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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.'' |
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| ||[wiki:EoTest eotest]||Even/odd data split for resolution evaluation after refinement|| | |
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| ||[wiki:/ProcPDB procpdb.py]||Simple PDB file manipulation|| ||[wiki:/ImInfo iminfo]||Dump information about image files|| |
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| ||[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|| '''Refinement-related Processing''' ||[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...|| '''AIRS Tools (Analysis of Intermediate Resolution Structures)''' ||[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 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
[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' |
Refinement Programs
[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 |
Utility Programs
[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 |
Refinement-related Processing
[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... |
AIRS Tools (Analysis of Intermediate Resolution Structures)
[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 |