eman1_programs
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.txt · Last modified: by steveludtke