/Users/bernard/b20/bsoft/src Directory Reference(3)

NAME
/Users/bernard/b20/bsoft/src Directory Reference

SYNOPSIS

  Directories
directory img
directory mg
directory model
directory mol
directory ps
directory rwimg
directory rwmodel
directory rwmol
directory rwparam
directory util

  Files
file b3v.cpp
Program to extract 3 orthogonal views from a map.
file badd.cpp
Program to catenate image files.
file baddmask.cpp
Program to catenate image files.
file bafm.cpp
Simulation of AFM experiments.
file balign.cpp
Aligns two images.
file balpha.cpp
Program to make and analyze alpha helices.
file bampweigh.cpp
Program to filter images.
file bar.cpp
Program to do simple arithmetic on images.
file bass.cpp
Program to assemble molecular components.
file bbackproj.cpp
3D reconstruction by backprojection
file bbif.cpp
Program to denoise images by bilateral filtering.
file bbild.cpp
Generates BILD output from a model.
file bcat.cpp
Program to catenate image files.
file bcatmol.cpp
A program to concatenate coordinates from different files.
file bcatseq.cpp
A program to concatenate protein sequences from different files.
file bcc.cpp
Program for calculating cross-correlations.
file bclass.cpp
Classifies raw single particle images with respect to multiple models.
file bcolour.cpp
Program to generate nice colour images.
file bcomplex.cpp
Program for handing complex images.
file bconvert.cpp
Program to catenate image files.
file bcormut.cpp
A program to analyze protein sequences for correlated mutations.
file bcrystal.cpp
Calculates coordinates for multiple unit cells.
file bctf.cpp
A program to determine and correct for the CTF (contrast transfer function) in electron micrographs.
file bcyl.cpp
Program to manipulate cylindrical images.
file bdelta.cpp
Generating a deltagraph with minimal input parameters.
file bdens.cpp
Program to calculate density in selected regions of a map.
file bdif.cpp
Analyze diffraction patterns.
file bdual.cpp
Program to handle dual tomographic tilt series.
file bedge.cpp
A program to float an image in a uniform background.
file beditimg.cpp
Segment images into density regions.
file bfcc.cpp
Fast cross-correlation search for the best fit of a 3D map to a template.
file bfft.cpp
General FFT for n-dimensional data.
file bfil.cpp
Extract filaments from a micrograph as straightened filaments or boxed particles.
file bfile.cpp
Program to read file contents directly and poke single values.
file bfilter.cpp
Program to filter images.
file bfilwidth.cpp
Program to calculate moving average images.
file bfind.cpp
Searches orientation space for the best fit of a 3D map to a template.
file bfix.cpp
Program to fix end-of-line characters in ascii files.
file bflat.cpp
Solvent flattening.
file bflood.cpp
Segment images into density regions.
file bftr.cpp
Program for resizing an image using Fourier transformation.
file bgex.cpp
Calculating and comparing atomic models and maps.
file bgraphseg.cpp
Segment images into density regions using a nondirected graph.
file bhead.cpp
Program to modify image parameters in the header.
file bheight.cpp
Projecting a 3D map and calculating comparison statistics of the projections.
file bhelcross.cpp
Dealing with images with helical symmetry.
file bhelix.cpp
Dealing with images with helical symmetry.
file bhisto.cpp
Image histograms.
file bico.cpp
Program to analyze icosahedral subtomograms.
file bimg.cpp
General image processing program.
file bint.cpp
Interpolation of 2D and 3D images.
file bkernel.cpp
Program to calculate filter kernels.
file blevel.cpp
A program to manipulate level masks.
file blocfilt.cpp
Local resolution analysis.
file blocres.cpp
Local resolution analysis.
file bmapdist.cpp
Calculates a distance criterion between a set of 2D images or 3D maps.
file bmark.cpp
Program to generate symmetry axes for mark group symmetries.
file bmask.cpp
Generating and manipulating masks.
file bmaskmod.cpp
Generating a model from a mask.
file bmatch.cpp
Program to search an image with multiple projections and orient them.
file bmatrix.cpp
Program to process matrices.
file bmaxpow.cpp
Determining orientations by maximum power of 3D reconstruction from single particle images.
file bmd.cpp
Molecular dynamics - humble beginnings.
file bmedian.cpp
Program to filter images.
file bmg.cpp
Manipulating project and micrograph structures.
file bmg2imod.cpp
Converts between IMOD files and a micrograph parameter file.
file bmgalign.cpp
Aligns micrographs specified in parameter files.
file bmgconvert.cpp
Convert between micrograph parameter formats.
file bmgft.cpp
Disk-based 3D reconstruction for a tomography series.
file bmgtransfer.cpp
Transfer pieces of information between micrograph paramater files.
file bmissing.cpp
Generating and manipulating masks.
file bmm.cpp
A program to do model mechanics.
file bmod2part.cpp
Converting from a pseudo-atomic model to particle parameters.
file bmodcol.cpp
A tool to color models.
file bmodcomp.cpp
A tool to compare polyhedra.
file bmodedit.cpp
A tool to create and edit models.
file bmodel.cpp
Manipulates models.
file bmodmap.cpp
A tool to genrate a map from a model.
file bmodmask.cpp
Generating a mask from an atomic model.
file bmodsel.cpp
Manipulates selections from sets of components as solutions of fits.
file bmodsym.cpp
Deals with model and component symmetries.
file bmodview.cpp
Manipulates models.
file bmol.cpp
