[Chimera-users] building D-amino acid peptides

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 6 15:00:07 PDT 2014

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

(3) invert the alpha-carbon of each residue, e.g. commands:

invert  :1 at ca
invert  :2 at ca
(… etc. …)
invert  :10 at 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:

invert  :1 at ha,cb


You can save the structure as a PDB file with menu: File… Save PDB, or command: write

I hope this helps,
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 at 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

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