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.

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?

Thanks very much!

Steve Aird