Individual Programs

Graphical:


High level commands:

  • eotest This program performs a 2 way even/odd test to determine the resolution of a reconstruction.
  • multirefine This performs refinement on a set of 3D models simultaneously
  • refine This is the main refinement loop in EMAN. It has a tremendous number of options.
  • refine2d.py This is a program for iterative MSA-based particle classification and averaging

  • Low level commands

    Experimental

  • align3dvec Rotational and translational alignment of 3d models via vectorization
  • alignhuge Determines the rotation and transformation between images in a focal pair
  • classalignml Aligns a set of images using maximum likelihood
  • classesbymra3 An experimental version of classesbymra
  • classesbymrafast This is an experimental classification program
  • cosec2iv This program converts helices in COSEC secondary structure elements file format to Open Inventor format
  • dejavu2iv This program converts helices in DejaVu secondary structure elements file format to Open Inventor format
  • focalpair Merges focal pairs into a single image with partial CTF correction
  • foldhunter This program is used to quantitatively fit a subunit/domain into a large structure density map at intermediate resolution.
  • foldhunterP This program is used to quantitatively fit a subunit/domain into a large structure density map at intermediate resolution.
  • helixhunter This program is used to locate possible helices in intermediate resolution maps.
  • helixhunter2 This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map
  • helixhunter2OMP This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map
  • helixhunter3 This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map
  • helixhunterP This program is used to locate possible helices in intermediate resolution maps. Parallelized.
  • iv2cosec This program converts helices in Open Inventor format to COSEC secondary structure elements file format
  • iv2dejavu This program converts helices in Open Inventor format to DejaVu secondary structure elements file format
  • ivFit This program fits the matched paires of helices returned by COSEC
  • make3dicos This program builds 3D models from a set of particles with icosahedral symmetry
  • make3dicos2 Do not use this program directly. It is called from make3dicos.
  • matrixembed This program will embed a mutual distance matrix generated by the 'matrix' option of classesbymra
  • matrixclass This program will take a distance matrix and a pre-embedded space
  • skeleton This program is used to produce a skeleton representation of a 3D map. The skeleton preserves the topology (i.e., connectivity) of the input map, yet with a reduced structure consisting only of curves (corresponding to tubular shapes in the map, such as helices) and surfaces (corresponding to platelike shapes in the map, such as beta-sheets). The skeleton can also be used to generate helix/sheet scores for given points in the map.
  • symAxisSearch This program is used to iteratively search for the local rotation symmtry axis
  • symeval Experimental - not documented yet
  • basiseotest.py This is the basisrefine equivalent to eotest
  • basismultirefine.py This is a highly experimental refinement procedure using a novel alignment/classification procedure
  • basisrefine.py This is a highly experimental refinement procedure using a novel alignment/classification procedure
  • classalignhelix.py This program will take helical cls files and make class-averages
  • classesbymradfilt.py This program is a new version of classesbymra using the dfilt option
  • classeshelix.py This program will align and classify helical segments vs a set of reference projections
  • classifykmeans.py This program will classify pre-aligned 2D or 3D images
  • evalsim3d.py A simple script that generates projections of a map and uses glmatrix to visually make a similarity comparison
  • extractmonomers.py This program will extract individual monomers from individual symmetric particles using masks after normal refinement
  • makeinitialmodel.py Interactively allows the user to make an initial model for iterative reconstruction
  • masksym.py This will apply the given symmetry to a mask, and optionally extend the mask
  • project3dhelix.py This program will make axial and near-axial projections of 3D volumes
  • sfmerge.py Combines a structure factor from CTFIT with a simulated curve for use in CTF correction