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'

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

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

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

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