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| ''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].'' | ''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]].'' |
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| ||[: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' || |
||[[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' || |
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| ||[: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 || |
||[[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 || |
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| ||[: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 || |
||[[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 || |
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| ||[: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 || |
||[[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 || |
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| ||[: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 || |
||[[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 || |
EMAN1 Individual Programs
There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list.
GUI Programs
Image browser and tutorial interface |
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Manual particle picking |
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CTF parameter determination and simulation |
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Viewing 3-D models in projection |
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Interactive slice-by-slice 3D model segmentation |
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2D crystal preprocessing and evaluation |
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Program for picking and evaluating non-square 'boxes' |
Refinement Programs
Make high-quality 2-D class-averages from stacks of raw particle images |
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3-D model refinement |
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Even/odd data split for resolution evaluation after refinement |
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Simultaneous multiple model 3-D refinement |
Utility Programs
Generic 2-D image processing |
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Generic 3-D image processing |
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Simple PDB file manipulation |
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Dump information about image files |
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Simple application-specific computer benchmarking program |
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Generate pseudoimage text files |
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Optimize pseudoimage files for rapid access |
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Convert PDB files to MRC density maps |
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Align 2-D particles to a common reference |
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Aligns a 3-D model to a similar 3-D model |
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Align a 3-D model so symmetry axes are along canonical axes |
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Compute or adjust the volume of a 3-D reconstruction |
Refinement-related Processing
Command-line automatic particle picking and box manipulation |
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Automatic CTF parameter determination |
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Perform phase flipping and other CTF-correction operations |
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Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve |
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Interactive script for generating initial models out of Gaussian blobs |
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Generate initial models from data with Cn and Dn symmetries |
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Generate initial models from data with icosahedral (532) symmetry |
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Generate an initial model from data with octahedral (432) symmetry |
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Initial model generation using common-lines. Usually a bad idea... |
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Observe particle orientation changes during refinement |
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Automatic segmentation of 3-D reconstructions |
AIRS Tools (Analysis of Intermediate Resolution Structures)
Dock a PDB file or density segment in a 3-D reconstruction |
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Identify/locate secondary structural elements in subnanometer resolution reconstructions |
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Program to locate alpha-helices in subnanometer resolution reconstructions |
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Skeletonization of 3-D models based on both lines and planes |