Differences between revisions 44 and 45
Revision 44 as of 2010-11-24 15:19:50
Size: 3382
Editor: SteveLudtke
Revision 45 as of 2010-12-20 21:42:39
Size: 3388
Editor: SteveLudtke
Deletions are marked like this. Additions are marked like this.
Line 6: Line 6:

== Generic Docs ==
 * [[StandardParms|Standard parameters accepted by multiple programs]]
Line 45: Line 48:
== Generic Docs ==
 * [[StandardParms|Standard parameters used in multiple programs]]

EMAN2 Programs


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

Generic Docs

Important Utilities

High Level Tasks

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

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

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

  • e2refine.py - Single particle reconstruction, iterative refinement

  • e2eotest.py - Single particle reconstruction, resolution assessment

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

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

Programs with a GUI

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

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

  • e2boxer.py - Particle picker for single particle analysis

  • e2helixboxer.py - Selection tool for helical objects

  • e2ctf.py - Contrast transfer estimation and correction

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

  • e2simmxxplor.py - Display classification similarity metrics for individual 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

  • 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.


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