== EMAN1 Individual Programs ==
''There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. [[http://blake.bcm.tmc.edu/eman/eman1/progs/programs.html|See the fixed documentation for a full list]].''

'''GUI Programs'''
||[[EMAN1/Programs/Eman|eman]] ||Image browser and tutorial interface ||
||[[EMAN1/Programs/Boxer|boxer]] ||Manual particle picking ||
||[[EMAN1/Programs/CTFit|ctfit]] ||CTF parameter determination and simulation ||
||[[EMAN1/Programs/V4|v4]] ||Viewing 3-D models in projection ||
||[[EMAN1/Programs/QSegment|qsegment]] ||Interactive slice-by-slice 3D model segmentation ||
||[[EMAN1/Programs/QIndex|qindex]] ||2D crystal preprocessing and evaluation ||
||[[EMAN1/Programs/HelixBoxer|helixboxer]] ||Program for picking and evaluating non-square 'boxes' ||


'''Refinement Programs'''
||[[EMAN1/Programs/Refine2D|refine2d.py]] ||Make high-quality 2-D class-averages from stacks of raw particle images ||
||[[EMAN1/Programs/Refine|refine]] ||3-D model refinement ||
||[[EoTest|eotest]] ||Even/odd data split for resolution evaluation after refinement ||
||[[EMAN1/Programs/MultiRefine|multirefine]] ||Simultaneous multiple model 3-D refinement ||


'''Utility Programs'''
||[[EMAN1/Programs/Proc2D|proc2d]] ||Generic 2-D image processing ||
||[[EMAN1/Programs/Proc3D|proc3d]] ||Generic 3-D image processing ||
||[[EMAN1/Programs/ProcPDB|procpdb.py]] ||Simple PDB file manipulation ||
||[[EMAN1/Programs/ImInfo|iminfo]] ||Dump information about image files ||
||[[EMAN1/Programs/SpeedTest|speedtest]] ||Simple application-specific computer benchmarking program ||
||[[LstCat|lstcat.py]] ||Generate pseudoimage text files ||
||[[LstFast|lstfast.py]] ||Optimize pseudoimage files for rapid access ||
||[[PdbToMrc|pdbtomrc]] ||Convert PDB files to MRC density maps ||
||[[Align2D|align2d]] ||Align 2-D particles to a common reference ||
||[[Align3D|align3d]] ||Aligns a 3-D model to a similar 3-D model ||
||[[Align3DSym|align3dsym]] ||Align a 3-D model so symmetry axes are along canonical axes ||
||[[Volume|volume]] ||Compute or adjust the volume of a 3-D reconstruction ||


'''Refinement-related Processing'''
||[[EMAN1/Programs/BatchBoxer|batchboxer]] ||Command-line automatic particle picking and box manipulation ||
||[[EMAN1/Programs/FitCtf|fitctf]] ||Automatic CTF parameter determination ||
||[[EMAN1/Programs/ApplyCtf|applyctf]] ||Perform phase flipping and other CTF-correction operations ||
||[[EMAN1/Programs/SfMerge|sfmerge.py]] ||Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve ||
||[[MakeInitialModel|makeinitialmodel.py]] ||Interactive script for generating initial models out of Gaussian blobs ||
||[[StartCSym|startcsym]] ||Generate initial models from data with Cn and Dn symmetries ||
||[[StartIcos|starticos]] ||Generate initial models from data with icosahedral (532) symmetry ||
||[[StartOct|startoct]] ||Generate an initial model from data with octahedral (432) symmetry ||
||[[StartAny|startAny]] ||Initial model generation using common-lines. Usually a bad idea... ||
||[[PtclTrace|ptcltrace]] ||Observe particle orientation changes during refinement ||
||[[Segment3D|segment3d]] ||Automatic segmentation of 3-D reconstructions ||


'''AIRS Tools (Analysis of Intermediate Resolution Structures)'''
||[[EMAN1/Programs/FoldHunter|foldhunter.py]] ||Dock a PDB file or density segment in a 3-D reconstruction ||
||[[EMAN1/Programs/SseHunter|ssehunter.py]] ||Identify/locate secondary structural elements in subnanometer resolution reconstructions ||
||[[EMAN1/Programs/HelixHunter|helixhunter.py]] ||Program to locate alpha-helices in subnanometer resolution reconstructions ||
||[[EMAN1/Programs/Skeleton|skeleton]] ||Skeletonization of 3-D models based on both lines and planes ||