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''UNDER CONSTRUCTION'' - Seriously. We are adding to the detailed docs every week. If you don't see what' you're looking for, please email us and ask, and we'll move it up in the queue. | |
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* [[EMAN2/Programs/e2scannereval|e2scannereval.py]] * [[EMAN2/Programs/e2boxer|e2boxer.py]] * [[EMAN2/Programs/e2helixboxer|e2helixboxer.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]] * [[EMAN2/Programs/e2proc2d|e2proc2d.py]] * [[EMAN2/Programs/e2proc3d|e2proc3d.py]] |
Note that running any EMAN2 program with the '--help' option will provide basic documentation for that program. |
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* [[StandardParms|Standard parameters used in multiple programs]] | * [[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|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/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. |
EMAN2 Programs
UNDER CONSTRUCTION - Seriously. We are adding to the detailed docs every week. If you don't see what' you're looking for, please email us and ask, and we'll move it up in the queue.
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
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
e2refinetorelion2d.py - Use Relion to perform maximum likelihood 2D Class Averaging.
e2refinetorelion3d.py - Use an EMAN2 refinement result to set up all necessary files to perform a Relion refinement.
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
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.