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<!DOCTYPE html>
<html lang='en'>
<head>
<title>RNA2D.js</title>
<meta charset='utf-8'>
<link href='static/css/bootstrap.min.css' rel='stylesheet'>
<link href='static/css/bootstrap-toggle-buttons.css' rel='stylesheet'>
<link href="static/css/chosen.css" rel='stylesheet'>
<link rel="stylesheet" href="static/css/github-fork-ribbon.css" />
<!--[if IE]>
<link rel="stylesheet" href="static/css/github-fork-ribbon.ie.css" />
<![endif]-->
<link href='static/css/main.css' rel='stylesheet'>
<script src='static/jmol/Jmol.js'></script>
<script src='static/js/sizzle.js'></script>
<script src='static/js/jquery.min.js'></script>
<script src='static/js/jquery.jmolTools.js'></script>
<script src='static/js/chosen.jquery.js'></script>
<script src='static/js/d3.js'></script>
<script src='static/js/bootstrap.min.js'></script>
<script src='rna2d.js'></script>
<script src='jquery.rna2d.js'></script>
<script src='static/js/app.js'></script>
</head>
<body>
<div class="github-fork-ribbon-wrapper right">
<div class="github-fork-ribbon">
<a href="https://github.com/blakesweeney/rna2d.js">Fork me on GitHub</a>
</div>
</div>
<div class='navbar navbar-inverse navbar-fixed-top'>
<div class='navbar-inner'>
<a class='brand' href='#'> RNA2d.js</a>
<ul class='nav'>
<li><a href='#modal' data-toggle="modal">About</a></li>
</ul>
</div>
</div>
<div class='container-fluid'>
<div class='page-header'>
<h1>RNA2d.js <small>Interact with RNA 2D structures</small></h1>
</div>
<div id='view-div' class='row'>
<div id="structures" class='span2'>
<select id="structure-select" class="chzn-select">
<option value="2AW7">2AW7</option>
<option value="1J5E">3F4G</option>
</select>
</div>
<div class="span3 offset2">
<div id='view-buttons' class='btn-group' data-toggle='buttons-radio'>
<button id='airpot-view' class="btn active view-control" data-view='airport'>
Airport
</button>
<button id='circular-view' class="btn view-control" data-view='circular'>
Circular
</button>
</div>
</div>
</div>
<div id='example' class='row'>
<div id='controls' class='span1'>
<a href="#modal" role="button" class="btn btn-primary btn-block" data-toggle="modal">Help</a>
<div class="btn-toolbar">
<!-- <h5>Mode</h5> -->
<button type="button" id="mode-toggle" class="btn btn-block"
data-normal-text="Select" data-loading-text="Click">Select</button>
</div>
<div id="control-groups" class="accordian">
<div id="motif-controls" class="accordion-group">
<div class="accordion-heading">
<a class="accordion-toggle" data-toggle="collapse" data-parent="#control-groups"
href="#motif-control-buttons">Motifs</a>
</div>
<div id="motif-control-buttons" class="accordion-body collapse">
<div class="accordion-inner">
<button id="il-toggle" type="button" class="btn btn-block
active motif-control" data-toggle="button" data-toggable='IL'>IL</button>
<button id="hl-toggle" type="button" class="btn btn-block
motif-control" data-toggle="button" data-toggable='HL'>HL</button>
</div>
</div>
</div>
<div id="nucleotide-controls" class="accordion-group">
<div class="accordion-heading">
<a class="accordion-toggle" data-toggle="collapse" data-parent="#control-groups"
href="#nucleotide-control-buttons">Units</a>
</div>
<div id="nucleotide-control-buttons" class="accordion-body collapse">
<div class="accordion-inner">
<div class="button-group">
<div class="btn-toolbar">
<button id="sequence-control" class="btn btn-small">
<i class="icon-tint"></i>
</button>
</div>
</div>
</div>
</div>
</div>
<div id="interaction-controls" class="accordion-group">
<div class="accordion-heading">
<a class="accordion-toggle" data-toggle="collapse"
data-parent="#control-groups" href="#interaction-control-buttons">Pairs</a>
</div>
<div id="interaction-control-buttons" class="accordion-body collapse in">
<div class="accordion-inner" data-toggle="buttons-checkbox">
<div class="btn-toolbar">
<button type="button" id='all-toggle'
class="btn btn-block interaction-toggle"
data-toggable='tWW,cWS,tWS,cWH,tWH,cSH,tSH,cSS,tSS,cHH,tHH'
data-activate='cWW'>
All
</button>
</div>
<div class="btn-toolbar">
<button type="button" id='cWW-toggle' class="btn btn-block
interaction-toggle active" data-toggable='cWW'>cWW</button>
