[Chimera-users] Mutate by D- res...

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 30 11:05:47 PDT 2008

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 Pettersen
                         UCSF Computer Graphics Lab

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 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
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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