Compatibility with PDB format files

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 192-193

Section 3.6.8.3.2. Compatibility with PDB format files

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^a Merck Research Laboratories, Rahway, New Jersey, USA,^bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,^cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,^dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,^eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and ^fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.8.3.2. Compatibility with PDB format files

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Data items in these categories are as follows:

(a) DATABASE_PDB_REV [Scheme scheme193]

(b) DATABASE_PDB_REV_RECORD [Scheme scheme194]

(d) DATABASE_PDB_TVECT [Scheme scheme196]

(e) DATABASE_PDB_CAVEAT [Scheme scheme197]

(f) DATABASE_PDB_REMARK [Scheme scheme198]

The bullet ( $[\bullet]$ ) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

A major goal of the design of the mmCIF data model was that a file could be transformed from Protein Data Bank (PDB) format to mmCIF format and back again without loss of information. This required the creation of mmCIF data items whose sole purpose is to capture PDB-specific records that do not map onto mmCIF data items. These records would never be created for a de novo mmCIF. This family of categories also belongs to the PDB category group (see Section 3.6.9.3).

The items in the categories DATABASE_PDB_MATRIX and DATABASE_PDB_TVECT are derived from the elements of transformation matrices and vectors used by the Protein Data Bank. The items in the categories DATABASE_PDB_REV and DATABASE_PDB_REV_RECORD record details about the revision history of the data block as archived by the Protein Data Bank.

The items in the DATABASE_PDB_CAVEAT category record comments about the data block flagged as `CAVEATS' by the Protein Data Bank at the time the original PDB archive file was created. A PDB CAVEAT record indicates that the entry contains severe errors. In PDB format, extended comments were stored as a sequence of fixed-length (80-character) format records, columns 9 and 10 being reserved for continuation sequence numbering. The mmCIF representation retains each record as a separate data value and does not attempt to merge continuation records to provide more readable running text. Hence the PDB CAVEAT entry [Scheme scheme199] would be represented in mmCIF as [Scheme scheme200]

The PDB format used `REMARK' records to store information relating to several aspects of the structure in free or loosely structured text. In some cases, the conventions used for individual types of REMARK record allow structured data to be extracted automatically and translated to specific mmCIF data items. Where this is not possible, the DATABASE_PDB_REMARK category may be used to retain the information that appeared in these parts of PDB format files. Unlike the CAVEAT records, it is possible to collect together several REMARK records sharing a common numbering into a single free-text field. For example, PDB practice has been to repeat the contents of CAVEAT records (see above) as records of type `REMARK 5'. While each separate CAVEAT record is converted to a separate mmCIF data value, the complete text of a REMARK 5 record may be gathered into a single mmCIF data value. Hence the CAVEAT example above would also appear in a PDB file as part of a `REMARK 5' as [Scheme scheme201] and would appear in an mmCIF as [Scheme scheme202]

Note that by convention the value of _database_PDB_remark.id matches the class of the REMARK record in the PDB file.

References

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 192-193