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== Generic Docs ==
 * [:StandardParms:Standard parameters used in multiple programs]
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 * e2scannereval.py
 * e2proc2d.py
 * e2proc3d.py
 * e2display.py
 * [:e2classaverage:e2classaverage.py]
 * [:e2fileinfo:e2fileinfo.py]
 * [:e2make3d:e2make3d.py]
 * [:e2project3d:e2project3d.py]
 * [:e2refine:e2refine.py]
'''This page is very incomplete, but running any EMAN2 program with the '--help' option will provide documentation for that program.'''

== Generic Docs ==
 * [[StandardParms|Standard parameters accepted by multiple programs]]

=== Important Utilities ===
 * [[EMAN2/Programs/e2proc2d|e2proc2d.py]] - Generic 2-D image processing
 * [[EMAN2/Programs/e2proc3d|e2proc3d.py]] - Generic 3-D image processing
 * [[EMAN2/Programs/e2bdb|e2bdb.py]] - Examine and manipulate EMAN2 database files
 * [[EMAN2/Programs/e2iminfo|e2iminfo.py]] - Examine image files
 * [[EMAN2/Programs/e2display|e2display.py]] - Main program for 2-D and 3-D visualization and interactive manipulation
 * [[EMAN2/Programs/e2filtertool|e2filtertool.py]] - A GUI for designing sequences of processors interactively, for filtration, masking, and other operations

=== High Level Tasks ===
 * [[EMAN2/Programs/e2refine2d|e2refine2d.py]] - 2-D iterative reference-free class-averaging
 * [[EMAN2/Programs/e2initialmodel|e2initialmodel.py]] - Single particle reconstruction, initial model generation
 * [[EMAN2/Programs/e2refine_easy|e2refine_easy.py]] - Single particle reconstruction, iterative refinement
 * [[EMAN2/Programs/e2refinemulti|e2refinemulti.py]] - Single particle reconstruction, iterative, multi-model refinement. Can be used to separate particles into multiple groups.
 * [[EMAN2/Programs/e2eotest|e2eotest.py]] - Single particle reconstruction, resolution assessment
 * [[EMAN2/Programs/e2evalrefine|e2evalrefine.py]] - Tools for comparing refinement runs and evaluating results
 * [[EMAN2/Programs/e2evalparticles|e2evalparticles.py]] - GUI tool for evaluating particle quality, and eliminating bad particles.
 * [[EMAN2/Programs/e2classifyligand|e2classifyligand.py]] - Classify data into two groups based on reference models/masks
 * [[EMAN2/Programs/e2rct|e2rct.py]] - Random Conical Tilt reconstruction
 * [[EMAN2/Programs/e2tiltvalidate.py|e2tiltvalidate.py]] - Tilt Validation

=== Programs with a GUI ===
 * [[EMAN2/Programs/e2projectmanager|e2projectmanager.py]] - This is the main GUI which will guide you through various specific tasks (like single particle reconstruction)
 * [[EMAN2/Programs/e2display|e2display.py]] - Main program for 2-D and 3-D visualization and interactive manipulation
 * [[EMAN2/Programs/e2boxer|e2boxer.py]] - Particle picker for single particle analysis
 * [[EMAN2/Programs/e2ctf|e2ctf.py]] - Contrast transfer estimation and correction
 * [[EMAN2/Programs/e2eulerxplor|e2eulerxplor.py]] - Display particle orientation distribution from e2refine.py results
 * [[EMAN2/Programs/e2evalparticles|e2evalparticles.py]] - GUI tool for evaluating particle quality, and eliminating bad particles.
 * [[EMAN2/Programs/e2evalimage|e2evalimage.py]] - Tool for interactive evaluation of micrography quality. Can open large sets of image, perform CTF evaluation, compute 2-D unit-cells, etc.
 * [[EMAN2/Programs/e2filtertool|e2filtertool.py]] - A GUI for designing sequences of processors interactively, for filtration, masking, and other operations
 * [[EMAN2/Programs/e2helixboxer|e2helixboxer.py]] - Selection tool for helical objects
 * [[EMAN2/Programs/e2RCTboxer|e2RCTboxer.py]] - Particle picker for focal pairs
 * [[EMAN2/Programs/e2simmxxplor|e2simmxxplor.py]] - Display classification similarity metrics for individual particles

=== Interacting with Other Software ===
 * Frealign
  * [[EMAN2/Programs/e2refinetofrealign|e2refinetofrealign.py]] - Use an EMAN2 refinement result to set up all necessary files to start a Frealign refinement.
  * [[EMAN2/Programs/e2runfrealign|e2runfrealign.py]] - Execute Frealign based on the results of e2refinetofrealign.
  * [[EMAN2/Programs/e2refinefromfrealign|e2refinefromfrealign.py]] - Collect the results from a standard Frealign run and re-interpret in EMAN2 terms.
 * Relion
  * [[EMAN2/Programs/e2refinetorelion2d|e2refinetorelion2d.py]] - Use Relion to perform maximum likelihood 2D Class Averaging.
  * [[EMAN2/Programs/e2refinetorelion3d|e2refinetorelion3d.py]] - Use an EMAN2 refinement result to set up all necessary files to perform a Relion refinement.
 *

=== Single Particle Tomography ===
 * [[EMAN2/Programs/e2tomoboxer|e2spt_boxer.py]] - Tomographic particle picker.
 * [[EMAN2/Programs/e2classaverage3d|e2classaverage3d.py]] - Tomographic class-averager. Will align and average stacks of (optionally classified) 3-D particles.

=== Low Level Tasks ===
 * [[EMAN2/Programs/e2scannereval|e2scannereval.py]] - Tool to look for scanner artifacts (film) or localized distortions (CCD frames)
 * [[EMAN2/Programs/e2classaverage|e2classaverage.py]] - Generate 2-D class-averages from sets of classified particles
 * [[EMAN2/Programs/e2classextract|e2classextract.py]] - Extract particles associated with class-averages in various ways
 * [[EMAN2/Programs/e2ctf|e2ctf.py]] - Contrast transfer function estimation and correction
 * [[EMAN2/Programs/e2make3d|e2make3d.py]] - Reconstruct a 3-D map from a set of 2-D projections/class-averages
 * [[EMAN2/Programs/e2project3d|e2project3d.py]] - Generate 2-D projections from 3-D maps
 * [[EMAN2/Programs/e2simmx|e2simmx.py]] - Compute exhaustive similarity comparison between set of particles and references
 * [[EMAN2/Programs/e2simmx2stage|e2simmx2stage.py]] - More efficient version of e2simmx.py (not exhaustive)

=== Experimental Programs ===
 * [[EMAN2/Programs/tomotrackbox|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.

{{attachment:slices_plus_cylinders.png}}

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

  • 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.

slices_plus_cylinders.png

EMAN2/Programs (last edited 2018-04-25 00:59:47 by TunayDurmaz)