Differences between revisions 40 and 41
Revision 40 as of 2010-09-14 12:31:01
Size: 2050
Editor: SteveLudtke
Comment:
Revision 41 as of 2010-09-14 12:37:19
Size: 3111
Editor: SteveLudtke
Comment:
Deletions are marked like this. Additions are marked like this.
Line 3: Line 3:
Note that unning any EMAN2 program with the '--help' option will provide basic documentation for that program. Note that running any EMAN2 program with the '--help' option will provide basic documentation for that program.
Line 14: Line 14:
 * [[EMAN2/Programs/e2workflow|e2refine2d.py]]
 * [[EMAN2/Programs/e2workflow|e2initialmodel.py]]
 * [[EMAN2/Programs/e2workflow|e2refine.py]]
 * [[EMAN2/Programs/e2workflow|e2eotest.py]]
 * [[EMAN2/Programs/e2workflow|e2evalrefine.py]]
 * [[EMAN2/Programs/e2workflow|e2classifyligand.py]]
 * [[EMAN2/Programs/e2workflow|e2refine2d.py]] - 2-D iterative reference-free class-averaging
 * [[EMAN2/Programs/e2workflow|e2initialmodel.py]] - Single particle reconstruction, initial model generation
 * [[EMAN2/Programs/e2workflow|e2refine.py]] - Single particle reconstruction, iterative refinement
 * [[EMAN2/Programs/e2workflow|e2eotest.py]] - Single particle reconstruction, resolution assessment
 * [[EMAN2/Programs/e2workflow|e2evalrefine.py]] - Tools for comparing refinement runs and evaluating results
 * [[EMAN2/Programs/e2workflow|e2classifyligand.py]] - Classify data into two groups based on reference models/masks
Line 24: Line 24:
 * [[EMAN2/Programs/e2boxer|e2boxer.py]]
 * [[EMAN2/Programs/e2helixboxer|e2helixboxer.py]]
 * [[EMAN2/Programs/e2boxer|e2ctf.py]]
 * [[EMAN2/Programs/e2helixboxer|e2eulerxplor.py]]
 * [[EMAN2/Programs/e2helixboxer|e2simmxxplor.py]]
 * [[EMAN2/Programs/e2boxer|e2boxer.py]] - Particle picker for single particle analysis
 * [[EMAN2/Programs/e2helixboxer|e2helixboxer.py]] - Selection tool for helical objects
 * [[EMAN2/Programs/e2boxer|e2ctf.py]] - Contrast transfer estimation and correction
 * [[EMAN2/Programs/e2helixboxer|e2eulerxplor.py]] - Display particle orientation distribution from e2refine.py results
 * [[EMAN2/Programs/e2helixboxer|e2simmxxplor.py]] - Display classification similarity metrics for individual particles
Line 32: Line 32:
 * [[EMAN2/Programs/e2scannereval|e2scannereval.py]]
 * [[EMAN2/Programs/e2classaverage|e2classaverage.py]]
 * [[EMAN2/Programs/e2ctf|e2ctf.py]]
 * [[EMAN2/Programs/e2make3d|e2make3d.py]]
 * [[EMAN2/Programs/e2project3d|e2project3d.py]]
 * [[EMAN2/Programs/e2simmx2stage|e2simmx.py]]
 * [[EMAN2/Programs/e2simmx2stage|e2simmx2stage.py]]
 * [[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/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/e2simmx2stage|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)

EMAN2 Programs

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

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)

Generic Docs

slices_plus_cylinders.png

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