EMAN2 Programs

This page is very incomplete, but running any EMAN2 program with the '--help' option will provide documentation for that program.

Generic Docs

• Standard parameters accepted by multiple programs

Important Utilities

• e2proc2d.py - Generic 2-D image processing

• e2proc3d.py - Generic 3-D image processing

• e2bdb.py - Examine and manipulate EMAN2 database files

• e2iminfo.py - Examine image files

• e2display.py - Main program for 2-D and 3-D visualization and interactive manipulation

• e2filtertool.py - A GUI for designing sequences of processors interactively, for filtration, masking, and other operations

High Level Tasks

• e2refine2d.py - 2-D iterative reference-free class-averaging

• e2initialmodel.py - Single particle reconstruction, initial model generation

• e2refine_easy.py - Single particle reconstruction, iterative refinement

• e2refinemulti.py - Single particle reconstruction, iterative, multi-model refinement. Can be used to separate particles into multiple groups.

• e2eotest.py - Single particle reconstruction, resolution assessment

• e2evalrefine.py - Tools for comparing refinement runs and evaluating results

• e2evalparticles.py - GUI tool for evaluating particle quality, and eliminating bad particles.

• e2classifyligand.py - Classify data into two groups based on reference models/masks

• e2rct.py - Random Conical Tilt reconstruction

• e2tiltvalidate.py - Tilt Validation

Programs with a GUI

• e2projectmanager.py - This is the main GUI which will guide you through various specific tasks (like single particle reconstruction)

• e2display.py - Main program for 2-D and 3-D visualization and interactive manipulation

• e2boxer.py - Particle picker for single particle analysis

• e2ctf.py - Contrast transfer estimation and correction

• e2eulerxplor.py - Display particle orientation distribution from e2refine.py results

• e2evalparticles.py - GUI tool for evaluating particle quality, and eliminating bad particles.

• e2evalimage.py - Tool for interactive evaluation of micrography quality. Can open large sets of image, perform CTF evaluation, compute 2-D unit-cells, etc.

• e2filtertool.py - A GUI for designing sequences of processors interactively, for filtration, masking, and other operations

• e2helixboxer.py - Selection tool for helical objects

• e2RCTboxer.py - Particle picker for focal pairs

• e2simmxxplor.py - Display classification similarity metrics for individual particles

Interacting with Other Software

• Frealign

  • e2refinetofrealign.py - Use an EMAN2 refinement result to set up all necessary files to start a Frealign refinement.

  • e2runfrealign.py - Execute Frealign based on the results of e2refinetofrealign.

  • e2refinefromfrealign.py - Collect the results from a standard Frealign run and re-interpret in EMAN2 terms.

• Relion

  • e2refinetorelion2d.py - Use Relion to perform maximum likelihood 2D Class Averaging.

  • e2refinetorelion3d.py - Use an EMAN2 refinement result to set up all necessary files to perform a Relion refinement.

Single Particle Tomography

• e2spt_boxer.py - Tomographic particle picker.

• e2classaverage3d.py - Tomographic class-averager. Will align and average stacks of (optionally classified) 3-D particles.

Low Level Tasks

• e2scannereval.py - Tool to look for scanner artifacts (film) or localized distortions (CCD frames)

• e2classaverage.py - Generate 2-D class-averages from sets of classified particles

• e2classextract.py - Extract particles associated with class-averages in various ways

• e2ctf.py - Contrast transfer function estimation and correction

• e2make3d.py - Reconstruct a 3-D map from a set of 2-D projections/class-averages

• e2project3d.py - Generate 2-D projections from 3-D maps

• e2simmx.py - Compute exhaustive similarity comparison between set of particles and references

• e2simmx2stage.py - More efficient version of e2simmx.py (not exhaustive)

Experimental Programs

• examples/tomotrackbox.py - This tomography program will allow you to individually reconstruct particles or sections from an aligned tilt series, and play with various options.

New Documentation (Work In Progress)

• new_docs - New docs extracted from programs' parsers.