== 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: ?)]]
 * [[Eman2NFS|Practical Advice on EMAN2 in environments with network-shared directories (like NFS)]]
 * [[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]]

=== Modular classes in EMAN2 ===
 * [[EMAN2/Modular/Processors|Processors]] - Filters, masks and other basic image processing operations
 * [[EMAN2/Modular/Cmps|Comparators]] (cmp) - Similarity metrics (cmp) for comparing two images/volumes
 * [[EMAN2/Modular/Aligners|Aligners]] - Algorithms for aligning one image/volume to another
 * [[EMAN2/Modular/Averagers|Averagers]] - Methods for averaging many images/volumes together
 * [[EMAN2/Modular/Projectors|Projectors]] - Generate 2-D projections of 3-D volumes (or 1-D projections of 2-D images)
 * [[EMAN2/Modular/Reconstructors|Reconstructors]] - Generate 3-D volumetric reconstructions from sets of 2-D images and orientation paramters
 * [[EMAN2/Modular/Analyzers|Analyzers]] - Perform various analyses on sets of images/volumes
 * [[EMAN2/Modular/Symmetries|Symmetries]] - Permissible symmetries to use in EMAN2
 * [[EMAN2/Modular/OrientGens|Orientation Generators]] (orientgen) - Methods for generating sets of orientations filling an asymmetric unit

=== Information on specific files used in 3-D single particle refinement ===
This section 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/ClassesFiles|Class-averages (classes_xx)]]
 * [[EMAN2/ThreedFiles|3-D reconstructions (threed_xx, threed_filt_xx, threed_mask_xx)]]

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