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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bshow__boxes_8tcl">
<title>/Users/bernard/b20/bsoft/tcltk/bshow_boxes.tcl File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/tcltk/bshow_boxes.tcl</primary></indexterm>
<para>

<para>Procedures to create, move and destroy particle boxes. </para>
 
</para>
<simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1af67283f31b607b7d71fbff50df6d0c8d">Particles</link></para>

<para>Dialog box to manipulate particle boxes on the main canvas. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ac279b25c267b48b84a2e846261139555">setBoxSize</link></para>

<para>Sets the 3 dimensions for a box from the entries. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a932fccfe37d7e7961fb6afe8b554f425">boxSelect</link> x y</para>

<para>Selects a box or bad area near a clicked location. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a90b97913cc6af0a60fdb5b7b9dcd4d0b">boxCreateSelect</link> x y t</para>

<para>Creates or selects a box or bad area near a clicked location. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a27c523861f5e536962f3545c11b5eecc">boxDrawOldNew</link> id</para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a78adb9a2701fc6c38de12252f2d963bf">boxMove</link> x y</para>

<para>Moves the selected box or bad area to the new coordinates. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a5725a8bb20df1de938bd0c2e5867ae94">boxDraw</link> id</para>

<para>Draws a box or bad area. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a0d2e5dfb4f16a834ecbfe6bec9e7900d">boxesDrawAll</link></para>

<para>Redraws all boxes and bad circles. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a2b122a14d6fe4989b857ed28a8a98256">boxDelete</link> x y</para>

<para>Deletes the selected box or bad area. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1abb20d76a7e67d2765e0227a1129141d9">boxDeleteAll</link></para>

<para>Deletes all boxes. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ad5c9c21470d78aa9a70f97de2d2d6635">boxDeleteCurrent</link></para>

<para>Deletes all boxes in current image. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ab637b888477d13f63f1a89c195c9589f">boxDeleteUnselected</link></para>

<para>Deletes all unselected boxes. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1abf64b677eb37f2dd21a36192a751a138">boxRenumber</link></para>

<para>Renumbers boxes. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1af1add8df1eaff8d5c6e6085373d98549">boxCenter</link></para>

<para>Centers boxes. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ae15c0170ebeee1aeb82a3ce9e3a2be85">templatePicker</link></para>

<para>Picks particles by cross-correlation with a template. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a13223d3e1e9775d086cb495e79705d84">setTemplateScale</link> scale</para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a7d6a2f9c11840a943a9c2bd84bc52cc6">readTemplate</link></para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a2541d6ef65f0f5cc1af69edc3b477f34">saveTemplate</link></para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ab3b9e5f67881431cea6945d18fe0f4a2">updateBoxTemplate</link> w</para>

<para>Updates and shows the particle template. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a23ff328347bc80ee857900dd14967206">doTemplatePicker</link> w</para>

<para>Picks particles using cross-correlation. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1aa0a20cf278dd99c7df21765037857dd4">variancePicker</link></para>

<para>Picks particles from a variance map. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a8e5883b41e9a449d8d808bf0d3c53ca6">doVariancePicker</link> w</para>

<para>Picks particles using variance map. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1aed08800ce104899b2521909a20072be7">updatePartSel</link> args</para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ac8fccba631287feb889baba2a3145e02">updateBoxParam</link></para>

<para>Updates box and bad area parameters. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a5c9e5432cea4f52ee8b0d5f1fb002200">updateBoxCounts</link></para>

<para>Updates box and bad area counts. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ad48035463cf52269b5c4f2385f81e590">updateBoxSelected</link></para>

<para>Updates selected box and bad area counts. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1acd38efbd080dd7791105015d3d761308">extractParticles</link></para>

<para>Extracts particles from the current set of box coordinates. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a776219225e369dd22f7e73a1206d874a">doExtractParticles</link> w</para>

<para>Extracts particles from the current set of box coordinates. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ae591b6efa1f21cb0bd43437bbe451cbb">alignParticles</link></para>

<para>Aligns particles by projection matching to a reference. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a30d3186871db1895885c9d9d6a305797">doAlignParticles</link> w</para>

<para>Executes marker tracking. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1ae371c2fffbc9321f571fedc4085173df">refineParticles</link></para>

<para>Refines particle orientations by central section matching to a reference. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1af39d1d513879df07585b041b2a53d956">doRefineParticles</link> w</para>

<para>Executes particle orientation refinement. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a42e5fff03a1bfd78ac48eea8e3c9f027">selectParticles</link></para>

<para>Selects particles after an alignment run. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a0542f751da1d62479f93b523ed9e5386">showSelectedParticles</link></para>

<para>Shows the current particle selection. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1adfa805534b6981c55a4836e901c7454b">doSelectParticles</link> w</para>

