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

Mark J van Raaij mjvanraaij at cnb.csic.es
Wed Feb 15 22:39:10 PST 2017

Do the chains you want to join have the same chain id? I think this may be necessary.
And you might want to make the numbering of the amino acids continuous to avoid any confusion.
I think then the peptide joining should work both in Chimera and Pymol.
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.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616

> On 16 Feb 2017, at 03:28, Steven Douglas Aird <steven.aird at oist.jp> wrote:
> 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
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> Email:  steven.aird at oist.jp <mailto:steven.aird at oist.jp>
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