Individual Programs
Graphical:
High level commands:
- 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.
- ttest This program performs a 2 way T-test to determine the resolution of a reconstruction.
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 performs MSA based filtering of a set of particles
- startnrclasses This program takes a set of particle images and generates reference free class averages
- 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
- 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
- alignhelix This will take a set of filament 'particles' and align them so they are vertical and centered
- classhelix This will take a set of filament 'particles' and generate a class-average
- 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
- 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
- euler This program calculates a cross common lines image between 2 source images
- 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
- volume This program calculates the volume/mass of a 3D map
- tiltseries Aligns a set of images from a tilt series and assigns Eulers
- Misc.
- basisfilter This takes an ortogonal 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!)
- fitctf This program estimates CTF parameters in batch. The results should be checked in CTFIT.
- iminfo This program provides basic information about image files
- 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
- speedtest This program runs a set of speed tests on the current machine.
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
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
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
symAxisSearch This program is used to iteratively search for the local rotation symmtry axis
symeval Experimental - not documented yet
helixpitch Determine the pitch of a helical object