Differences between revisions 48 and 65 (spanning 17 versions)
Revision 48 as of 2011-03-21 12:48:48
Size: 4173
Editor: SteveLudtke
Comment:
Revision 65 as of 2018-04-25 00:59:47
Size: 5841
Editor: TunayDurmaz
Comment: new docs
Deletions are marked like this. Additions are marked like this.
Line 3: Line 3:
''UNDER CONSTRUCTION''

N
ote that running any EMAN2 program with the '--help' option will provide basic documentation for that program.
'''This page is very incomplete, but running any EMAN2 program with the '--help' option will provide documentation for that program.'''
Line 16: Line 14:
 * [[EMAN2/Programs/e2filtertool|e2filtertool.py]] - A GUI for designing sequences of processors interactively, for filtration, masking, and other operations
Line 18: Line 17:
 * [[EMAN2/Programs/e2workflow|e2workflow.py]] - The GUI workflow interface. Suggested for all reconstruction projects.
Line 21: Line 19:
 * [[EMAN2/Programs/e2refine|e2refine.py]] - Single particle reconstruction, iterative refinement  * [[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.
Line 24: Line 23:
 * [[EMAN2/Programs/e2evalparticles|e2evalparticles.py]] - GUI tool for evaluating particle quality, and eliminating bad particles.
Line 25: Line 25:
 * [[EMAN2/Programs/e2rct|e2rct.py]] - Random Conical Tilt reconstruction
 * [[EMAN2/Programs/e2tiltvalidate.py|e2tiltvalidate.py]] - Tilt Validation
Line 27: Line 29:
 * [[EMAN2/Programs/e2workflow|e2workflow.py]] - The GUI workflow interface. Suggested for all reconstruction projects.  * [[EMAN2/Programs/e2projectmanager|e2projectmanager.py]] - This is the main GUI which will guide you through various specific tasks (like single particle reconstruction)
Line 30: Line 32:
 * [[EMAN2/Programs/e2helixboxer|e2helixboxer.py]] - Selection tool for helical objects
Line 33: Line 34:
 * [[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
Line 40: Line 46:
 * XMIPP
 * IMOD
 * 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.
 *
Line 44: Line 52:
 * [[EMAN2/Programs/e2tomoboxer|e2tomoboxer.py]] - Tomographic particle picker.  * [[EMAN2/Programs/e2tomoboxer|e2spt_boxer.py]] - Tomographic particle picker.
Line 50: Line 58:
 * [[EMAN2/Programs/e2classextract|e2classextract.py]] - Extract particles associated with class-averages in various ways
Line 57: Line 66:
 * [[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.   * [[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.

=== New Documentation (Work In Progress) ===
 * [[EMAN2/Programs/new_docs|new_docs]] - New docs extracted from programs' parsers.

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.

New Documentation (Work In Progress)

  • new_docs - New docs extracted from programs' parsers.

slices_plus_cylinders.png

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