== EMAN2 Concepts and Conventions ==

 * [[EMAN2/ProjectDatabase|Projects, e2desktop.py and the database]]
 * [[EMAN2/BoxSize|Particle box-size and refinement speed, what size to use]]
 * [[EMAN2/Symmetry|EMAN2 and the asymmetric unit]]
 * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]]
 * [[EMAN2/CtfModel|CTF model used in EMAN2]]
 * [[Eman2TransformInPython|Transformations in the context of projections, reconstructions, and in general]]
 * [[EMAN2/AlignersDescription|More information regarding the aligners]]
 * [[Eman2Metadata|Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr]]
 * [[Eman2AppMetadata|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 ===
This documents the contents of all of the files produced by running e2refine.py in one of the refine_xx directories.
 * [[EMAN2/ProjectionFiles|Map projection files (projections_xx, proj_stg1_xx)]]
 * [[EMAN2/SimmxFiles|Similarity matrix image files (simmx_xx, simmx_stg1_xx, proj_simmx_xx)]]
 * [[EMAN2/ClassmxFiles|Classification matrix image files (classify_xx)]]
 * [[EMAN2/ClsResultFiles|Class-Averaging Results matrix image files (cls_result_xx)]]
 * [[EMAN2/ThreedFiles|3-D reconstructions (threed_xx, threed_filt_xx, threed_mask_xx)]]

{{attachment:single_image_iso_c.png}}