EMAN2 Programs

UNDER CONSTRUCTION - Seriously. We are adding to the detailed docs every week. If you don't see what' you're looking for, please email us and ask, and we'll move it up in the queue.

Note that running any EMAN2 program with the '--help' option will provide basic 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

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

• 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

• 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

• e2workflow.py - The GUI workflow interface. Suggested for all reconstruction projects.

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

• 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.