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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_dir_68267d1309a1af8e8297ef4c3efbcdba">
<title>/Users/bernard/b20/bsoft/src Directory Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src Directory Reference</primary></indexterm>
<simplesect>
    <title>Directories    </title>
        <itemizedlist>
            <listitem><para>directory <link linkend="_dir_7673ec780970b264223275c6ce2fb0e1">img</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_1d197ef0d9947f4cc1ac44e7f59e2b57">mg</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_5dd65160827af56e6353642206b80129">model</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_d222c3909b771dd1cf1b375528c5865e">mol</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_6e3f4de94181a0c26fe036ae85a353f0">ps</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_e6602f3dc482aab2c4dbb37953c911fd">rwimg</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_f347dd41100e820f728e8b665c3b5705">rwmodel</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_9b49ebcb002c4d7ed155dd26f01900e7">rwmol</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_5cff5ebabf0008b7b580a164f8978e8c">rwparam</link></para>
</listitem>
            <listitem><para>directory <link linkend="_dir_b7878ad5ecbf2506f4125b9d34c97e45">util</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Files    </title>
        <itemizedlist>
            <listitem><para>file <link linkend="_b3v_8cpp">b3v.cpp</link></para>

<para>Program to extract 3 orthogonal views from a map. </para>
</listitem>
            <listitem><para>file <link linkend="_badd_8cpp">badd.cpp</link></para>

<para>Program to catenate image files. </para>
</listitem>
            <listitem><para>file <link linkend="_baddmask_8cpp">baddmask.cpp</link></para>

<para>Program to catenate image files. </para>
</listitem>
            <listitem><para>file <link linkend="_bafm_8cpp">bafm.cpp</link></para>

<para>Simulation of AFM experiments. </para>
</listitem>
            <listitem><para>file <link linkend="_balign_8cpp">balign.cpp</link></para>

<para>Aligns two images. </para>
</listitem>
            <listitem><para>file <link linkend="_balpha_8cpp">balpha.cpp</link></para>

<para>Program to make and analyze alpha helices. </para>
</listitem>
            <listitem><para>file <link linkend="_bampweigh_8cpp">bampweigh.cpp</link></para>

<para>Program to filter images. </para>
</listitem>
            <listitem><para>file <link linkend="_bar_8cpp">bar.cpp</link></para>

<para>Program to do simple arithmetic on images. </para>
</listitem>
            <listitem><para>file <link linkend="_bass_8cpp">bass.cpp</link></para>

<para>Program to assemble molecular components. </para>
</listitem>
            <listitem><para>file <link linkend="_bbackproj_8cpp">bbackproj.cpp</link></para>

<para>3D reconstruction by backprojection </para>
</listitem>
            <listitem><para>file <link linkend="_bbif_8cpp">bbif.cpp</link></para>

<para>Program to denoise images by bilateral filtering. </para>
</listitem>
            <listitem><para>file <link linkend="_bbild_8cpp">bbild.cpp</link></para>

<para>Generates BILD output from a model. </para>
</listitem>
            <listitem><para>file <link linkend="_bcat_8cpp">bcat.cpp</link></para>

<para>Program to catenate image files. </para>
</listitem>
            <listitem><para>file <link linkend="_bcatmol_8cpp">bcatmol.cpp</link></para>

<para>A program to concatenate coordinates from different files. </para>
</listitem>
            <listitem><para>file <link linkend="_bcatseq_8cpp">bcatseq.cpp</link></para>

<para>A program to concatenate protein sequences from different files. </para>
</listitem>
            <listitem><para>file <link linkend="_bcc_8cpp">bcc.cpp</link></para>

<para>Program for calculating cross-correlations. </para>
</listitem>
            <listitem><para>file <link linkend="_bclass_8cpp">bclass.cpp</link></para>

<para>Classifies raw single particle images with respect to multiple models. </para>
</listitem>
            <listitem><para>file <link linkend="_bcolour_8cpp">bcolour.cpp</link></para>

<para>Program to generate nice colour images. </para>
</listitem>
            <listitem><para>file <link linkend="_bcomplex_8cpp">bcomplex.cpp</link></para>

<para>Program for handing complex images. </para>
</listitem>
            <listitem><para>file <link linkend="_bconvert_8cpp">bconvert.cpp</link></para>

<para>Program to catenate image files. </para>
</listitem>
            <listitem><para>file <link linkend="_bcormut_8cpp">bcormut.cpp</link></para>

