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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. 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. [javascript:void(0);/*1208454045851*/ See the fixed documentation for a full list].''
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||[wiki:/Eman eman]||Image browser and tutorial interface||
||[wiki:/Boxer boxer]||Manual particle picking||
||[wiki:/CTFit ctfit]||CTF parameter determination and simulation||
||[wiki:/V4 v4]||Viewing 3-D models in projection||
||[wiki:/QSegment qsegment]||Interactive slice-by-slice 3D model segmentation||
||[wiki:/QIndex qindex]||2D crystal preprocessing and evaluation||
||[wiki:/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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||[wiki:/Refine2D refine2d.py]||Make high-quality 2-D class-averages from stacks of raw particle images||
||[wiki:/Refine refine]||3-D model refinement||
||[wiki:EoTest eotest]||Even/odd data split for resolution evaluation after refinement||
||[wiki:/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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||[wiki:/Proc2D proc2d]||Generic 2-D image processing||
||[wiki:/Proc3D proc3d]||Generic 3-D image processing||
||[wiki:/ProcPDB procpdb.py]||Simple PDB file manipulation||
||[wiki:/ImInfo iminfo]||Dump information about image files||
||[wiki:/SpeedTest speedtest]||Simple application-specific computer benchmarking program||
||[wiki:LstCat lstcat.py]||Generate pseudoimage text files||
||[wiki:LstFast lstfast.py]||Optimize pseudoimage files for rapid access||
||[wiki:PdbToMrc pdbtomrc]||Convert PDB files to MRC density maps||
||[wiki:Align2D align2d]||Align 2-D particles to a common reference||
||[wiki:Align3D align3d]||Aligns a 3-D model to a similar 3-D model||
||[wiki:Align3DSym align3dsym]||Align a 3-D model so symmetry axes are along canonical axes||
||[wiki: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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||[wiki:/BatchBoxer batchboxer]||Command-line automatic particle picking and box manipulation||
||[wiki:/FitCtf fitctf]||Automatic CTF parameter determination||
||[wiki:/ApplyCtf applyctf]||Perform phase flipping and other CTF-correction operations||
||[wiki:/SfMerge sfmerge.py]||Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve||
||[wiki:MakeInitialModel makeinitialmodel.py]||Interactive script for generating initial models out of Gaussian blobs||
||[wiki:StartCSym startcsym]||Generate initial models from data with Cn and Dn symmetries||
||[wiki:StartIcos starticos]||Generate initial models from data with icosahedral (532) symmetry||
||[wiki:StartOct startoct]||Generate an initial model from data with octahedral (432) symmetry||
||[wiki:StartAny startAny]||Initial model generation using common-lines. Usually a bad idea...||
||[wiki:PtclTrace ptcltrace]||Observe particle orientation changes during refinement||
||[wiki: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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||[wiki:/FoldHunter foldhunter.py]||Dock a PDB file or density segment in a 3-D reconstruction||
||[wiki:/SseHunter ssehunter.py]||Identify/locate secondary structural elements in subnanometer resolution reconstructions||
||[wiki:/HelixHunter helixhunter.py]||Program to locate alpha-helices in subnanometer resolution reconstructions||
||[wiki:/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. [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

EMAN1/Programs (last edited 2008-11-26 04:42:29 by localhost)