The PDBx/mmCIF format is modified format based on CIF (a file format used to describe crystal structures) and has been adapted for macromolecules. Both PDBx/mmCIF as well as CIF are based on the STAR format. The PDBx/mmCIF format will become the default PDB format from 2014.
The PDBx/mmCIF dictionary is available from following URL:
An ASCII file format consisting of 80 columns also called the "flat-file" format. Although it is the format that has been used since the inception of the PDB (albeit analogue), due to it's inherit limitations it has been deprecated in favour of the PDBx/mmCIF format. Some of the structures already have no flat file version available. It will be phased out from 2016.
- See PDB Format for details.
PDBML is the canonical XML format of PDB entries adapted from the PDBx/mmCIF specification and originally-introduced in the following publication:
The schema file which defines the PDBML data description rules is available via following URL:
There are 3 variants on the standard PDBML format:
Currently, the PDB data commonly provided by each wwPDB partner doesn't include detailed functional and experimental information.
PDBj however has collected such additional information and provides it in an XML format named PDBMLadd.
Previously we had developed a PDBML variant which had the additional information integrated with the regular PDBML-noatom information, making it incompatible with the official PDBML specification. Recently we deprecated this version of the PDBMLplus format and replaced it with a format which separately defines the additional content as an extensions to the original PDBML specification. The additional content is stored in a new format called PDBMLadd and is available from our ftp site, as well as on the download pages of each individual entries. Users who want to download the combined data (PDBML and PDBMLadd) can download the combined entry via the individual entry pages, or use the appropriate REST service. It is of course also possible to download the entries separately and afterwards combine them.
The NMR restraints file is mandatory for NMR structures deposited after February 1, 2008. For more details, please see the main page on the NMR restraints files.
[NMR Chemical shift]
The NMR chemical shift file is mandatory for NMR structures deposited after December 6, 2010. For more details, please see the main page on the Chemical shift files.
Stores structure factors amplitudes/intensities in mmCIF format.
The structure factors file is mandatory for X-ray diffraction structures deposited after February 1, 2008.
For more details, please see the main page on Structure factors files.
- See wwPDB/RDF for details.
PDB data (noatom) is also available in RDF (Resource Description Framework) format. The RDF files are automatically generated from PDBML files using an XSLT transform script. The ontology has also been defined based on the PDB mmCIF Exchange Dictionary. An RDF file is available for each PDB entry. For example, the RDF data for PDB entry 1GOF is accessible at https://rdf.wwpdb.org/pdb/1GOF.