[Chimera-users] D-amino acids

Francesco Pietra chiendarret at gmail.com
Fri Mar 6 11:07:45 PST 2009

Hi Elaine:

As I was interested in inverting the configuration at the alph carbon
of amino acids in a peptide, I came across (between ==)

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 30 10:53:33 PDT 2008

Hi Yasser,
Sorry, mutation with the Rotamers tool (or swapaa command) is only to
L-amino acids.

Some less convenient alternatives:

- use Build Structure (under Tools... Structure Editing) to build out
the D- side chain manually.  Note the resulting bond lengths and
angles are approximate.

- open another structure that contains the D- amino acid, match the
backbone atoms of the residue you wish to substitute, write out
coordinates "relative to" the first structure, then manually edit the
PDB file to substitute that sidechain for the one originally in the

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 27, 2008, at 12:33 PM, Yasser Almeida Hernández wrote:

> Can Chimera mutate by D-residues? If this is possible, how i can do
> it?
> Thanks...
> --
> Yasser Almeida Hernández
> Estudiante, 4to Año Bioquímica
> Facultad de Biología
> Universidad de la Habana

What about doing that with a molecular mechanics package? Most such
packages have the capability of enantiomerize. Then, back to Chimera.
Your view?


francesco pietra

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