EMDB Map Format

The EM Data Bank (EMDB) accepts and distributes 3D map volumes derived from several types of EM reconstruction methods, including single particle averaging, helical averaging, 2D crystallography, and tomography. Since its inception in 2002, the EMDB map distribution format has followed CCP4 definition, which is widely recognized by software packages used by the structural biology community. CCP4 map format is closely related to the MRC map format used in the 3DEM community; CCP4 is slightly more restrictive, in that voxel positions are limited to a grid that includes the Cartesian coordinate origin (0,0,0).

In July 2010, all 765 released EMDB maps were remediated to improve the uniformity of CCP4 format header parameters across the archive, including correction of density statistics and voxel dimensions. The CCP4 map format description is reproduced here along with the operational implementation for 3DEM map volumes employed in the remediation effort.