2017-01-18 : 4464 EMDB map entries, 1427 PDB coordinate entries PDBe | RCSB    

One-stop shop for 3DEM deposition and retrieval


Announcement: EMDB header format update

On 16 January 2013, the EMDB archive plans to adopt an updated format, v.1.9.0, for the entry header file (XML file associated with each map). This means that EMDB header files distributed from wwPDB partner sites will conform to the 1.9.0 format, and EMDataBank deposition/annotation/search services will start using this format.

We are announcing this planned change in advance so that developers can make any necessary modifications to software/services that make use of EMDB header files. Please contact us at help@emdatabank.org with any questions or concerns.

The candidate schema is available for download here: ftp://ftp.ebi.ac.uk/pub/databases/emdb/doc/XML-schemas/Header-schema/current/emdb.xsd. A complete list of changes can be found at the beginning of the schema file.

v. 1.9.0 EMDB xml schema highlights:
  • Two new descriptors 'method' and 'specimen state' allow a map to be separately defined by both its specimen state and reconstruction methodology. These replace 'aggregation state' descriptor of v.1.8 and earlier schema versions, which mixed this information and did not permit, e.g., tomography on 2D crystals or subtomogram averaging on helical samples.
  • The methodology descriptor now explicitly includes tomography and subtomogram averaging as enumeration values.
  • Obsolete/supersede entry information is now provided.