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PDB FILE FORMATS, ANNOTATION PROCEDURES, AND REMEDIATION Regarding recent discussions about the PDB the following notes are made from the wwPDB partners * PDB File Formats Entries in PDB format comply with the PDB Contents Guide v2.3 (July 1998). Entries in mmCIF format comply with the PDB Exchange Dictionary v1.037 (January 2007). Entries in XML format comply with the PDBML Schema v1.037 (January 2007). Documentation for these formats is available at http://www.wwpdb.org/docs.html * Annotation Procedures There are some data items for which the processing procedures are ambiguous. Over the course of the last 12 months the annotation teams at the wwPDB deposition sites have worked to formalize many aspects of PDB annotation policies and procedures. As a result, a consistent set of annotation procedures are being defined. Documentation for annotation procedures and policies is available at http://www.wwpdb.org/docs.html * Remediation All existing entries have been reviewed and errors have been corrected where possible. One major change is that the atomic names will conform to IUPAC standards. In addition, the chemical component dictionary has been updated and extended to include more information about the chemical structures of each component. The wwPDB Advisory Committee has reviewed and approved this effort. Remediation project information is available at http://remediation.wwpdb.org/. Please consult this site to review test data files and the new dictionary. The full new data set in PDB, mmCIF and XML formats will become available for review in April 2007. For the wwPDB partners, Helen Berman (RCSB PDB) Haruki Nakamura (PDBj) Kim Henrick (EBI) John Markley (BMRB)
