| b3v | Generates 3 orthogonal views of a map. |
| badd | Adds multiple images to generate a new composite image. |
| baddmask | Adds multiple masks to generate a new composite mask. |
| bafm | Simulates AFM imaging. |
| balign | The second input image is aligned to the first, transformed and output. |
| balpha | Creates and manipulates alpha helices. |
| bampweigh | Weighs the amplitudes of a map using a reference map's amplitudes. |
| bar | Does simple arithmetic on images. |
| bass | Assemble molecular components specified in a model. |
| bbackproj | Reconstructs 3D maps from single particles by backprojection. |
| bbif | Denoises by bilateral filtering. |
| bbild | Generates BILD output from a model. |
| bcat | Catenates a list of images into a multi-image file. |
| bcatmol | Concatenates sets of coordinates with shifts from sets of files. |
| bcatseq | Concatenates protein sequences from different files. |
| bcc | Calculates cross-correlation using fast Fourier transforms. |
| bclass | Classifies raw single particle images with respect to multiple reference maps. |
| bcolour | Generates nice colour images. |
| bcomplex | Converts complex image forms. |
| bconvert | Converts a list of images into a new format, using the original names and replacing the extension. |
| bcormut | Analyzes for correlated mutations in aligned protein sequences. |
| bcrystal | Calculates coordinates for multiple unit cells. |
| bctf | Applies, determines or corrects for the CTF (contrast transfer function) in electron micrographs. |
| bcyl | Unwraps an image to its cylindrical projection. |
| bdelta | Generates and analyzes deltagraphs. |
| bdens | Calculate density in selected regions of a map. |
| bdif | Analyzes diffraction patterns. |
| bdual | Handles dual tomographic tilt series of micrographs. |
| bedge | Smooths the edge of an image to a uniform background. |
| beditimg | Creates a new image or modifies an input image by inserting or deleting regions. |
| bfcc | Fast cross-correlation for the best fit of a 3D map to a template. |
| bfft | Fast Fourier transforms to and from image and reflection formats. |
| bfil | Extracts filaments from a micrograph as straightened filaments or boxed particles. |
| bfile | Examines and modifies binary files. |
| bfilter | Filters images. |
| bfilwidth | Analyzes the periodicity of a filament from width changes. |
| bfind | Searches orientation space for the best fit of a 3D map to a template. |
| bfix | Replaces single characters in a file. |
| bflat | Does phase extension by solvent flattening. |
| bflood | Segments images using the watershed or flooding algorithm. |
| bftr | Resizing an image using Fourier transformation. |
| bgex | Calculates and compares atomic models and maps. |
| bgraphseg | Segment images into density regions using a nondirected graph. |
| bhead | Reports on and modifies image parameters in the image header. |
| bheight | Calculates 2D height images from a 3D map. |
| bhelcross | Calculates the 2D cross section for a helical filament. |
| bhelix | Symmetrizes and projects images with helical symmetry. |
| bhisto | Calculates the histogram of an image and associated statistics. |
| bico | Analyzes icosahedral subtomograms. |
| bimg | Manipulates images in a few general ways. |
| bint | Applies geometric transformations requiring interpolation to 2D and 3D images. |
| bkernel | Calculates filter kernels. |
| blocfilt | |
| blocres | The local (-box) and shell (-shell) resolution calculations are mutually exclusive. |
| bmapdist | Calculates distance criterions between a set of 2D images or 3D maps. |
| bmark | Operates on sets of micrograph markers. |
| bmask | Generates and uses binary masks of the size given or of the input image. |
| bmatch | Searching an image with a set of 2D templates/references |
| bmatrix | Processes matrices. |
| bmaxpow | Finds orientations of particle images based on maximizing reciprocal space reconstruction power. |
| bmd | Calculates forces on an atomic structure and adjust coordinates. |
| bmedian | Filters images. |
| bmg | Manipulates micrograph parameter files. |
| bmg2imod | Converts between IMOD files and a micrograph parameter file. |
| bmgalign | Aligns micrographs within sets such as focal series specified in parameter files. |
| bmgconvert | Converts micrograph parameter files. |
| bmgft | Fourier transforms micrographs from a tomographic tilt series. |
| bmgtransfer | Transfer pieces of information from input micrograph parameter files |
| bmissing | Generates binary masks corresponding to reciprocal space regions. |
| bmm | Mechanical modeling. |
| bmod2part | Converting between model components and reconstruction particle parameters. |
| bmodcol | Colors models based on selection. |
| bmodcomp | Compares models internally or to reference models. |
| bmodedit | Creates models. |
| bmodel | Manipulates models. |
| bmodmap | Generates a map from a model. |
| bmodmask | Generates a mask from a model if an output image is specified. |
