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| * [[EMAN2/Programs/e2scannereval|e2scannereval.py]] * [[EMAN2/Programs/e2boxer|e2boxer.py]] * [[EMAN2/Programs/e2boxer2|e2boxer2.py]] * [[EMAN2/Programs/e2classaverage|e2classaverage.py]] * [[EMAN2/Programs/e2ctf|e2ctf.py]] * [[EMAN2/Programs/e2desktop|e2desktop.py]] * [[EMAN2/Programs/e2display|e2display.py]] * [[EMAN2/Programs/e2eulerxplor|e2eulerxplor.py]] * [[EMAN2/Programs/e2fileinfo|e2fileinfo.py]] * [[EMAN2/Programs/e2flick|e2flick.py]] * [[EMAN2/Programs/e2make3d|e2make3d.py]] * [[EMAN2/Programs/e2project3d|e2project3d.py]] * [[EMAN2/Programs/e2refine|e2refine.py]] * [[EMAN2/Programs/e2refine2d|e2refine2d.py]] * [[EMAN2/Programs/e2simmx2stage|e2simmx2stage.py]] * [[EMAN2/Programs/e2workflow|e2workflow.py]] |
''UNDER CONSTRUCTION'' Note that running any EMAN2 program with the '--help' option will provide basic 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 === High Level Tasks === * [[EMAN2/Programs/e2workflow|e2workflow.py]] - The GUI workflow interface. Suggested for all reconstruction projects. * [[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|e2refine.py]] - Single particle reconstruction, iterative refinement * [[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/e2classifyligand|e2classifyligand.py]] - Classify data into two groups based on reference models/masks * [[EMAN2/Programs/e2rct|e2rct.py]] - Random Conical Tilt reconstruction === Programs with a GUI === * [[EMAN2/Programs/e2workflow|e2workflow.py]] - The GUI workflow interface. Suggested for all reconstruction projects. * [[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/e2helixboxer|e2helixboxer.py]] - Selection tool for helical objects * [[EMAN2/Programs/e2RCTboxer|e2RCTboxer.py]] - Particle picker for focal pairs * [[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/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. * XMIPP * IMOD === Single Particle Tomography === * [[EMAN2/Programs/e2tomoboxer|e2tomoboxer.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/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. |
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| * [[EMAN2/Programs/e2proc2d|e2proc2d.py]] * [[EMAN2/Programs/e2proc3d|e2proc3d.py]] == Generic Docs == * [[StandardParms|Standard parameters used in multiple programs]] |
EMAN2 Programs
UNDER CONSTRUCTION
Note that running any EMAN2 program with the '--help' option will provide basic 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
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
e2rct.py - Random Conical Tilt reconstruction
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
e2RCTboxer.py - Particle picker for focal pairs
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
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.
- XMIPP
- IMOD
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
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.
