== EMAN2 Programs == '''This page is very incomplete, but running any EMAN2 program with the '--help' option will provide 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 * [[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|e2spt_boxer.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. {{attachment:slices_plus_cylinders.png}}