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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. [javascript:void(0);/*1208454045851*/ See the fixed documentation for a full list].'' | |
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| ''''' Under Construction ''''' | '''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 || |
EMAN1 Individual Programs
There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. [javascript:void(0);/*1208454045851*/ 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 |