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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. [[http://blake.bcm.tmc.edu/eman/eman1/progs/programs.html|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||		 ||[[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: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...||		 ||[[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||		 ||[[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

eman

Image browser and tutorial interface

boxer

Manual particle picking

ctfit

CTF parameter determination and simulation

v4

Viewing 3-D models in projection

qsegment

Interactive slice-by-slice 3D model segmentation

qindex

2D crystal preprocessing and evaluation

helixboxer

Program for picking and evaluating non-square 'boxes'

Refinement Programs

refine2d.py

Make high-quality 2-D class-averages from stacks of raw particle images

refine

3-D model refinement

eotest

Even/odd data split for resolution evaluation after refinement

multirefine

Simultaneous multiple model 3-D refinement

Utility Programs

proc2d

Generic 2-D image processing

proc3d

Generic 3-D image processing

procpdb.py

Simple PDB file manipulation

iminfo

Dump information about image files

speedtest

Simple application-specific computer benchmarking program

lstcat.py

Generate pseudoimage text files

lstfast.py

Optimize pseudoimage files for rapid access

pdbtomrc

Convert PDB files to MRC density maps

align2d

Align 2-D particles to a common reference

align3d

Aligns a 3-D model to a similar 3-D model

align3dsym

Align a 3-D model so symmetry axes are along canonical axes

volume

Compute or adjust the volume of a 3-D reconstruction

Refinement-related Processing

batchboxer

Command-line automatic particle picking and box manipulation

fitctf

Automatic CTF parameter determination

applyctf

Perform phase flipping and other CTF-correction operations

sfmerge.py

Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve

makeinitialmodel.py

Interactive script for generating initial models out of Gaussian blobs

startcsym

Generate initial models from data with Cn and Dn symmetries

starticos

Generate initial models from data with icosahedral (532) symmetry

startoct

Generate an initial model from data with octahedral (432) symmetry

startAny

Initial model generation using common-lines. Usually a bad idea...

ptcltrace

Observe particle orientation changes during refinement

segment3d

Automatic segmentation of 3-D reconstructions

AIRS Tools (Analysis of Intermediate Resolution Structures)

foldhunter.py

Dock a PDB file or density segment in a 3-D reconstruction

ssehunter.py

Identify/locate secondary structural elements in subnanometer resolution reconstructions

helixhunter.py

Program to locate alpha-helices in subnanometer resolution reconstructions

skeleton

Skeletonization of 3-D models based on both lines and planes

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