[Chimera-users] building D-amino acid peptides

[Elaine Meng]

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.html#start>

(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:

addh
invert  :1 at 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 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