| bmodsel | |
| bmodsym | Manipulates models. |
| bmodview | Manipulates models. |
| bmol | Edits, analyzes and transforms atomic coordinate files. |
| bmoledit | Manipulates atomic coordinate files. |
| bmolhel | Performs helical symmetry operations on molecules. |
| bmolsym | Performs symmetry operations on molecules. |
| bmontage | Generates a montage from a 3D image or a set of 2D images |
| bmonte | Minimizes the energy of a set of molecular structures using a Monte Carlo Metropolis algorithm. |
| bmultifit | Searches orientation space for a set of solutions for the fit of a template within a 3D map. |
| bmultimask | Manipulates composite/level masks. |
| bmultislice | Simulates electron imaging using a multi-slice approach. |
| bnad | Denoises by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion. |
| bnorm | Normalizes a set of images based on their histograms. |
| bop | Binary operations for 2D and 3D images. |
| borient | Determines the orientations and origins of single particles with respect to a reference. |
| bparam | Manipulate molecular parameter files. |
| bpart | Manipulates single particle images. |
| bpartmulti | |
| bpartsel | |
| bpatch | Patches a list of tiles together with overlap. |
| bpath | Analyzes paths and cycles in a model. |
| bphase | Calculates the phase difference between two images. |
| bpick | Picks and extracts single particles from 2D (micrograph) or 3D (tomogram) images. |
| bplane | Generates and manipulates plane models. |
| bpoly | Manipulate model polyhedral coordinate files. |
| bproject | Projects a 3D map and calculating comparison statistics of the projections. |
| bradial | Calculates radial profiles of 2D and 3D images. |
| bradsec | Generates symmetry-adjusted radial sections from 3D images. |
| brandom | Generates random content images. |
| brecadd | Averages reconstructions or subvolumes of reconstructions based on |
| brecmod | Merges data from micrograph and model files. |
| breconstruct | Reconstructs 2D and 3D maps from single particle images. |
| brefine | Refines the orientations of particle images with respect to a reference map. |
| bresolve | Determines the resolution (FSC and DPR) from two images. |
| bscale | Scales a map with respect to a reference. |
| bsegment | Analyzes images for segmentation. |
| bseq | Manipulates DNA and protein sequences. |
| bseqaln | Analyzes aligned protein sequences. |
| bseries | Aligns series of micrographs using consecutive pairwise cross-correlation. |
| bsf | Calculates structure factors from atomic models. |
| bshell | Generates and operates on shell models. |
| bsim | Simulates TEM images from atomic coordinates. |
| bspiral | Generates a polyhedron using the spiral algorithm. |
| bsplit | Splits multi-image files of the following formats: |
| bsplitmol | Splits sets of coordinates to different numbered files. |
| bspr | Analyzing single particle reconstructions. |
| bstar | Examines and modifies STAR format files. |
| bsupix | Segments an image into superpixels. |
| bsurf | Calculates a 3D surface from an AFM image. |
| bsym | Analyzes for and applies point group symmetry to images. |
| bsymcomp | Finds the best orientation that fits a symmetrized template. |
| btile | Splits an image into overlapping tiles. |
| btomaln | Aligns a tilt series of micrographs by progressive reconstruction. |
| btomo | Manipulates parameter files for tilt series and aligns them by cross-correlation. |
| btompart | Averages reconstructions or subvolumes of reconstructions based on |
| btomrec | Reconstructs a tomogram from an aligned tilt series in Fourier space. |
| btomres | Program to determine the resolution of a tilt series. |
| btrack | Track fiducial markers in a tomographic tilt series of micrographs. |
| btree | Draws phylogenetic trees as postscript. |
| btube | Symmetrizes helical tubes with hexagonal lattices. |
| bwater | Generates and does molecular dynamics on blocks of water. |
| bxb | Extracting a part of a density map and building a new map based on a model. |
| bxml | Reads, writes and validates XML files. |
| bzfft | Assembles slabs and back-transform z-lines for tomogram reconstruction. |
| dcount | Determines the occupancy of components in the maps associated with models. |
| dhand | Compares projections of two oppositely handed reconstructions to images |
| dimgstats | Calculates statistical measures within a set of images or between sets of images. |
| dmerge | Merges corresponding single particle images in a series. |
| emgrand | Randomizes particle parameters. |
| jave | Averages multiple images together. |
| jpartdif | Calculates the difference in the particle parameters, |
| jsubtomo | Finds particles (subtomograms) in a tomographic reconstruction and refines their orientations and origins. |
| jviews | Creates and modifies particle views. |
| radon | Program to do radon transforms. |
| radonrecon | Program to reconstruct a quarter (PI*PI) radon transform from projections. |