<para>Executes particle selection. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1a87e70f718d57bd776ee419607c3cdeaa">particleReconstruct</link></para>

<para>Reconstructs a single particle. </para>
</listitem>
            <listitem><para><link linkend="_bshow__boxes_8tcl_1addc7c268a49169331783b62cd50ebef5">doReconstruct</link> w</para>

<para>Executes tomogram reconstruction. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Procedures to create, move and destroy particle boxes. </para>

<para><formalpara><title>Author: </title>

<para>Bernard Heymann </para>
</formalpara>
<formalpara><title>Date: </title>

<para>Created: 20010516 </para>

<para>Modified: 20191017 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bshow__boxes_8tcl_1ae591b6efa1f21cb0bd43437bbe451cbb"/>    <section>
    <title>alignParticles()</title>
<indexterm><primary>alignParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>alignParticles</secondary></indexterm>
<para><computeroutput>alignParticles</computeroutput></para><para>

<para>Aligns particles by projection matching to a reference. </para>
</para>
<para>
Definition at line 986 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1af1add8df1eaff8d5c6e6085373d98549"/>    <section>
    <title>boxCenter()</title>
<indexterm><primary>boxCenter</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxCenter</secondary></indexterm>
<para><computeroutput>boxCenter</computeroutput></para><para>

<para>Centers boxes. </para>
</para>
<para>
Definition at line 504 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a90b97913cc6af0a60fdb5b7b9dcd4d0b"/>    <section>
    <title>boxCreateSelect()</title>
<indexterm><primary>boxCreateSelect</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxCreateSelect</secondary></indexterm>
<para><computeroutput>boxCreateSelect x y t </computeroutput></para><para>

<para>Creates or selects a box or bad area near a clicked location. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Box position in canvas coordinates. </para>
</entry>
                            </row>
                            <row>
                                <entry>t</entry>
                                <entry>
<para>Type: &quot;part&quot;/&quot;bad&quot; </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 258 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a2b122a14d6fe4989b857ed28a8a98256"/>    <section>
    <title>boxDelete()</title>
<indexterm><primary>boxDelete</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxDelete</secondary></indexterm>
<para><computeroutput>boxDelete x y </computeroutput></para><para>

<para>Deletes the selected box or bad area. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Box or bad area position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 445 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1abb20d76a7e67d2765e0227a1129141d9"/>    <section>
    <title>boxDeleteAll()</title>
<indexterm><primary>boxDeleteAll</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxDeleteAll</secondary></indexterm>
<para><computeroutput>boxDeleteAll</computeroutput></para><para>

<para>Deletes all boxes. </para>
</para>
<para>
Definition at line 464 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ad5c9c21470d78aa9a70f97de2d2d6635"/>    <section>
    <title>boxDeleteCurrent()</title>
<indexterm><primary>boxDeleteCurrent</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxDeleteCurrent</secondary></indexterm>
<para><computeroutput>boxDeleteCurrent</computeroutput></para><para>

<para>Deletes all boxes in current image. </para>
</para>
<para>
Definition at line 476 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ab637b888477d13f63f1a89c195c9589f"/>    <section>
    <title>boxDeleteUnselected()</title>
<indexterm><primary>boxDeleteUnselected</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxDeleteUnselected</secondary></indexterm>
<para><computeroutput>boxDeleteUnselected</computeroutput></para><para>

<para>Deletes all unselected boxes. </para>
</para>
<para>
Definition at line 485 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a5725a8bb20df1de938bd0c2e5867ae94"/>    <section>
    <title>boxDraw()</title>
<indexterm><primary>boxDraw</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxDraw</secondary></indexterm>
<para><computeroutput>boxDraw id </computeroutput></para><para>

<para>Draws a box or bad area. </para>
</para>

<para>Draws a box and circle with the current box size and number for a selected box, or draws a red circle with the current bad size for a selected bad area.</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>id</entry>
                                <entry>
<para>Box or bad area identifier. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 325 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a27c523861f5e536962f3545c11b5eecc"/>    <section>
    <title>boxDrawOldNew()</title>
<indexterm><primary>boxDrawOldNew</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxDrawOldNew</secondary></indexterm>
<para><computeroutput>boxDrawOldNew id </computeroutput></para><para>
Definition at line 275 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a0d2e5dfb4f16a834ecbfe6bec9e7900d"/>    <section>
    <title>boxesDrawAll()</title>
<indexterm><primary>boxesDrawAll</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxesDrawAll</secondary></indexterm>
<para><computeroutput>boxesDrawAll</computeroutput></para><para>

<para>Redraws all boxes and bad circles. </para>
</para>
<para>
Definition at line 410 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a78adb9a2701fc6c38de12252f2d963bf"/>    <section>
    <title>boxMove()</title>
<indexterm><primary>boxMove</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxMove</secondary></indexterm>
<para><computeroutput>boxMove x y </computeroutput></para><para>

