You can also make Chimera add D amino acids via a relatively simple change in its Python code.  If you edit <your Chimera installation>/share/Rotamers/__init__.py, you will find a line that looks like this:

        xform, rmsd = matchPositions(_coordArray([n, ca, c]),

(approximately line #53).  Change it to this:

        xform, rmsd = matchPositions(_coordArray([c, ca, n]),

i.e. swap the 'c' and then 'n'.  This will have the effect of making it place the CB atom at the D position instead of the L position.  Of course, when you are done make sure to swap the c and the n back or Chimera will add D amino acids forever.  The other thing to keep in mind is that the rotamer libraries are developed for L amino acids and therefore are basically of little assistance in choosing a side chain conformation for D amino acids.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

On Jun 30, 2008, at 10:53 AM, Elaine Meng wrote:

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  
structure.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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
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