See this newsletter:<div><br></div><div><a href="http://www.phenix-online.org/newsletter/CCN_2011_01.pdf">http://www.phenix-online.org/newsletter/CCN_2011_01.pdf</a></div><div><br></div><div>pages 3-5: FAQ</div><div>There are two methods to add links between atoms in Phenix. Which one should I use?</div>
<div><br></div><div>Let us know if this doesn't fully answer your question.</div><div><br></div><div>Ralf</div><div><br><br><div class="gmail_quote">On Sat, May 12, 2012 at 6:58 PM, Vitali Stanevich <span dir="ltr"><<a href="mailto:stanevich@wisc.edu" target="_blank">stanevich@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br><br>I am trying to refine protein structure with MCLR ligand - this is cyclic hepta-peptide which has some non-standard amino acids. Sequence is DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It's exactly the same compound as chain G at 3dw8 PDB entry.<br>
<br>I could successfully import amino acids in coot through "get monomer" option, renumber and combine in one chain. Problem is that whenever I use phenix.refine it returns all residues nonbonded. Corresponding carboxyl and amino groups are in close proximity to make a bond. I tried to write LINKR record in .pdb - with no success:<br>
...<br>LINKR������������ 1ZN G�� 5�������������������� FGA G�� 6������������� trans<br>LINKR������������ FGA G�� 6�������������������� DAM G�� 7������������� trans<br>...<br><br>Is there a way to create peptide bonds in this inhibitor chain? I'm using phenix Version: 1.7.3.<br>
<br>Thanks in advance,<br>Vitali<br><br>
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