[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'

[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

[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

[wiki:Align2D align2d]

Align 2-D particles to a common reference

[wiki:Align3D align3d]

Aligns a 3-D model to a similar 3-D model

[wiki:Align3DSym align3dsym]

Align a 3-D model so symmetry axes are along canonical axes

[wiki:Volume volume]

Compute or adjust the volume of a 3-D reconstruction

[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:/SfMerge sfmerge.py]

Merge a low resolution 1-D structure factor from ctfit with a high resolution solution scattering curve

[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...

[wiki:PtclTrace ptcltrace]

Observe particle orientation changes during refinement

[wiki:Segment3D segment3d]

Automatic segmentation of 3-D reconstructions

[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

[wiki:/Skeleton skeleton]

Skeletonization of 3-D models based on both lines and planes