<para>Moves the selected box or bad area to the new coordinates. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Box position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 296 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1abf64b677eb37f2dd21a36192a751a138"/>    <section>
    <title>boxRenumber()</title>
<indexterm><primary>boxRenumber</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxRenumber</secondary></indexterm>
<para><computeroutput>boxRenumber</computeroutput></para><para>

<para>Renumbers boxes. </para>
</para>
<para>
Definition at line 495 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a932fccfe37d7e7961fb6afe8b554f425"/>    <section>
    <title>boxSelect()</title>
<indexterm><primary>boxSelect</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>boxSelect</secondary></indexterm>
<para><computeroutput>boxSelect x y </computeroutput></para><para>

<para>Selects a box or bad area near a clicked location. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>x</entry>
                                <entry>
<para></para>
</entry>
                            </row>
                            <row>
                                <entry>y</entry>
                                <entry>
<para>Box position in canvas coordinates. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 240 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a30d3186871db1895885c9d9d6a305797"/>    <section>
    <title>doAlignParticles()</title>
<indexterm><primary>doAlignParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doAlignParticles</secondary></indexterm>
<para><computeroutput>doAlignParticles w </computeroutput></para><para>

<para>Executes marker tracking. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1060 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a776219225e369dd22f7e73a1206d874a"/>    <section>
    <title>doExtractParticles()</title>
<indexterm><primary>doExtractParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doExtractParticles</secondary></indexterm>
<para><computeroutput>doExtractParticles w </computeroutput></para><para>

<para>Extracts particles from the current set of box coordinates. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>Dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 958 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1addc7c268a49169331783b62cd50ebef5"/>    <section>
    <title>doReconstruct()</title>
<indexterm><primary>doReconstruct</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doReconstruct</secondary></indexterm>
<para><computeroutput>doReconstruct w </computeroutput></para><para>

<para>Executes tomogram reconstruction. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1351 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1af39d1d513879df07585b041b2a53d956"/>    <section>
    <title>doRefineParticles()</title>
<indexterm><primary>doRefineParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doRefineParticles</secondary></indexterm>
<para><computeroutput>doRefineParticles w </computeroutput></para><para>

<para>Executes particle orientation refinement. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1164 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1adfa805534b6981c55a4836e901c7454b"/>    <section>
    <title>doSelectParticles()</title>
<indexterm><primary>doSelectParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doSelectParticles</secondary></indexterm>
<para><computeroutput>doSelectParticles w </computeroutput></para><para>

<para>Executes particle selection. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>dialog window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 1256 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a23ff328347bc80ee857900dd14967206"/>    <section>
    <title>doTemplatePicker()</title>
<indexterm><primary>doTemplatePicker</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doTemplatePicker</secondary></indexterm>
<para><computeroutput>doTemplatePicker w </computeroutput></para><para>

<para>Picks particles using cross-correlation. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>the window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 686 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a8e5883b41e9a449d8d808bf0d3c53ca6"/>    <section>
    <title>doVariancePicker()</title>
<indexterm><primary>doVariancePicker</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>doVariancePicker</secondary></indexterm>
<para><computeroutput>doVariancePicker w </computeroutput></para><para>

<para>Picks particles using variance map. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>the window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 748 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1acd38efbd080dd7791105015d3d761308"/>    <section>
    <title>extractParticles()</title>
<indexterm><primary>extractParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>extractParticles</secondary></indexterm>
<para><computeroutput>extractParticles</computeroutput></para><para>

<para>Extracts particles from the current set of box coordinates. </para>
</para>
<para>
Definition at line 881 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a87e70f718d57bd776ee419607c3cdeaa"/>    <section>
    <title>particleReconstruct()</title>
<indexterm><primary>particleReconstruct</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>particleReconstruct</secondary></indexterm>
<para><computeroutput>particleReconstruct</computeroutput></para><para>

<para>Reconstructs a single particle. </para>
</para>
<para>
Definition at line 1284 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1af67283f31b607b7d71fbff50df6d0c8d"/>    <section>
    <title>Particles()</title>
<indexterm><primary>Particles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>Particles</secondary></indexterm>
<para><computeroutput>Particles</computeroutput></para><para>

<para>Dialog box to manipulate particle boxes on the main canvas. </para>
</para>
<para>
Definition at line 31 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a7d6a2f9c11840a943a9c2bd84bc52cc6"/>    <section>
    <title>readTemplate()</title>
<indexterm><primary>readTemplate</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>readTemplate</secondary></indexterm>
<para><computeroutput>readTemplate</computeroutput></para><para>
Definition at line 621 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ae371c2fffbc9321f571fedc4085173df"/>    <section>
    <title>refineParticles()</title>
<indexterm><primary>refineParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>refineParticles</secondary></indexterm>
<para><computeroutput>refineParticles</computeroutput></para><para>

