A number of changes are being proposed to the existing data format. We are presenting these changes here for consideration. In accordance with PDB's Format Change Policy (http://www.pdb.bnl.gov/format_change_policy.html), there will be an open sixty-day discussion period during which we will entertain comments and suggestions regarding these changes. Send comments to Enrique Abola (abola1@bnl.gov) or to Nancy Manning (oeder@bnl.gov). Discussion on the PDB Listserver is encouraged as well.
Changes being proposed here, if adopted, will not appear in released entries before March 31, 1997. A public announcement will be made some weeks prior to their appearance in released entries.
Methylene hydrogen atoms will be labeled as 2HX and 3HX where X is the remoteness indicator of the atom. For example, hydrogen atoms attached to C beta of an amino acid will be named 2HB and 3HB. Our current convention is to name these 1HB and 2HB. This change will make PDB more compliant with IUPAC recommendations.
The use of the shortened Hermann-Mauguin symbol for monoclinic crystals will be reinstated. This will be applied to crystals in the standard b-unique cell setting. Thus the space group symbol P 21 will be used instead of P 1 21 1. Crystals using other settings will be designated with the full international Hermann-Mauguin symbol (e.g., P 21 1 1).
Modified nucleic acids will be represented using the same rules that are used by the PDB for representing modified amino acids. We will assign a unique three-letter code for modified residues. For example, we will use BRU for brominated uridine rather than +U. In addition, all atoms belonging to the residue will be grouped together in the coordinate records. Our current practice is to list atoms that modify nucleotides after the TER record.