PDBML

PDBML: XML for PDB

Japanese version:PDBML

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:

• http://www.pdbj.org/schema/pdbx-v40.xsd

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).