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<!DOCTYPE html>
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<title>Chapter 11 3Dmol mapping description | MicrobioSee User Manual</title>
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<meta name="author" content="Jinhui Li, Yimeng Sang, Sen Zeng." />
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<li><a href="https://microbiosee.gxu.edu.cn">MicrobioSee Guide</a></li>
<li class="divider"></li>
<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> MicrobioSee Users’ Guide</a>
<ul>
<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#microbiosee-a-visualization-tool-for-microbial-multiomics."><i class="fa fa-check"></i><b>1.1</b> Microbiosee: a visualization tool for microbial multiomics.</a></li>
<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#issues-and-contact"><i class="fa fa-check"></i><b>1.2</b> Issues and Contact</a></li>
<li class="chapter" data-level="1.3" data-path="index.html"><a href="index.html#license"><i class="fa fa-check"></i><b>1.3</b> License</a></li>
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<li class="chapter" data-level="2" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html"><i class="fa fa-check"></i><b>2</b> Alpha diversity mapping description</a>
<ul>
<li class="chapter" data-level="2.1" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#upload-sample-data"><i class="fa fa-check"></i><b>2.1</b> Upload sample data</a></li>
<li class="chapter" data-level="2.2" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#different-alpha-index-values-and-statistical-methods"><i class="fa fa-check"></i><b>2.2</b> Different alpha index values ,and statistical methods</a></li>
<li class="chapter" data-level="2.3" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#different-drawing-tools"><i class="fa fa-check"></i><b>2.3</b> Different drawing tools</a>
<ul>
<li class="chapter" data-level="2.3.1" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#box-plot"><i class="fa fa-check"></i><b>2.3.1</b> box-plot</a></li>
<li class="chapter" data-level="2.3.2" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#pirates"><i class="fa fa-check"></i><b>2.3.2</b> pirates</a></li>
<li class="chapter" data-level="2.3.3" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#cloudyrain"><i class="fa fa-check"></i><b>2.3.3</b> cloudyrain</a></li>
<li class="chapter" data-level="2.3.4" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#violin"><i class="fa fa-check"></i><b>2.3.4</b> violin</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html"><i class="fa fa-check"></i><b>3</b> Beta diversity mapping description</a>
<ul>
<li class="chapter" data-level="3.1" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#upload-sample-data-1"><i class="fa fa-check"></i><b>3.1</b> Upload sample data</a></li>
<li class="chapter" data-level="3.2" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#different-beta-diversity-analysis-tools"><i class="fa fa-check"></i><b>3.2</b> Different beta diversity analysis tools</a>
<ul>
<li class="chapter" data-level="3.2.1" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#different-drawing-tools-1"><i class="fa fa-check"></i><b>3.2.1</b> Different drawing tools</a></li>
<li class="chapter" data-level="3.2.2" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#pcoa"><i class="fa fa-check"></i><b>3.2.2</b> PCoA</a></li>
<li class="chapter" data-level="3.2.3" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#pca"><i class="fa fa-check"></i><b>3.2.3</b> PCA</a></li>
<li class="chapter" data-level="3.2.4" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#nmds"><i class="fa fa-check"></i><b>3.2.4</b> NMDS</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="stack-column-charts-mapping-description.html"><a href="stack-column-charts-mapping-description.html"><i class="fa fa-check"></i><b>4</b> Stack column charts mapping description</a>
<ul>
<li class="chapter" data-level="4.1" data-path="stack-column-charts-mapping-description.html"><a href="stack-column-charts-mapping-description.html#upload-sample-data-2"><i class="fa fa-check"></i><b>4.1</b> Upload sample data</a></li>
<li class="chapter" data-level="4.2" data-path="stack-column-charts-mapping-description.html"><a href="stack-column-charts-mapping-description.html#draw"><i class="fa fa-check"></i><b>4.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="venn-mapping-description.html"><a href="venn-mapping-description.html"><i class="fa fa-check"></i><b>5</b> Venn mapping description</a>
<ul>
<li class="chapter" data-level="5.1" data-path="venn-mapping-description.html"><a href="venn-mapping-description.html#upload-sample-data-3"><i class="fa fa-check"></i><b>5.1</b> Upload sample data</a></li>