<para>A program to analyze protein sequences for correlated mutations. </para>
</listitem>
            <listitem><para>file <link linkend="_bcrystal_8cpp">bcrystal.cpp</link></para>

<para>Calculates coordinates for multiple unit cells. </para>
</listitem>
            <listitem><para>file <link linkend="_bctf_8cpp">bctf.cpp</link></para>

<para>A program to determine and correct for the CTF (contrast transfer function) in electron micrographs. </para>
</listitem>
            <listitem><para>file <link linkend="_bcyl_8cpp">bcyl.cpp</link></para>

<para>Program to manipulate cylindrical images. </para>
</listitem>
            <listitem><para>file <link linkend="_bdelta_8cpp">bdelta.cpp</link></para>

<para>Generating a deltagraph with minimal input parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_bdens_8cpp">bdens.cpp</link></para>

<para>Program to calculate density in selected regions of a map. </para>
</listitem>
            <listitem><para>file <link linkend="_bdif_8cpp">bdif.cpp</link></para>

<para>Analyze diffraction patterns. </para>
</listitem>
            <listitem><para>file <link linkend="_bdual_8cpp">bdual.cpp</link></para>

<para>Program to handle dual tomographic tilt series. </para>
</listitem>
            <listitem><para>file <link linkend="_bedge_8cpp">bedge.cpp</link></para>

<para>A program to float an image in a uniform background. </para>
</listitem>
            <listitem><para>file <link linkend="_beditimg_8cpp">beditimg.cpp</link></para>

<para>Segment images into density regions. </para>
</listitem>
            <listitem><para>file <link linkend="_bfcc_8cpp">bfcc.cpp</link></para>

<para>Fast cross-correlation search for the best fit of a 3D map to a template. </para>
</listitem>
            <listitem><para>file <link linkend="_bfft_8cpp">bfft.cpp</link></para>

<para>General FFT for n-dimensional data. </para>
</listitem>
            <listitem><para>file <link linkend="_bfil_8cpp">bfil.cpp</link></para>

<para>Extract filaments from a micrograph as straightened filaments or boxed particles. </para>
</listitem>
            <listitem><para>file <link linkend="_bfile_8cpp">bfile.cpp</link></para>

<para>Program to read file contents directly and poke single values. </para>
</listitem>
            <listitem><para>file <link linkend="_bfilter_8cpp">bfilter.cpp</link></para>

<para>Program to filter images. </para>
</listitem>
            <listitem><para>file <link linkend="_bfilwidth_8cpp">bfilwidth.cpp</link></para>

<para>Program to calculate moving average images. </para>
</listitem>
            <listitem><para>file <link linkend="_bfind_8cpp">bfind.cpp</link></para>

<para>Searches orientation space for the best fit of a 3D map to a template. </para>
</listitem>
            <listitem><para>file <link linkend="_bfix_8cpp">bfix.cpp</link></para>

<para>Program to fix end-of-line characters in ascii files. </para>
</listitem>
            <listitem><para>file <link linkend="_bflat_8cpp">bflat.cpp</link></para>

<para>Solvent flattening. </para>
</listitem>
            <listitem><para>file <link linkend="_bflood_8cpp">bflood.cpp</link></para>

<para>Segment images into density regions. </para>
</listitem>
            <listitem><para>file <link linkend="_bftr_8cpp">bftr.cpp</link></para>

<para>Program for resizing an image using Fourier transformation. </para>
</listitem>
            <listitem><para>file <link linkend="_bgex_8cpp">bgex.cpp</link></para>

<para>Calculating and comparing atomic models and maps. </para>
</listitem>
            <listitem><para>file <link linkend="_bgraphseg_8cpp">bgraphseg.cpp</link></para>

<para>Segment images into density regions using a nondirected graph. </para>
</listitem>
            <listitem><para>file <link linkend="_bhead_8cpp">bhead.cpp</link></para>

<para>Program to modify image parameters in the header. </para>
</listitem>
            <listitem><para>file <link linkend="_bheight_8cpp">bheight.cpp</link></para>

<para>Projecting a 3D map and calculating comparison statistics of the projections. </para>
</listitem>
            <listitem><para>file <link linkend="_bhelcross_8cpp">bhelcross.cpp</link></para>

