# 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.