<li class="chapter" data-level="5.2" data-path="venn-mapping-description.html"><a href="venn-mapping-description.html#draw-1"><i class="fa fa-check"></i><b>5.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="upset-mapping-description.html"><a href="upset-mapping-description.html"><i class="fa fa-check"></i><b>6</b> Upset mapping description</a>
<ul>
<li class="chapter" data-level="6.1" data-path="upset-mapping-description.html"><a href="upset-mapping-description.html#upload-sample-data-4"><i class="fa fa-check"></i><b>6.1</b> Upload sample data</a></li>
<li class="chapter" data-level="6.2" data-path="upset-mapping-description.html"><a href="upset-mapping-description.html#draw-2"><i class="fa fa-check"></i><b>6.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="bubble-mapping-description.html"><a href="bubble-mapping-description.html"><i class="fa fa-check"></i><b>7</b> Bubble mapping description</a>
<ul>
<li class="chapter" data-level="7.1" data-path="bubble-mapping-description.html"><a href="bubble-mapping-description.html#upload-sample-data-5"><i class="fa fa-check"></i><b>7.1</b> Upload sample data</a></li>
<li class="chapter" data-level="7.2" data-path="bubble-mapping-description.html"><a href="bubble-mapping-description.html#draw-3"><i class="fa fa-check"></i><b>7.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="volcano-mapping-description.html"><a href="volcano-mapping-description.html"><i class="fa fa-check"></i><b>8</b> Volcano mapping description</a>
<ul>
<li class="chapter" data-level="8.1" data-path="volcano-mapping-description.html"><a href="volcano-mapping-description.html#upload-sample-data-6"><i class="fa fa-check"></i><b>8.1</b> Upload sample data</a></li>
<li class="chapter" data-level="8.2" data-path="volcano-mapping-description.html"><a href="volcano-mapping-description.html#draw-4"><i class="fa fa-check"></i><b>8.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="scatter-mapping-description.html"><a href="scatter-mapping-description.html"><i class="fa fa-check"></i><b>9</b> Scatter mapping description</a>
<ul>
<li class="chapter" data-level="9.1" data-path="scatter-mapping-description.html"><a href="scatter-mapping-description.html#upload-sample-data-7"><i class="fa fa-check"></i><b>9.1</b> Upload sample data</a></li>
<li class="chapter" data-level="9.2" data-path="scatter-mapping-description.html"><a href="scatter-mapping-description.html#draw-5"><i class="fa fa-check"></i><b>9.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="rose-mapping-description.html"><a href="rose-mapping-description.html"><i class="fa fa-check"></i><b>10</b> Rose mapping description</a>
<ul>
<li class="chapter" data-level="10.1" data-path="rose-mapping-description.html"><a href="rose-mapping-description.html#upload-sample-data-8"><i class="fa fa-check"></i><b>10.1</b> Upload sample data</a></li>
<li class="chapter" data-level="10.2" data-path="rose-mapping-description.html"><a href="rose-mapping-description.html#draw-6"><i class="fa fa-check"></i><b>10.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html"><i class="fa fa-check"></i><b>11</b> 3Dmol mapping description</a>
<ul>
<li class="chapter" data-level="11.1" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#upload-sample-data-9"><i class="fa fa-check"></i><b>11.1</b> Upload sample data</a></li>
<li class="chapter" data-level="11.2" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#draw-7"><i class="fa fa-check"></i><b>11.2</b> Draw</a></li>
<li class="chapter" data-level="11.3" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#the-tool-provides-two-ways-to-draw-3d-drawings."><i class="fa fa-check"></i><b>11.3</b> The tool provides two ways to draw 3d drawings.</a>
<ul>
<li class="chapter" data-level="11.3.1" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#datafile-way"><i class="fa fa-check"></i><b>11.3.1</b> Datafile way</a></li>
<li class="chapter" data-level="11.3.2" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#pdb-id-way"><i class="fa fa-check"></i><b>11.3.2</b> PDB id way</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="12" data-path="rose-mapping-description-1.html"><a href="rose-mapping-description-1.html"><i class="fa fa-check"></i><b>12</b> Rose mapping description</a>
<ul>
<li class="chapter" data-level="12.1" data-path="rose-mapping-description-1.html"><a href="rose-mapping-description-1.html#upload-sample-data-10"><i class="fa fa-check"></i><b>12.1</b> Upload sample data</a></li>
