<div dir="ltr">Natalia<div><br></div><div>I have attached a restraints file that should automatically link. I generated the file with eLBOW and then edited that atom names to be the standard main chain names. If you edit the PDB file to reflect the atoms it should use the standard peptide links.</div><div><br></div><div>For the record, I changed</div><div><br></div><div>N1 -> N</div><div>CA1 -> CA</div><div>C3 -> C</div><div>O3 -> O</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 : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Jun 2, 2015 at 8:15 PM, Kevin Jude <span dir="ltr"><<a href="mailto:kjude@stanford.edu" target="_blank">kjude@stanford.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I just went through this with a blue FP. Carsten is correct about how to define the peptide bonds, but an easier way is to use JLigand. The tutorial at <a href="http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link" target="_blank">http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link</a> is helpful. You will have to define the i-1 and i+1 links in separate .cif files if you use JLigand.<div><br></div><div>HTH</div><div>kmj</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Tue, Jun 2, 2015 at 4:40 PM, Schubert, Carsten [JRDUS] <span dir="ltr"><<a href="mailto:CSCHUBER@its.jnj.com" target="_blank">CSCHUBER@its.jnj.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Nat,<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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">bonds in COOT do not mean much, as they do not translate into bonded interactions in the refinement programs. Phenix for instance tries to figure out the bonding
by itself through some distance based heuristics. However in your case it looks as if the CRO residue may not be defined as a polymer, i.e. part of a protein chain in the monomer library you are using. In Windows the monomer library is located in C:\WinCoot\share\coot\lib\data\monomers.
Look at the difference in the headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The aminoacids or modified aminoacids considered part of the peptide chain have all ‘peptide’ in the header, CRO does not. That is probably the reason why coot does
not make any bonds. This would probably cause problems later on with Phenix as well. You could pull out the CRO.cif into your directory, modify it to make it a peptide and read it into coot and phenix during refinement. I would also run it through REEL to
make sure the definitions are kosher.<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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">HTH
<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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> Carsten<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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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""> Natalia Ketaren [<a href="mailto:nketaren@mail.rockefeller.edu" target="_blank">mailto:nketaren@mail.rockefeller.edu</a>]
<br>
<b>Sent:</b> Tuesday, June 02, 2015 5:42 PM<br>
<b>To:</b> Schubert, Carsten [JRDUS]<br>
<b>Subject:</b> Re: Changing an amino acid to an unusual amino acid<u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Hi Carsten, <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Th residue is a part of the correct chain. It just doesn’t make an bonds with the residues on either side of it. Is this common for unusual amino acids when adding to the main chain?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Cheers,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div><span>
<p class="MsoNormal">Nat<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">_____________________________<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif";color:black">Natalia E. Ketaren, PhD<br>
Postdoctoral Associate<br>
Rout Laboratory<br>
Box 213<br>
The Rockefeller University<br>
1230 York Avenue<br>
New York, NY 10065<br>
<br>
Tel: <a href="tel:%28212%29%20327-8136" value="+12123278136" target="_blank">(212) 327-8136</a><br>
Fax: <a href="tel:%28212%29%20327-7193" value="+12123277193" target="_blank">(212) 327-7193</a><br>
<a href="mailto:Natalia.Ketaren@rockefeller.edu" target="_blank">Natalia.Ketaren@rockefeller.edu</a><br>
website: <a href="http://lab.rockefeller.edu/rout/" target="_blank">http://lab.rockefeller.edu/rout/</a><br>
NCDIR: <a href="http://www.ncdir.org/" target="_blank">http://www.ncdir.org/</a><u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</span><div><div><div>
<div>
<p class="MsoNormal">On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] <<a href="mailto:CSCHUBER@its.jnj.com" target="_blank">CSCHUBER@its.jnj.com</a>> wrote:<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Natalia,</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">if the missing/wrong chain IDs are really the problem you can change them in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky, since you
probably have to use the correct residue range to change an individual residue into an existing chain. In your case I would write out the PDB file and use a text editor to change the chain ID and move the residue into its correct place in the file.</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">HTH</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> Carsten</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
</div>
<div>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<div>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>
[<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">mailto:phenixbb-bounces@phenix-online.org</a>]<span> </span><b>On Behalf Of<span> </span></b>Natalia Ketaren<br>
<b>Sent:</b><span> </span>Tuesday, June 02, 2015 5:17 PM<br>
<b>To:</b><span> </span><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b><span> </span>[phenixbb] Changing an amino acid to an unusual amino acid</span><u></u><u></u></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Hello All,<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">I’m working on a GFP structure and I’m trying to incorporate the CRO (chromophore) residue into the structure using coot. My process is to use Extension->Modelling—>Replace residues, where it’s suppose to replace a Tyr residue. I type the
3 letter code, CRO, the residue appears, I’m able to real space refine it, but it does not incorporate CRO into the desired chain. Would someone be able to help me figure out what I’m doing wrong? And possibly walk me through a solution?<u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Cheers,<u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Nat<u></u><u></u></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif"">_____________________________</span><u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Helvetica","sans-serif"">Natalia E. Ketaren, PhD<br>
Postdoctoral Associate<br>
Rout Laboratory<br>
Box 213<br>
The Rockefeller University<br>
1230 York Avenue<br>
New York, NY 10065<br>
<br>
Tel: <a href="tel:%28212%29%20327-8136" value="+12123278136" target="_blank">(212) 327-8136</a><br>
Fax: <a href="tel:%28212%29%20327-7193" value="+12123277193" target="_blank">(212) 327-7193</a><br>
<a href="mailto:Natalia.Ketaren@rockefeller.edu" target="_blank"><span style="color:purple">Natalia.Ketaren@rockefeller.edu</span></a><br>
website:<span> </span><a href="http://lab.rockefeller.edu/rout/" target="_blank"><span style="color:purple">http://lab.rockefeller.edu/rout/</span></a><br>
NCDIR:<span> </span><a href="http://www.ncdir.org/" target="_blank"><span style="color:purple">http://www.ncdir.org/</span></a></span><u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div></div></div>
</div>
</div>
<br></div></div><span>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><br></span></blockquote></div><br></div>
<br>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><br></blockquote></div><br></div></div>