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 |