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.
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.
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.
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.

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