*Bsoft programs*

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. |

blevel | Manipulates level masks. |

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. |

bmaskmod | Generates a model from a mask. |

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 | Refines membrane models. |

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 | Selects and manipulates models and components. |

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 | Selection and analysis of single particles from multiple parameter files. |

bpartsel | Selects single particles for reconstruction and further processing. |

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 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. |

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. |