Hi Jesse, We're glad you like Chimera, and are always happy to hear about classroom use! As you probably saw, "Build Structure" doesn't have an option for D-amino acids. However, you can use it to build the L-amino acid version of the peptide, then invert the chirality of each residue. In a little more detail: (1) start Build Structure (in menu under Tools… Structure Editing) (2) in that tool, use the "Start Structure" section to create the L-amino acid version of your peptide sequence: enter the sequence, Apply, then in the next dialog set the phi/psi angles <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> (3) invert the alpha-carbon of each residue, e.g. commands: invert :1@ca invert :2@ca (… etc. …) invert :10@ca Or, if you want to control exactly which two substituents on CA are swapped, you can name them in the command instead of the CA. If you wanted the H to be one of the swapped substituents, you would have to add explicit hydrogens first. For example, commands: addh invert :1@ha,cb (etc.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> You can save the structure as a PDB file with menu: File… Save PDB, or command: write <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> 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 Oct 6, 2014, at 10:52 AM, JESSE JAYNES <jjsqrd@bellsouth.net> wrote:
I am a long time user of Chimra and greatly appreciate the software. I am also a professor at Tuskegee university and I use it in the classroom. I am Mac user.
I have a question.
How can I model an all D-form of a 10 amino acid peptide and generate its pdb?
Thank you!
Jesse M. Jaynes