[Chimera-users] D-amino acids

[Elaine Meng]

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 at 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
>