<para>Dealing with images with helical symmetry. </para>
</listitem>
            <listitem><para>file <link linkend="_bhelix_8cpp">bhelix.cpp</link></para>

<para>Dealing with images with helical symmetry. </para>
</listitem>
            <listitem><para>file <link linkend="_bhisto_8cpp">bhisto.cpp</link></para>

<para>Image histograms. </para>
</listitem>
            <listitem><para>file <link linkend="_bico_8cpp">bico.cpp</link></para>

<para>Program to analyze icosahedral subtomograms. </para>
</listitem>
            <listitem><para>file <link linkend="_bimg_8cpp">bimg.cpp</link></para>

<para>General image processing program. </para>
</listitem>
            <listitem><para>file <link linkend="_bint_8cpp">bint.cpp</link></para>

<para>Interpolation of 2D and 3D images. </para>
</listitem>
            <listitem><para>file <link linkend="_bkernel_8cpp">bkernel.cpp</link></para>

<para>Program to calculate filter kernels. </para>
</listitem>
            <listitem><para>file <link linkend="_blevel_8cpp">blevel.cpp</link></para>

<para>A program to manipulate level masks. </para>
</listitem>
            <listitem><para>file <link linkend="_blocfilt_8cpp">blocfilt.cpp</link></para>

<para>Local resolution analysis. </para>
</listitem>
            <listitem><para>file <link linkend="_blocres_8cpp">blocres.cpp</link></para>

<para>Local resolution analysis. </para>
</listitem>
            <listitem><para>file <link linkend="_bmapdist_8cpp">bmapdist.cpp</link></para>

<para>Calculates a distance criterion between a set of 2D images or 3D maps. </para>
</listitem>
            <listitem><para>file <link linkend="_bmark_8cpp">bmark.cpp</link></para>

<para>Program to generate symmetry axes for mark group symmetries. </para>
</listitem>
            <listitem><para>file <link linkend="_bmask_8cpp">bmask.cpp</link></para>

<para>Generating and manipulating masks. </para>
</listitem>
            <listitem><para>file <link linkend="_bmaskmod_8cpp">bmaskmod.cpp</link></para>

<para>Generating a model from a mask. </para>
</listitem>
            <listitem><para>file <link linkend="_bmatch_8cpp">bmatch.cpp</link></para>

<para>Program to search an image with multiple projections and orient them. </para>
</listitem>
            <listitem><para>file <link linkend="_bmatrix_8cpp">bmatrix.cpp</link></para>

<para>Program to process matrices. </para>
</listitem>
            <listitem><para>file <link linkend="_bmaxpow_8cpp">bmaxpow.cpp</link></para>

<para>Determining orientations by maximum power of 3D reconstruction from single particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_bmd_8cpp">bmd.cpp</link></para>

<para>Molecular dynamics - humble beginnings. </para>
</listitem>
            <listitem><para>file <link linkend="_bmedian_8cpp">bmedian.cpp</link></para>

<para>Program to filter images. </para>
</listitem>
            <listitem><para>file <link linkend="_bmg_8cpp">bmg.cpp</link></para>

<para>Manipulating project and micrograph structures. </para>
</listitem>
            <listitem><para>file <link linkend="_bmg2imod_8cpp">bmg2imod.cpp</link></para>

<para>Converts between <link linkend="_struct_i_m_o_d">IMOD</link> files and a micrograph parameter file. </para>
</listitem>
            <listitem><para>file <link linkend="_bmgalign_8cpp">bmgalign.cpp</link></para>

<para>Aligns micrographs specified in parameter files. </para>
</listitem>
            <listitem><para>file <link linkend="_bmgconvert_8cpp">bmgconvert.cpp</link></para>

<para>Convert between micrograph parameter formats. </para>
</listitem>
            <listitem><para>file <link linkend="_bmgft_8cpp">bmgft.cpp</link></para>

<para>Disk-based 3D reconstruction for a tomography series. </para>
</listitem>
            <listitem><para>file <link linkend="_bmgtransfer_8cpp">bmgtransfer.cpp</link></para>

<para>Transfer pieces of information between micrograph paramater files. </para>
</listitem>
            <listitem><para>file <link linkend="_bmissing_8cpp">bmissing.cpp</link></para>

<para>Generating and manipulating masks. </para>
</listitem>
            <listitem><para>file <link linkend="_bmm_8cpp">bmm.cpp</link></para>