A tool to edit and analyze coordinate files.
file bmoledit.cpp
A tool to edit coordinate files.
file bmolhel.cpp
A program to perform helical symmetry operations on coordinate files.
file bmolsym.cpp
A tool to perform symmetry operations on coordinate files.
file bmontage.cpp
A program to generate a montage from a 3D image or a set of 2D images.
file bmonte.cpp
Program to use a monte carlo metroplis algorithm to energy minimize molecular positions.
file bmultifit.cpp
Searching for a template in a map and returning multiple hits in a model.
file bmultimask.cpp
Generating and manipulating composite masks.
file bmultislice.cpp
Multi-slice simulation of the electron imaging process.
file bnad.cpp
Image denoising by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion.
file bnorm.cpp
Program to normalize a set of images based on their histograms.
file bop.cpp
A program to operate on image pairs.
file borient.cpp
Determines orientation angles and x,y origins of single particle images.
file bparam.cpp
A tool to extract parameters from coordinate files.
file bpart.cpp
Calculates centers of single particle images.
file bpartmulti.cpp
Selection of single particle parameters from multiple files for classification.
file bpartsel.cpp
Selection of single particles for 3D reconstruction.
file bpatch.cpp
Program to patch tiled image files.
file bpath.cpp
A program to analyze paths and cycles in a model.
file bphase.cpp
A program to examine phase differences between image pairs.
file bpick.cpp
Pick particles in a micrograph given the particle coordinates, or pick particles in a focal series of micrographs with alignment of the micrographs.
file bplane.cpp
A tool to expand models.
file bpoly.cpp
A tool to manipulate polyhedral coordinate files.
file bproject.cpp
Projecting a 3D map and calculating comparison statistics of the projections.
file bradial.cpp
Polar images and radial averages.
file bradsec.cpp
Generates radial sections from 3D images.
file brandom.cpp
Program to generate random images.
file brecadd.cpp
Program to average selected reconstructions.
file brecmod.cpp
A tool to merge data from micrograph reconstruction and model files.
file breconstruct.cpp
3D reconstruction from single particle images
file brefine.cpp
Reciprocal space refinement of orientation parameters of particle images.
file bresolve.cpp
Calculate resolution estimates and Fourier shell statistics.
file bscale.cpp
Program to find the scaling of map with respect to a reference.
file bsegment.cpp
Segment images into density regions.
file bseq.cpp
A program to manipulate DNA and protein sequences.
file bseqaln.cpp
A program to analyze aligned protein sequences.
file bseries.cpp
Program to align and analyze series of images.
file bsf.cpp
Calculating structure factors from atomic models.
file bshell.cpp
Generates a shell point component model.
file bsim.cpp
A tool to generate a project with random orientations for a molecule and to simulate TEM images from given orientations.
file bspiral.cpp
A tool to generate polyhedra using the spiral algorithm.
file bsplit.cpp
Program to seperate a multi-image file into individual image files.
file bsplitmol.cpp
A program to concatenate coordinates from different files.
file bspr.cpp
3D reconstruction from single particle images
file bstar.cpp
Examines STAR format files.
file bsupix.cpp
Segment images.
file bsurf.cpp
AFM image analysis and reconstruction.
file bsym.cpp
Program to generate symmetry axes for point group symmetries.
file bsymcomp.cpp
Finds the best orientation that fits a symmetrized template.
file btile.cpp
Program to split an image into overlapping tiles.
file btomaln.cpp
Program to do fiducialless alignment of a tilt series.
file btomo.cpp
Program to process tomographic series of images.
file btompart.cpp
Program to extract single particle images from a tilt series and generate individual reconstructions.
file btomrec.cpp
Disk-based 3D reconstruction for a tomography series.
file btomres.cpp
Program to determine the resolution of a tilt series.
file btrack.cpp
Program to track fiducial markers in a tomographic series of images.
file btree.cpp
Program to process trees.
file btube.cpp
Symmetrizes helical tubes with hexagonal lattices.
file bwater.cpp
Molecular dynamics - humble beginnings.
file bxb.cpp
Extracting a part of a density map and building a new map.
file bxml.cpp
Reads, writes and validates XML files.
file bzfft.cpp
Disk-based z-line transforms for big reconstructions.
file dcount.cpp
A program to determine the occupancy of components in models.
file dhand.cpp
Compare projections of two oppositely handed reconstructions to images of tilted specimens.
file dimgstats.cpp
Calculates statistical measures within a set of images or between sets of images.
file dmerge.cpp
Merge images in a defocal or other series, align images before adding together.
file emgrand.cpp
Generate random values for micrograph parameters.
file jave.cpp
Program to average files and weigh the average in Real/Fourier space.
file jpartdif.cpp
Analysis of particle differences between two starfiles.
file jsubtomo.cpp
Finds particles (subtomograms) in a tomographic reconstruction and refines their origins and orientations.
file jviews.cpp
Generates views covering an asymmetric unit or all symmetry related views.
file radon.cpp
Program to do radon transforms.
file radonrecon.cpp
Program to do radon transforms.