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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_1d197ef0d9947f4cc1ac44e7f59e2b57">
<title>/Users/bernard/b20/bsoft/src/mg Directory Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/mg Directory Reference</primary></indexterm>
<simplesect>
    <title>Files    </title>
        <itemizedlist>
            <listitem><para>file <link linkend="_mg__align_8cpp">mg_align.cpp</link></para>

<para>Functions to align micrographs or coordinates from micrographs and apply the resultant transformation. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__class_8cpp">mg_class.cpp</link></para>

<para>Classifies raw single particle images with respect to multiple models. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__ctf_8cpp">mg_ctf.cpp</link></para>

<para>Functions for CTF (contrast transfer function) processing. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__ctf__fit_8cpp">mg_ctf_fit.cpp</link></para>

<para>Functions for CTF (contrast transfer function) processing. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__extract_8cpp">mg_extract.cpp</link></para>

<para>Functions to extract particles from micrographs. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__hand_8cpp">mg_hand.cpp</link></para>

<para>Functions for comparing projections of two oppositely handed reconstructions to images of tilted specimens. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__helix_8cpp">mg_helix.cpp</link></para>

<para>Functions to process helical data. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__img__proc_8cpp">mg_img_proc.cpp</link></para>

<para>Functions for image processing from micrograph structures. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__marker_8cpp">mg_marker.cpp</link></para>

<para>Functions for dealing with markers and linkers. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__merge_8cpp">mg_merge.cpp</link></para>

<para>Library functions to merge images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__multiple_8cpp">mg_multiple.cpp</link></para>

<para>Selection of single particle parameters from multiple files for classification. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__multislice_8cpp">mg_multislice.cpp</link></para>

<para>Generates and manipulates projects for multislice calculations. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__orient_8cpp">mg_orient.cpp</link></para>

<para>Determines orientation angles and x,y origins of single particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__particle__select_8cpp">mg_particle_select.cpp</link></para>

<para>Select particles. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__particles_8cpp">mg_particles.cpp</link></para>

<para>Calculates centers of single particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__pick_8cpp">mg_pick.cpp</link></para>

<para>Functions for picking single particle images from a micrograph. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__processing_8cpp">mg_processing.cpp</link></para>

<para>Functions for micrograph processing. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__random_8cpp">mg_random.cpp</link></para>

<para>Functions for applying some randomization to parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__reconstruct_8cpp">mg_reconstruct.cpp</link></para>

<para>Functions for reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__refine_8cpp">mg_refine.cpp</link></para>

<para>Reciprocal space refinement of orientation parameters of particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__subtomo_8cpp">mg_subtomo.cpp</link></para>

<para>Functions to find particles (subtomograms) in a tomographic reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomo__rec_8cpp">mg_tomo_rec.cpp</link></para>

<para>Functions to do a tomographic reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomo__resol_8cpp">mg_tomo_resol.cpp</link></para>

<para>Functions to assess the resoltion of a tomographic tilt series. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomo__track_8cpp">mg_tomo_track.cpp</link></para>

<para>Functions to track fiducial markers in a tomographic series of images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomography_8cpp">mg_tomography.cpp</link></para>

<para>Functions to manage tomographic series of images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__xtal_8cpp">mg_xtal.cpp</link></para>

<para>Functions to process crystallographic data. </para>
</listitem>
        </itemizedlist>
</simplesect>
</section>
