Chimera refuses to attach short peptide to protein C-terminus
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@oist.jp<mailto:steven.aird@oist.jp>
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 http://wwwuser.cnb.csic.es/~mjvanraaij
On 16 Feb 2017, at 03:28, Steven Douglas Aird <steven.aird@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 Japan 904-0495
Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird@oist.jp <mailto:steven.aird@oist.jp>
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Hi Steven, You can only add a bond between atoms that are already in the same model. I’m guessing the protein and tripeptide are opened from two different files, which would make them two different models. Also, you do not want to make a bond from a C-terminal oxygen to the N-terminal nitrogen… a peptide bond is from the carbonyl carbon to the nitrogen. However, I think you can do what you want… instructions for 2 possible scenarios: - If the tripeptide is already in the correct position relative to the protein: Just combine the two models into one and then add the bond. You can do this with the “combine” command or using the Model Panel (Favorites… Model Panel, choose the 2 models on the left and then the “copy/combine” function on the right). Then in the combined model you can add the bond in Build Structure like you tried to do before, or with the command “bond” (I assume the C-terminal C only has one oxygen on it, so there is still “room” for the N… if it has two oxygens you’d need to delete one first). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> - If the tripeptide is not already in the correct position relative to the protein: Use the Join Models part of Build Structure (menu: Structure Editing… Build Structure) to simultaneously move the tripeptide to form the peptide bond and join the two models into one. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 15, 2017, at 6:28 PM, Steven Douglas Aird <steven.aird@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
participants (3)
-
Elaine Meng -
Mark J van Raaij -
Steven Douglas Aird