Hi Francesco, I myself haven't used molecular mechanics packages separate from Chimera for a while, but it sounds fine to use them to do any building, then open the result in Chimera. It should work if the PDB or Mol2 files they make are reasonably correct. The only thing to do is just try it -- probably details are different for the different programs. Otherwise I don't have anything to add to my previous reply -- what I said about Chimera is still true. Best, Elaien ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 6, 2009, at 11:07 AM, Francesco Pietra wrote:
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 structure.
I hope this helps, Elaine ----- 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 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 ================================
What about doing that with a molecular mechanics package? Most such packages have the capability of enantiomerize. Then, back to Chimera. Your view?
thanks
francesco pietra