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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. [javascript:void(0);/*1208454002719*/ See the fixed documentation for a full list].'' |
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| == Description == Note: Despite the experimental tags, the 'phasecls' and 'fscls' almost always produce better results than the default linear variance classifier. Note that these options are mutually exclusive. |
'''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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| This is the main refinement command in EMAN. You should have your starting images in 'start.img' and your initial 3D model in threed.0a.mrc. The 'refine' command will then refine this model iteratively. Note that the 'total number of iterations' specifies the number of iterations the program will finish with. If 5 iterations have been run, then 'refine 8 ...' is run, the program will pick up after 5 iterations and run only 3 more cycles. If you want to start over again from the first iteration, you must remove all of the 'threed.?.mrc' files (except for 0a) and all of the 'classes.?.mrc' files. | |
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| Most of the options are simply passed through to other programs. Typical options for this program can be determined by running [/eman/eman1/progs/eman.html eman] and following the reconstruction procedure it provides. | '''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 || |
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| The tree option may not work in certian parallel configurations, such as grid configurations where the filesystem isn't cross-mounted. | '''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);/*1208454002719*/ 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 |