EMAN2 Output Files

This page documents all of the various files produced by various tasks and workflows in EMAN2. While the format of the actual files will be one of the standard EMAN2 supported image formats in most cases, these pages will explain the contents of files with specific standard names.

General File Information

• File formats & data storage conventions

• Parameters/Metadata appearing in EMData attributes (and stored on disk with the image)

Information on specific output files in 3-D single particle refinement runs (e2refine_easy.py and e2refinemulti.py)

This section documents the contents of all of the files produced by running e2refine.py in one of the refine_xx directories. This listing is in the order that the files are created.

• projections_xx.hdf, proj_stg1_xx.hdf - Map projection files

• simmx_xx.hdf, simmx_stg1_xx.hdf, proj_simmx_xx.hdf - Similarity matrix image files

• classify_xx.hdf - Classification matrix image files

• cls_result_xx.hdf - Class-Averaging Results matrix image files

• classes_xx.hdf - Class-averages

• threed_even_unmasked.hdf, threed_odd_unmasked.hdf - Reconstructions from the final completed iteration without masking or final filtration, suitable for use with ResMap

• threed_xx.hdf, threed_filt_xx.hdf, threed_mask_xx.hdf - 3-D reconstructions

If you are struggling with a failed refinement, look at the produced files in this order until you find something unexpected, and that may give some clues as to what went wrong.

Information on specific output files from 2-D reference-free class-averaging (e2refine2d.py)

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 and aligned) to be used for the current iteration. Other than sorting/alingment, same as classes_XX files

• 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