[Chimera-users] Chimera refuses to attach short peptide to protein C-terminus

Steven Douglas Aird steven.aird at oist.jp
Wed Feb 15 18:28:37 PST 2017

Dear Sirs:

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

Steven D. Aird
Technical Editor
Faculty Affairs Division
Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son
Kunigami-gun, Okinawa-ken
Japan  904-0495

Phone:  098-982-3584
Cell:  080-4154-9504
Email:  steven.aird at oist.jp<mailto:steven.aird at oist.jp>

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