[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
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!
Steven D. Aird
Faculty Affairs Division
Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son
Email: steven.aird at oist.jp<mailto:steven.aird at oist.jp>
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