<para>A program to do model mechanics. </para>
</listitem>
            <listitem><para>file <link linkend="_bmod2part_8cpp">bmod2part.cpp</link></para>

<para>Converting from a pseudo-atomic model to particle parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodcol_8cpp">bmodcol.cpp</link></para>

<para>A tool to color models. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodcomp_8cpp">bmodcomp.cpp</link></para>

<para>A tool to compare polyhedra. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodedit_8cpp">bmodedit.cpp</link></para>

<para>A tool to create and edit models. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodel_8cpp">bmodel.cpp</link></para>

<para>Manipulates models. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodmap_8cpp">bmodmap.cpp</link></para>

<para>A tool to genrate a map from a model. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodmask_8cpp">bmodmask.cpp</link></para>

<para>Generating a mask from an atomic model. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodsel_8cpp">bmodsel.cpp</link></para>

<para>Manipulates selections from sets of components as solutions of fits. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodsym_8cpp">bmodsym.cpp</link></para>

<para>Deals with model and component symmetries. </para>
</listitem>
            <listitem><para>file <link linkend="_bmodview_8cpp">bmodview.cpp</link></para>

<para>Manipulates models. </para>
</listitem>
            <listitem><para>file <link linkend="_bmol_8cpp">bmol.cpp</link></para>

<para>A tool to edit and analyze coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_bmoledit_8cpp">bmoledit.cpp</link></para>

<para>A tool to edit coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_bmolhel_8cpp">bmolhel.cpp</link></para>

<para>A program to perform helical symmetry operations on coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_bmolsym_8cpp">bmolsym.cpp</link></para>

<para>A tool to perform symmetry operations on coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_bmontage_8cpp">bmontage.cpp</link></para>

<para>A program to generate a montage from a 3D image or a set of 2D images. </para>
</listitem>
            <listitem><para>file <link linkend="_bmonte_8cpp">bmonte.cpp</link></para>

<para>Program to use a monte carlo metroplis algorithm to energy minimize molecular positions. </para>
</listitem>
            <listitem><para>file <link linkend="_bmultifit_8cpp">bmultifit.cpp</link></para>

<para>Searching for a template in a map and returning multiple hits in a model. </para>
</listitem>
            <listitem><para>file <link linkend="_bmultimask_8cpp">bmultimask.cpp</link></para>

<para>Generating and manipulating composite masks. </para>
</listitem>
            <listitem><para>file <link linkend="_bmultislice_8cpp">bmultislice.cpp</link></para>

<para>Multi-slice simulation of the electron imaging process. </para>
</listitem>
            <listitem><para>file <link linkend="_bnad_8cpp">bnad.cpp</link></para>

<para>Image denoising by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion. </para>
</listitem>
            <listitem><para>file <link linkend="_bnorm_8cpp">bnorm.cpp</link></para>

<para>Program to normalize a set of images based on their histograms. </para>
</listitem>
            <listitem><para>file <link linkend="_bop_8cpp">bop.cpp</link></para>

<para>A program to operate on image pairs. </para>
</listitem>
            <listitem><para>file <link linkend="_borient_8cpp">borient.cpp</link></para>

<para>Determines orientation angles and x,y origins of single particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_bparam_8cpp">bparam.cpp</link></para>

<para>A tool to extract parameters from coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_bpart_8cpp">bpart.cpp</link></para>

<para>Calculates centers of single particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_bpartmulti_8cpp">bpartmulti.cpp</link></para>

<para>Selection of single particle parameters from multiple files for classification. </para>
</listitem>
            <listitem><para>file <link linkend="_bpartsel_8cpp">bpartsel.cpp</link></para>

<para>Selection of single particles for 3D reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_bpatch_8cpp">bpatch.cpp</link></para>

<para>Program to patch tiled image files. </para>
</listitem>
            <listitem><para>file <link linkend="_bpath_8cpp">bpath.cpp</link></para>

<para>A program to analyze paths and cycles in a model. </para>
</listitem>
            <listitem><para>file <link linkend="_bphase_8cpp">bphase.cpp</link></para>

<para>A program to examine phase differences between image pairs. </para>
</listitem>
            <listitem><para>file <link linkend="_bpick_8cpp">bpick.cpp</link></para>

<para>Pick particles in a micrograph given the particle coordinates, or pick particles in a focal series of micrographs with alignment of the micrographs. </para>
</listitem>
            <listitem><para>file <link linkend="_bplane_8cpp">bplane.cpp</link></para>