</div>
<div class="btn-toolbar">
<button type="button" id='tWW-toggle' class="btn btn-block
tWW interaction-toggle" data-toggable='tWW'>tWW</button>
</div>
<div class="btn-toolbar">
<button type="button" id="cWS-toggle" class="btn btn-block
cWS interaction-toggle" data-toggable='cWS'>cWS</button>
</div>
<div class="btn-toolbar">
<button type="button" id="tWS-toggle" class="btn btn-block
tWS interaction-toggle" data-toggable='tWS'>tWS</button>
</div>
<div class="btn-toolbar">
<button type="button" id="cWH-toggle" class="btn btn-block
cWH interaction-toggle" data-toggable='cWH'>cWH</button>
</div>
<div class="btn-toolbar">
<button type="button" id="tWH-toggle" class="btn btn-block
tWH interaction-toggle" data-toggable='tWH'>tWH</button>
</div>
<div class="btn-toolbar">
<button type="button" id="cSH-toggle" class="btn btn-block
cSH interaction-toggle" data-toggable='cSH'>cSH</button>
</div>
<div class="btn-toolbar">
<button type="button" id="tSH-toggle" class="btn btn-block
tSH interaction-toggle" data-toggable='tSH'>tSH</button>
</div>
<div class="btn-toolbar">
<button type="button" id="cSS-toggle" class="btn btn-block
cSS interaction-toggle" data-toggable='cSS'>cSS</button>
</div>
<div class="btn-toolbar">
<button type="button" id="tSS-toggle" class="btn btn-block
tSS interaction-toggle" data-toggable='tSS'>tSS</button>
</div>
<div class="btn-toolbar">
<button type="button" id="cHH-toggle" class="btn btn-block
cHH interaction-toggle" data-toggable='cHH'>cHH</button>
</div>
<div class="btn-toolbar">
<button type="button" id="tHH-toggle" class="btn btn-block
tHH interaction-toggle" data-toggable='tHH'>tHH</button>
</div>
</div>
</div>
</div>
</div>
</div>
<div class='span6'>
<!-- 2D structure -->
<div id='rna-2d'></div>
</div>
<div class='jmol-viewer'>
<div id="overflow" class="alert alert-error" style="display: none">
<button type="button" class="close" data-dismiss="alert">×</button>
<strong>Error!</strong> Can only select 200 nts at a time
</div>
<div id='jmol' class='well'>
<script type="text/javascript">
jmolInitialize("./static/jmol");
jmolSetDocument(0);
jmolSetAppletColor("#ffffff");
</script>
</div>
<div id="about-selection" class="well" style="display: none">
</div>
</div>
</div>
<div id="modal" class='modal hide fade' tabindex="-1" role="dialog">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h3>RNA2D.js</h3>
</div>
<div class="modal-body">
<p>
<a href='https://github.com/blakesweeney/rna2d.js'>RNA2D.js</a>
is a tool to visualize and interact with RNA Secondary
structures. It is meant to create the standard airport diagrams and
provide a way to interact with them. Currently, we can easily
integrate the 2D visualization with the 3D visualization provided by
<a href='https://github.com/AntonPetrov/jmolTools'>jmolTools</a>.
</p>
<a class="btn btn-primary" href="http://rna.bgsu.edu/main/interacting-with-2d-structures" target="_blank">More details</a>
<h4>Interactivity</h4>
<p>
In the default select mode,
click and drag to create a selection box. All nucleotides within
the selection box will be displayed in a jmol window to the right.
</p>
<p>
The selection box is dragable and resizeable. Click inside and
drag to move it. Click on the border and drag to resize it.
</p>
<p>
In click mode, click on a interaction to display the interaction
in 3D. To switch to the click mode use the selection mode control.
</p>
<p>
Interactions are displayed as black bars connecting nucleotides,
by default only cWW interactions are displayed. To display other
interactions use the interaction controls.
</p>
</div>
<div class="modal-footer">
<button class="btn" data-dismiss="modal" aria-hidden="true">Close</button>
</div>
</div>
<div class='row'>
<div class='span9'>
<h2>Data</h2>
<p>
This example uses the 16S <i>E. coli</i> secondary structure provided
<a href='http://www.rna.ccbb.utexas.edu/'>Comparative RNA Web Site and
Project</a> and interaction annotations of <a
href='http://www.rcsb.org/pdb/explore.do?structureId=2aw7'>2AW7</a>
(<a href='http://rna.bgsu.edu/rna3dhub/pdb/2AW7'>RNA 3D Hub</a>) from
<a href='http://rna.bgsu.edu/main/software/fr3d/'>FR3D</a>.
</p>
</div>
</div>
</div>
</body>
</html>