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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