<para>A tool to expand models. </para>
</listitem>
            <listitem><para>file <link linkend="_bpoly_8cpp">bpoly.cpp</link></para>

<para>A tool to manipulate polyhedral coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_bproject_8cpp">bproject.cpp</link></para>

<para>Projecting a 3D map and calculating comparison statistics of the projections. </para>
</listitem>
            <listitem><para>file <link linkend="_bradial_8cpp">bradial.cpp</link></para>

<para>Polar images and radial averages. </para>
</listitem>
            <listitem><para>file <link linkend="_bradsec_8cpp">bradsec.cpp</link></para>

<para>Generates radial sections from 3D images. </para>
</listitem>
            <listitem><para>file <link linkend="_brandom_8cpp">brandom.cpp</link></para>

<para>Program to generate random images. </para>
</listitem>
            <listitem><para>file <link linkend="_brecadd_8cpp">brecadd.cpp</link></para>

<para>Program to average selected reconstructions. </para>
</listitem>
            <listitem><para>file <link linkend="_brecmod_8cpp">brecmod.cpp</link></para>

<para>A tool to merge data from micrograph reconstruction and model files. </para>
</listitem>
            <listitem><para>file <link linkend="_breconstruct_8cpp">breconstruct.cpp</link></para>

<para>3D reconstruction from single particle images </para>
</listitem>
            <listitem><para>file <link linkend="_brefine_8cpp">brefine.cpp</link></para>

<para>Reciprocal space refinement of orientation parameters of particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_bresolve_8cpp">bresolve.cpp</link></para>

<para>Calculate resolution estimates and Fourier shell statistics. </para>
</listitem>
            <listitem><para>file <link linkend="_bscale_8cpp">bscale.cpp</link></para>

<para>Program to find the scaling of map with respect to a reference. </para>
</listitem>
            <listitem><para>file <link linkend="_bsegment_8cpp">bsegment.cpp</link></para>

<para>Segment images into density regions. </para>
</listitem>
            <listitem><para>file <link linkend="_bseq_8cpp">bseq.cpp</link></para>

<para>A program to manipulate DNA and protein sequences. </para>
</listitem>
            <listitem><para>file <link linkend="_bseqaln_8cpp">bseqaln.cpp</link></para>

<para>A program to analyze aligned protein sequences. </para>
</listitem>
            <listitem><para>file <link linkend="_bseries_8cpp">bseries.cpp</link></para>

<para>Program to align and analyze series of images. </para>
</listitem>
            <listitem><para>file <link linkend="_bsf_8cpp">bsf.cpp</link></para>

<para>Calculating structure factors from atomic models. </para>
</listitem>
            <listitem><para>file <link linkend="_bshell_8cpp">bshell.cpp</link></para>

<para>Generates a shell point component model. </para>
</listitem>
            <listitem><para>file <link linkend="_bsim_8cpp">bsim.cpp</link></para>

<para>A tool to generate a project with random orientations for a molecule and to simulate TEM images from given orientations. </para>
</listitem>
            <listitem><para>file <link linkend="_bspiral_8cpp">bspiral.cpp</link></para>

<para>A tool to generate polyhedra using the spiral algorithm. </para>
</listitem>
            <listitem><para>file <link linkend="_bsplit_8cpp">bsplit.cpp</link></para>

<para>Program to seperate a multi-image file into individual image files. </para>
</listitem>
            <listitem><para>file <link linkend="_bsplitmol_8cpp">bsplitmol.cpp</link></para>

<para>A program to concatenate coordinates from different files. </para>
</listitem>
            <listitem><para>file <link linkend="_bspr_8cpp">bspr.cpp</link></para>

<para>3D reconstruction from single particle images </para>
</listitem>
            <listitem><para>file <link linkend="_bstar_8cpp">bstar.cpp</link></para>

<para>Examines STAR format files. </para>
</listitem>
            <listitem><para>file <link linkend="_bsupix_8cpp">bsupix.cpp</link></para>

<para>Segment images. </para>
</listitem>
            <listitem><para>file <link linkend="_bsurf_8cpp">bsurf.cpp</link></para>

<para>AFM image analysis and reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_bsym_8cpp">bsym.cpp</link></para>

<para>Program to generate symmetry axes for point group symmetries. </para>
</listitem>
            <listitem><para>file <link linkend="_bsymcomp_8cpp">bsymcomp.cpp</link></para>

