src Directory Reference

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	baberr.cpp
	Program to generate images from aberration weights and analyze them.
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	bess.cpp
	Electron scattering simulation.
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	bfocal.cpp
	Processing focal series.
file	bftr.cpp
	Program for resizing an image using Fourier transformation.
file	bgex.cpp
	Calculating and comparing atomic models and maps.
file	bgradient.cpp
	Calculating image gradients.
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	bimport.cpp
	Generate parameter files from a cisTEM hierarchy.
file	bint.cpp
	Interpolation of 2D and 3D images.
file	bkernel.cpp
	Program to calculate filter kernels.
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	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	bmodfit.cpp
	A tool to fit 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
	Process single particle images in various ways.
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	bscatter.cpp
	Program to calculate scattering cross sections.
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.