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EMAN2 Programs

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

Generic Docs

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

Single Particle Tomography

  • e2tomoboxer.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.

slices_plus_cylinders.png

EMAN2/Programs (last edited 2017-02-14 06:55:40 by SteveLudtke)