<para>Finds the best orientation that fits a symmetrized template. </para>
</listitem>
            <listitem><para>file <link linkend="_btile_8cpp">btile.cpp</link></para>

<para>Program to split an image into overlapping tiles. </para>
</listitem>
            <listitem><para>file <link linkend="_btomaln_8cpp">btomaln.cpp</link></para>

<para>Program to do fiducialless alignment of a tilt series. </para>
</listitem>
            <listitem><para>file <link linkend="_btomo_8cpp">btomo.cpp</link></para>

<para>Program to process tomographic series of images. </para>
</listitem>
            <listitem><para>file <link linkend="_btompart_8cpp">btompart.cpp</link></para>

<para>Program to extract single particle images from a tilt series and generate individual reconstructions. </para>
</listitem>
            <listitem><para>file <link linkend="_btomrec_8cpp">btomrec.cpp</link></para>

<para>Disk-based 3D reconstruction for a tomography series. </para>
</listitem>
            <listitem><para>file <link linkend="_btomres_8cpp">btomres.cpp</link></para>

<para>Program to determine the resolution of a tilt series. </para>
</listitem>
            <listitem><para>file <link linkend="_btrack_8cpp">btrack.cpp</link></para>

<para>Program to track fiducial markers in a tomographic series of images. </para>
</listitem>
            <listitem><para>file <link linkend="_btree_8cpp">btree.cpp</link></para>

<para>Program to process trees. </para>
</listitem>
            <listitem><para>file <link linkend="_btube_8cpp">btube.cpp</link></para>

<para>Symmetrizes helical tubes with hexagonal lattices. </para>
</listitem>
            <listitem><para>file <link linkend="_bwater_8cpp">bwater.cpp</link></para>

<para>Molecular dynamics - humble beginnings. </para>
</listitem>
            <listitem><para>file <link linkend="_bxb_8cpp">bxb.cpp</link></para>

<para>Extracting a part of a density map and building a new map. </para>
</listitem>
            <listitem><para>file <link linkend="_bxml_8cpp">bxml.cpp</link></para>

<para>Reads, writes and validates XML files. </para>
</listitem>
            <listitem><para>file <link linkend="_bzfft_8cpp">bzfft.cpp</link></para>

<para>Disk-based z-line transforms for big reconstructions. </para>
</listitem>
            <listitem><para>file <link linkend="_dcount_8cpp">dcount.cpp</link></para>

<para>A program to determine the occupancy of components in models. </para>
</listitem>
            <listitem><para>file <link linkend="_dhand_8cpp">dhand.cpp</link></para>

<para>Compare projections of two oppositely handed reconstructions to images of tilted specimens. </para>
</listitem>
            <listitem><para>file <link linkend="_dimgstats_8cpp">dimgstats.cpp</link></para>

<para>Calculates statistical measures within a set of images or between sets of images. </para>
</listitem>
            <listitem><para>file <link linkend="_dmerge_8cpp">dmerge.cpp</link></para>

<para>Merge images in a defocal or other series, align images before adding together. </para>
</listitem>
            <listitem><para>file <link linkend="_emgrand_8cpp">emgrand.cpp</link></para>

<para>Generate random values for micrograph parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_jave_8cpp">jave.cpp</link></para>

<para>Program to average files and weigh the average in Real/Fourier space. </para>
</listitem>
            <listitem><para>file <link linkend="_jpartdif_8cpp">jpartdif.cpp</link></para>

<para>Analysis of particle differences between two starfiles. </para>
</listitem>
            <listitem><para>file <link linkend="_jsubtomo_8cpp">jsubtomo.cpp</link></para>

<para>Finds particles (subtomograms) in a tomographic reconstruction and refines their origins and orientations. </para>
</listitem>
            <listitem><para>file <link linkend="_jviews_8cpp">jviews.cpp</link></para>

<para>Generates views covering an asymmetric unit or all symmetry related views. </para>
</listitem>
            <listitem><para>file <link linkend="_radon_8cpp">radon.cpp</link></para>

<para>Program to do radon transforms. </para>
</listitem>
            <listitem><para>file <link linkend="_radonrecon_8cpp">radonrecon.cpp</link></para>

<para>Program to do radon transforms. </para>
</listitem>
        </itemizedlist>
</simplesect>
</section>
