I sent a message to the pdb-l mailing list asking about mapping between .pdb * names and .cif ' names for atoms.
I was hoping for a computer-like 'algorithm' rather than an encyclopedia-like reference to chemistry nomenclature pages. I don't really care how the atoms are named ... I only want a succinct set of rules for turning a * name into a ' name and viceversa. I recieved the response below. I looked at a few pages, and it is more than I can digest. It would be helpful for me if someone with some expertise in the area could look into this, distill it down a bit, and tell me how to map between the * notation of .pdb files and the ' nomenclature of .cif files. Thanks, Miguel ---------------------------- Original Message ---------------------------- Subject: Re: pdb-l: * in .pdb <-> ' in .cif From: "Kim Henrick" <[EMAIL PROTECTED]> Date: Tue, June 15, 2004 12:13 To: "Miguel" <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] -------------------------------------------------------------------------- look at http://www.bmrb.wisc.edu/referenc/aa_chem.html http://www.bmrb.wisc.edu/referenc/nomenclature/ and the references here for atom naming and mappings between pdb and various other naming systems if you go to http://www.ebi.ac.uk/msd-srv/chempdb/ and search for 3-letter code ==> A and display atoms you can get mapping between iupac and pdb or pickup http://www.ebi.ac.uk/msd-srv/docs/cif/peptide.cif http://www.ebi.ac.uk/msd-srv/docs/cif/nuc_comp.cif these files have some of the mappings iupac/pdb however all these mappings are not necessarily exactly what say ccp4 or cns use in house - they may use C1' while deposition changes this to C1* and the mmcif / msd / bmrb dont follow the same left- right- adjustments in pdb format - held as _chem_comp_atom.rcsb_align flag in mmcif - and iupac isnt the same as changing 1H5* into 1H5' - it is rather H5'1 (& H5'2) and mmcif uses H5' (& H5'') for iupac see http://www.chem.qmul.ac.uk/iupac/misc/pnuc1.html#130 see the files in the pdb ftp area under directory data/monomers/ components.cif (PDB names) components_iupac.cif (mmcif iupac names) kim Kim HENRICK [EMAIL PROTECTED] ::telephone: +44 (0) 1223 494629 TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . ------------------------------------------------------- This SF.Net email is sponsored by The 2004 JavaOne(SM) Conference Learn from the experts at JavaOne(SM), Sun's Worldwide Java Developer Conference, June 28 - July 1 at the Moscone Center in San Francisco, CA REGISTER AND SAVE! http://java.sun.com/javaone/sf Priority Code NWMGYKND _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
