Diff for "EMAN1/Programs"

Differences between revisions 6 and 17 (spanning 11 versions)

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

-  ⇤ ← Revision 6 as of 2006-11-09 21:13:27 → 
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  Editor: MikyungHan
  Comment:
+   ← Revision 17 as of 2008-11-26 04:42:29 → ⇥
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  Editor: localhost
  Comment: converted to 1.6 markup
-Deletions are marked like this.
+Additions are marked like this.
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-'''''Under Construction'''''
+''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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- proc2d
== This program performs various processing operations on images and sets of images (WARNING: auto normalization removed) ==
== Usage: ==
proc2d 3244.img start.hed invert apix=5 lp=18
+'''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' ||
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+Line 13:
-proc2d start.hed start.hed invert inplace
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+Line 14:
-== Description ==
IMPORTANT NOTE: proc2d no longer automatically normalizes output images. Use the 'norm' or 'edgenorm' flag to re-enable this.
+'''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 ||
-Line 14:
+Line 20:
-This program is used to perform a variety of generic 2D image processing tasks. Like all of the EMAN programs, it will read any supported file format. By default it outputs to an Imagic file although there are options to change this. Note that, by default, images are appended to the end of the output file if it already exists. All images in one file MUST have the same size. ie - if you try to copy 50x50 images to the end of a file that already contains 100x100 images, an error will result. Note the 'first=' and 'last=' options allow a subset of the input file to be processed. The 'inplace' keyword may be used to cause output images to overwrite the input images rather than being appended to the end of the file.
+'''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 ||