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PDBML is the canonical XML format for the PDB data which was first introduced in the following article:

PDBML: the representation of archival macromolecular structure data in XML.
Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM.
Bioinformatics, 2005, 21(7):988-992. PubMed:15509603 full text

The schema file to define PDBML data description rule is available from following URL:

And can also be viewed using our interactive XML viewer.

The file name of a PDBML file is pdbid.xml. For example, 1a00.xml, 1gof.xml, etc. These files are also called ”all” files since it contains all data.

There are variants of PDBML files called ”noatom” and ”extatom” files which are described in the following pages:

  • PDBML-noatom In short, ”noatom” files are PDBML files without the atom_site category (i.e., no atomic coordinates).
  • PDBML-extatom In short, ”extatom” files contain only atomic coordinates and related information, but in a more concise format than the atom_site element of PDBML. This is similar to the ”ATOM” lines of the classical PDB format (but not exactly the same).
2012-07-13 (last edited: 4 months ago)2016-11-16
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