Your solution sounds good. However, another way to skin this cat could be to define the unnatural residue as an amino acid residue and link it up to the other amino acid residues using the standard peptide bond description -- which, I believe, should be picked up automatically if the unconventional residue is defined as D-peptide in the _chem_comp.group in the cif dictionary file and has its backbone atoms named conventionally (or defining a TRANS link in the pdb file should fix that), i.e treat the ligand as a polypeptide chain with a nonconventional residue in it. Might be more fiddly to start with but cleaner on the long run?
As for the text editing solution: JLigand seems to be the fashionable tool of choice for defining links between residues these days.
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-----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Ian Clifton
> Sent: 09 January 2013 12:44
> To: [log in to unmask]
> Subject: [ccp4bb] How to make an unnatural amino acid ligand?
>
> I need to make dictionaries for a ligand that includes an unnatural
> amino acid (D chirality, and unnatural side‐chain) amongst a short
> sequence of natural amino acids. Sounds easy, but how to do it? I’m
> thinking of first making my unnatural amino acid in isolation, then
> using an editor to fix up the generated dictionaries to have the
> correct
> partial charges etc. for the main‐chain atoms, using standard
> dictionary
> entries as a template. Is there a better or sounder way to do it?
>
> Thanks,
> --
> Ian ◎
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