<li class="chapter" data-level="12.2" data-path="rose-mapping-description-1.html"><a href="rose-mapping-description-1.html#draw-8"><i class="fa fa-check"></i><b>12.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="histogram-mapping-description.html"><a href="histogram-mapping-description.html"><i class="fa fa-check"></i><b>13</b> Histogram mapping description</a>
<ul>
<li class="chapter" data-level="13.1" data-path="histogram-mapping-description.html"><a href="histogram-mapping-description.html#upload-sample-data-11"><i class="fa fa-check"></i><b>13.1</b> Upload sample data</a></li>
<li class="chapter" data-level="13.2" data-path="histogram-mapping-description.html"><a href="histogram-mapping-description.html#draw-9"><i class="fa fa-check"></i><b>13.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="pie-mapping-description.html"><a href="pie-mapping-description.html"><i class="fa fa-check"></i><b>14</b> Pie mapping description</a>
<ul>
<li class="chapter" data-level="14.1" data-path="pie-mapping-description.html"><a href="pie-mapping-description.html#upload-sample-data-12"><i class="fa fa-check"></i><b>14.1</b> Upload sample data</a></li>
<li class="chapter" data-level="14.2" data-path="pie-mapping-description.html"><a href="pie-mapping-description.html#draw-10"><i class="fa fa-check"></i><b>14.2</b> draw</a></li>
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<section class="normal" id="section-">
<div id="dmol-mapping-description" class="section level1" number="11">
<h1><span class="header-section-number">Chapter 11</span> 3Dmol mapping description</h1>
<div id="upload-sample-data-9" class="section level2" number="11.1">
<h2><span class="header-section-number">11.1</span> Upload sample data</h2>
<p>Such as this.</p>
<p>For more patterns on input files, you can download them from our <strong>Download Sample Files button</strong>.</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200185.png" style="zoom: 50%;" /></p>
<table>
<colgroup>
<col width="100%" />
</colgroup>
<thead>
<tr class="header">
<th>x</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>HEADER HYDROLASE 15-JUL-20 6ZSL</td>
</tr>
<tr class="even">
<td>TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 HELICASE AT 1.94 ANGSTROM</td>
</tr>
<tr class="odd">
<td>TITLE 2 RESOLUTION</td>
</tr>
<tr class="even">
<td>COMPND MOL_ID: 1;</td>
</tr>
<tr class="odd">
<td>COMPND 2 MOLECULE: SARS-COV-2 HELICASE NSP13;</td>
</tr>
<tr class="even">
<td>COMPND 3 CHAIN: B, A;</td>
</tr>
<tr class="odd">
<td>COMPND 4 SYNONYM: PP1AB,ORF1AB POLYPROTEIN,SARS-COV-2 HELICASE NSP13;</td>
</tr>
<tr class="even">
<td>COMPND 5 EC: 3.4.19.12,3.4.22.-,3.4.22.69,2.7.7.48,3.6.4.12,3.6.4.13,3.1.13.-,</td>
</tr>
<tr class="odd">
<td>COMPND 6 3.1.-.-,2.1.1.-;</td>
</tr>
</tbody>
</table>
</div>
<div id="draw-7" class="section level2" number="11.2">
<h2><span class="header-section-number">11.2</span> Draw</h2>
</div>
<div id="the-tool-provides-two-ways-to-draw-3d-drawings." class="section level2" number="11.3">
<h2><span class="header-section-number">11.3</span> The tool provides two ways to draw 3d drawings.</h2>
<ul>
<li>Enter the <strong>protein id</strong> in the PDB database, and the 3D map can be automatically generated.</li>
<li>According to the <strong>format</strong> of the sample number, upload the data of the corresponding protein and generate a map.</li>
</ul>
<div id="datafile-way" class="section level3" number="11.3.1">
<h3><span class="header-section-number">11.3.1</span> Datafile way</h3>
<p>Input document <strong>format</strong> (‘pdb,’ ‘sdf,’ ‘xyz,’ ‘pqr,’ or ‘mol2’).</p>
<p><em>Note that the selected format must be consistent with the format of the uploaded file before drawing.</em></p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200186.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200187.png" style="zoom:33%;" /></p>
<p>Whether to <strong>keep or strip hydrogens</strong> from imported model.</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200188.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200189.png" style="zoom:33%;" /></p>
<p><strong>style of cartoon</strong> rendering (“trace,” “oval,” “rectangle” (default), “parabola,” “edged”).</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200190.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200191.png" style="zoom:33%;" /></p>
</div>
<div id="pdb-id-way" class="section level3" number="11.3.2">
<h3><span class="header-section-number">11.3.2</span> PDB id way</h3>
<p>Enter the <strong>protein id</strong> in the PDB database, and the 3D map can be automatically generated.</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200192.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112200193.png" style="zoom:33%;" /></p>
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