<para>Refines particle orientations by central section matching to a reference. </para>
</para>
<para>
Definition at line 1091 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a2541d6ef65f0f5cc1af69edc3b477f34"/>    <section>
    <title>saveTemplate()</title>
<indexterm><primary>saveTemplate</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>saveTemplate</secondary></indexterm>
<para><computeroutput>saveTemplate</computeroutput></para><para>
Definition at line 641 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a42e5fff03a1bfd78ac48eea8e3c9f027"/>    <section>
    <title>selectParticles()</title>
<indexterm><primary>selectParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>selectParticles</secondary></indexterm>
<para><computeroutput>selectParticles</computeroutput></para><para>

<para>Selects particles after an alignment run. </para>
</para>
<para>
Definition at line 1198 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ac279b25c267b48b84a2e846261139555"/>    <section>
    <title>setBoxSize()</title>
<indexterm><primary>setBoxSize</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>setBoxSize</secondary></indexterm>
<para><computeroutput>setBoxSize</computeroutput></para><para>

<para>Sets the 3 dimensions for a box from the entries. </para>
</para>
<para>
Definition at line 208 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a13223d3e1e9775d086cb495e79705d84"/>    <section>
    <title>setTemplateScale()</title>
<indexterm><primary>setTemplateScale</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>setTemplateScale</secondary></indexterm>
<para><computeroutput>setTemplateScale scale </computeroutput></para><para>
Definition at line 601 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a0542f751da1d62479f93b523ed9e5386"/>    <section>
    <title>showSelectedParticles()</title>
<indexterm><primary>showSelectedParticles</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>showSelectedParticles</secondary></indexterm>
<para><computeroutput>showSelectedParticles</computeroutput></para><para>

<para>Shows the current particle selection. </para>
</para>
<para>
Definition at line 1245 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ae15c0170ebeee1aeb82a3ce9e3a2be85"/>    <section>
    <title>templatePicker()</title>
<indexterm><primary>templatePicker</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>templatePicker</secondary></indexterm>
<para><computeroutput>templatePicker</computeroutput></para><para>

<para>Picks particles by cross-correlation with a template. </para>
</para>
<para>
Definition at line 513 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1a5c9e5432cea4f52ee8b0d5f1fb002200"/>    <section>
    <title>updateBoxCounts()</title>
<indexterm><primary>updateBoxCounts</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>updateBoxCounts</secondary></indexterm>
<para><computeroutput>updateBoxCounts</computeroutput></para><para>

<para>Updates box and bad area counts. </para>
</para>
<para>
Definition at line 827 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ac8fccba631287feb889baba2a3145e02"/>    <section>
    <title>updateBoxParam()</title>
<indexterm><primary>updateBoxParam</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>updateBoxParam</secondary></indexterm>
<para><computeroutput>updateBoxParam</computeroutput></para><para>

<para>Updates box and bad area parameters. </para>
</para>
<para>
Definition at line 780 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ad48035463cf52269b5c4f2385f81e590"/>    <section>
    <title>updateBoxSelected()</title>
<indexterm><primary>updateBoxSelected</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>updateBoxSelected</secondary></indexterm>
<para><computeroutput>updateBoxSelected</computeroutput></para><para>

<para>Updates selected box and bad area counts. </para>
</para>
<para>
Definition at line 857 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1ab3b9e5f67881431cea6945d18fe0f4a2"/>    <section>
    <title>updateBoxTemplate()</title>
<indexterm><primary>updateBoxTemplate</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>updateBoxTemplate</secondary></indexterm>
<para><computeroutput>updateBoxTemplate w </computeroutput></para><para>

<para>Updates and shows the particle template. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>w</entry>
                                <entry>
<para>the window. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                </para>
<para>
Definition at line 659 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1aed08800ce104899b2521909a20072be7"/>    <section>
    <title>updatePartSel()</title>
<indexterm><primary>updatePartSel</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>updatePartSel</secondary></indexterm>
<para><computeroutput>updatePartSel args </computeroutput></para><para>
Definition at line 769 of file bshow_boxes.tcl.</para>
    </section><anchor xml:id="_bshow__boxes_8tcl_1aa0a20cf278dd99c7df21765037857dd4"/>    <section>
    <title>variancePicker()</title>
<indexterm><primary>variancePicker</primary><secondary>bshow_boxes.tcl</secondary></indexterm>
<indexterm><primary>bshow_boxes.tcl</primary><secondary>variancePicker</secondary></indexterm>
<para><computeroutput>variancePicker</computeroutput></para><para>

<para>Picks particles from a variance map. </para>
</para>
<para>
Definition at line 710 of file bshow_boxes.tcl.</para>
</section>
</section>
</section>
