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. > -------------------------------------------------------------------------- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Ian Clifton > Sent: 09 January 2013 12:44 > To: [email protected] > 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 ◎
