EMAN2 Concepts and Conventions
File Formats, Data storage conventions, and the internal database (what is BDB: ?)
Transformations in the context of projections, reconstructions, and in general
Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project
Information on specific files used in 3-D single particle refinement
Similarity matrix image files (simmx_xx, simmx_stg1_xx, proj_simmx_xx)
3-D reconstructions (threed_xx, threed_filt_xx, threed_mask_xx)