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EMAN2 Concepts and Conventions

Modular functions in EMAN2

Many aspects of EMAN2 are modular, meaning new functions can be easily added for a variety of tasks. These categories are used in the GUI and from the command-line, and are not just useful for programmers. For example, the '--process' option in and uses 'processors' as defined below.

  • Overview of how to use modular functions

  • Processors - Filters, masks and other basic image processing operations

  • Comparators (cmp) - Similarity metrics (cmp) for comparing two images/volumes

  • Aligners - Algorithms for aligning one image/volume to another

  • Averagers - Methods for averaging many images/volumes together

  • Projectors - Generate 2-D projections of 3-D volumes (or 1-D projections of 2-D images)

  • Reconstructors - Generate 3-D volumetric reconstructions from sets of 2-D images and orientation paramters

  • Analyzers - Perform various analyses on sets of images/volumes

  • Symmetries - Permissible symmetries to use in EMAN2

  • 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 in one of the refine_xx directories.

Information on specific files used in 2-D reference-free class-averaging

You may also wish to look at: e2refine2d

  • input_fp - rotational/translational invariants for each particle

  • input_fp_basis - MSA basis vectors (images) from input_fp

  • input_fp_basis_proj - MSA subspace projections of the input_fp invariants

  • classmx_00 - Initial classification of particles, same format as classmx above

  • classes_init - Initial set of class-averages from invariant method (not very good usually)

  • allrefs_XX - All of the references (sorted) to be used for the current iteration

  • basis_XX - MSA basis from allrefs_xx

  • aliref_XX - Subset of allrefs used for alignment of raw particles

  • simmx_XX - Similarity matrix in same format as simmx above

  • input_XX_proj - Aligned particles projected into basis_XX subspace

  • classmx_XX - Classification matrix for the current iteration (as above)

  • classes_XX - Class averages at the end of the iteration. The highest numbered classes_XX file is the final output of the program