atom names. I have attached a restraints file that I created using</div><div><br></div><div>phenix.elbow --chemical_component=NLE</div><div><br></div><div>I will update the restraints library in Phenix.</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>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></div></div></div></div></div>
<br><div class="gmail_quote"></div></div><div class="gmail_extra"><div class="gmail_quote">On Mon, Dec 1, 2014 at 1:19 PM, Joel Tyndall <span dir="ltr"><<a href="mailto:joel.tyndall@otago.ac.nz" target="_blank">joel.tyndall@otago.ac.nz</a>></span> wrote:<br></div></div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Do you need to define links to define the bonds?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [mailto:<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Daniel Keedy<br>
<b>Sent:</b> Tuesday, 2 December 2014 8:10 a.m.<br>
<b>To:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] norleucine (NLE) restraints<u></u><u></u></span></p><div><div>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Hi everybody,<u></u><u></u></p>
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<p class="MsoNormal" style="line-height:14.85pt">First-time poster! I'm trying to re-refine 2f4k.pdb, but phenix.refine chokes on the non-standard norleucine (NLE) amino acid. I've tried phenix.elbow and phenix.ready_set using different version of PHENIX,
with the NLE cards as either HETATM or ATOM, all to no avail. SHELX was used to refine the structure originally, but I'd like to use PHENIX to re-refine it. Any ideas on how to define these restraints?<u></u><u></u></p>
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<p class="MsoNormal" style="line-height:14.85pt"><u></u> <u></u></p>
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<p class="MsoNormal" style="line-height:14.85pt">Daniel Keedy<u></u><u></u></p>
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<p class="MsoNormal" style="line-height:14.85pt">James Fraser Lab<u></u><u></u></p>
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<p class="MsoNormal" style="line-height:14.85pt">UCSF<u></u><u></u></p>
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