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

Information on specific input/output files for different EMAN2 programs

For Single Particle Analysis (SPA)

For SPA refinement (single model - e2refine_easy.py and multimodel - e2refinemulti.py)

Input files:

Output files (in temporal order of creation), _xx denotes the iteration number:

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. Don't be shy about posting to the Google Group for help!

Particle quality assessment

The program e2evalrefine.py --evalptclqual is normally used to assess the quality of individual particles after running e2refine_easy. This produces a file in the Project Folder called ptclfsc_XX.txt where XX is the number of the refine_XX folder. This file is a multicolumn text file with the following contents. It can be displayed with e2display --plot :

For SPA 2-D reference-free class-averaging (e2refine2d.py)

You may also wish to look at: e2refine2d Input files:

Output files:

For Single Particle Tomography (SPT, "subtomogram averaging")

Single stage alignment of subtomograms to a reference (e2spt_align.py)

Output Files:

For SPT initial model generation by hierarchical ascendant classification (HAC, e2spt_hac.py)

For SPT initial model generation by binary tree alignment (BTA, e2spt_binarytree.py)

For SPT initial model generation by self symmetry alignment (SSA, e2symsearch3d.py)

For SPT iterative refinement runs (e2spt_classaverage.py)

Input files:

Output files:

For SPT multiple model refinement (e2spt_refinemulti.py)

EMAN2/ProgramFiles (last edited 2017-02-18 21:07:08 by SteveLudtke)