On 10:25 Wed 03 Jun , Dirk Kostrewa wrote: > we want to deposit some structures containing amino acids and nucleic > acids, but apparently the nomenclature for nucleic acids has changed. In > former times (PDB version 2.x), there was a complete description for the > PDB nomenclature, but I can't find it anymore for the current PDB version > 3.2 (http://www.wwpdb.org/docs.html)! When I browse through slightly > older description, there is only a hint that the IUPAC nomenclature was > adapted, with a broken link. Is there still an official PDB nomenclature > that I can use to get our structures PDB-conform? I find it strange, that > there seems to be no easily accessible PDB nomenclature description > anymore ...
You might try the Richardson's tool Remediator: <http://kinemage.biochem.duke.edu/software/remediator.php>. It says "Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2)." -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University
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