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.
Low level commands
- Classification
- classes This implements reference-free k-means classification based on a set of footprint files
- classesbycl This classifies a set of centered particles using self common lines.
- classesbymra This program classifies a set of particles based on a set of references (usually projections).
- classesbymra2 This program classifies a set of particles based on multiple sets of references and splits the results between 2 directories.
- classesrefs Classifies particles using a set of invariants
- clsregen This program uses particle.log to regenerate cls files for a particular iteration.
- imgdump Dump an image's dimensions and raw data into a file.
- startnrclasses This program takes a set of particle images and generates reference free class averages
- basisclsregen.py Regenerates cls files for a particular iteration produced with 'basisrefine'
- Alignment
- align2d This program will align a set of images to a reference
- align3d Rotational and translational alignment of 3d models
- align3dsym This will rotate a 3D model so its symmetric axes are aligned on the predefined axes
- align3dsymslow This will rotate a 3D model so its symmetric axes are aligned on the predefined axes
- cenalignacf This program will center a set of particles using an autocorrelation function
- cenalignint This iteratively centers a set of particles, using only integer shifts to avoid interpolation artifacts.
- classalign2 Aligns a set of images iteratively to generate a class-average.
- classalignall This will align the images in all of the cls*img files in the current directory
- geodcmp This will determine a set of orthogonal basis images from a set of aligned particles
- raw2mrc This program will import raw binary data and write a MRC file
- svdcmp This will determine a set of orthogonal basis images from a set of aligned particles
- powdcmp This will determine a set of orthogonal basis images from a set of projections
- Reconstruction
- c1startup This program uses cross-common lines to generate a 3D model from a set of projections
- clean3d This program uses make3diter and proc3d to iteratively make models match class averages
- make3d This program builds 3D models from a set of class averages using Fourier techniques
- make3diter Iteratively improves 3D models using real-space methods.
- make3diter2 Iteratively improves 3D models using real-space methods.
- make3dreal This program builds a 3d model from a set of projections (class averages) using unfiltered back-projection
- make3dnonorm This program builds 3D models from a set of class averages using Fourier techniques
- startAny This program will generate a 3D model from a set of class averages, using cross common lines.
- startcsym This program generates a preliminary 3d model for objects with Cn or Dn symmetry
- starticos This program generates a preliminary 3d model for objects with icosahedral symmetry
- startoct This program generates a preliminary 3d model for objects with octahedral symmetry
- Transformation/Analysis
- avg3d This program will average a set of aligned 3d images together
- cloud This program performs MSA based filtering of a set of particles
- ctfavg Averages a set of 2D images with ctf correction
- ctfavg2 Averages a set of 2D images with ctf correction
- euler This program calculates a cross common lines image between 2 source images
- eulerclassrefine This program will try to refine the Euler angles for a set of class-averages using the concept of common-lines
- eulerproj This program reassigns Euler angles to a set of class averages by projection matching
- eulerrefine This program is used internally by startAny
- fftavg This program reads a set of images, transforms them, and generates and averaged power spectrum
- footprint This program generates a set of rotational and translational invariants for use in classification
- footprint2 This program generates a set of rotational and translational invariants for use in classification
- footprint3 This program generates a set of rotational and translational invariants for use in classification
- footprintr This program generates a set of rotational and translational invariants for use in classification
- fpweight This program assigns weights to the various axes in a footprint file
- msa This performs multivariate statistical analysis on a set of invariants
- msa2 This performs multivariate statistical analysis on 2 sets of invariants
- project3d Generate projections of a 3D model
- ptcltrace Trace how classification of a single particle changes
- segment3d Split a 3d map into several pieces.
- symbest This program searches a large set of particles for those with the best symmetry.
- symsort Sorts a set of images in order of symmetry quality
- tiltseries Aligns a set of images from a tilt series and assigns Eulers
- volume This program calculates the volume/mass of a 3D map
- Misc.
- applyctf Applies/corrects CTF to sets of particle images
- basisfilter This takes an orthogonal basis set as created by svdcmp and uses it to operate on a set of images
- batchboxer This program is used for offline boxing of micrographs (MRC format ONLY!)
- circleboxer This program is used for offline boxing of micrographs using circular contrast regions
- classesbybasis This will classify and align a set of particles based on an orthogonal basis as produced by svdcmp or geodcmp
- fitctf This program estimates CTF parameters in batch. The results should be checked in CTFIT.
- iminfo This program provides basic information about image files
- make3dsirt Misc. 3d image processing
- mx2img This program converts a distance matrix to an MRC image
- pdb2mrc This program will generate a 3D electron density map from PDB files
- proc2d This program performs various processing operations on images and sets of images (WARNING: auto normalization removed)
- proc3d Misc. 3d image processing
- projtree Generates a list of projections used for high speed particle classification
- runpar Run a list of programs in parallel on one or several machines
- snrboxer This program is used for offline boxing of micrographs (MRC format ONLY!)
- speedtest This program runs a set of speed tests on the current machine.
- xtalcen This program will take a diffraction pattern, locate the center, remove the beamstop and do a background subtraction
- dejavu2pdb This program generates a pdb backbone for dejaVu helices
- foldhunter.py Python script for quickly running foldhunterP in chimera
- helix.py This program generates a Ca trace of dejaVu helices
- helixhunter.py Python script for quickly running helixhunter in chimera
- sheethunter2.py Beta sheet identification
- lstcat.py Generates a 'lst' file from a set of input image stacks
- makeboxref.py Generates an optimal set of reference projections from a 3D model for use in automatic particle selection
- procpdb.py This program is for performing simple operations on PDB files
- sheethunter2.py Beta sheet identification
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
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