<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Do the chains you want to join have the same chain id? I think this may be necessary.<div class="">And you might want to make the numbering of the amino acids continuous to avoid any confusion.</div><div class="">I think then the peptide joining should work both in Chimera and Pymol.<br class=""><div class="">If these conditions are met and you know all atoms are in the right place, you might also just add the peptides into the pdb file with a text editor - then Chimera (or Pymol) should automatically generate the peptide bond when displaying the file.</div><div class=""><br class=""></div><div class=""><div class=""></div></div></div><div class="">
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<br class=""><div><blockquote type="cite" class=""><div class="">On 16 Feb 2017, at 03:28, Steven Douglas Aird <<a href="mailto:steven.aird@oist.jp" class="">steven.aird@oist.jp</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Dear Sirs:
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<div class="">I am modeling novel proteins on homologous structures from other organisms using SWISS-MODEL. After the model is completed I import the PDB file into Chimera to form disulfides and to produce publication quality graphics. I thought all was going
well until I discovered that SWISS-MODEL was actually truncating one or both termini of my target sequences by 1-5 residues.</div>
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<div class="">In one case, I created the missing C-terminal tripeptide using MacPyMol, but MacPyMol will not not add the tripeptide to the C-terminus, because it is designed only to create intramolecular bonds. So I imported the protein and the tripeptide
into Chimera. I selected the C-terminal oxygen of the protein and the N-terminal nitrogen of the tripeptide and tried to create a peptide bond using Build Structure>Adjust Bonds>Add Bond. Chimera claims that only one atom is selected, but in fact, both are
selected. I do not want to try to build a tripeptide one atom at a time. Is there any way to do ligate the tripeptide?</div>
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<div class="">Thanks very much!</div>
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<div class="">Steve Aird</div>
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Steven D. Aird<br class="">
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Okinawa Institute of Science and Technology Graduate University<br class="">
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