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molecule_view.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="icon" type="image/png" href="./Images/C60_logo_circle.png">
<link rel="stylesheet" href="site_style.css">
<!--<meta name="viewport" content="width=device-width, initial-scale=1.0" />-->
<title>JSmol Tutorial</title>
<!--<link rel="stylesheet" href="site_style.css">-->
<!--<script type="text/javascript" src="jsmol/JSmol.min.js"></script>-->
<!--<script type="text/javascript" src="jmol-16.1.11/jsmol/JSmol.min.js"></script>-->
<!--<script src="/jmol-16.1.11/jsmol/js/Jmol2.js"></script>-->
<!--<script> jmolInitialize("/jmol-16.1.11/jsmol");</script>-->
<!--
<script type="text/javascript">
Jmol._isAsync = false;
// last update 2/18/2014 2:10:06 PM
var jmolApplet0; // set up in HTML table, below
// logic is set by indicating order of USE -- default is HTML5 for this test page, though
var s = document.location.search;
// Developers: The _debugCode flag is checked in j2s/core/core.z.js,
// and, if TRUE, skips loading the core methods, forcing those
// to be read from their individual directories. Set this
// true if you want to do some code debugging by inserting
// System.out.println, document.title, or alert commands
// anywhere in the Java or Jmol code.
Jmol._debugCode = (s.indexOf("debugcode") >= 0);
jmol_isReady = function(applet) {
document.title = (applet._id + " - Jmol " + Jmol.___JmolVersion)
Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
}
var Info = {
width: 420,
height: 300,
debug: false,
color: "0xFFFFFF",
addSelectionOptions: true,
use: "HTML5", // JAVA HTML5 WEBGL are all options
j2sPath: "jmol-16.1.11/jsmol/j2s", // this needs to point to where the j2s directory is.
jarPath: "jmol-16.1.11/jsmol/j2s/java",// this needs to point to where the java directory is.
jarFile: "JmolAppletSigned.jar",
isSigned: true,
script: "set zoomlarge false;set antialiasDisplay;load data/caffeine.mol",
serverURL: "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
readyFunction: jmol_isReady,
disableJ2SLoadMonitor: true,
disableInitialConsole: true,
allowJavaScript: true
//defaultModel: "$dopamine",
//console: "none", // default will be jmolApplet0_infodiv, but you can designate another div here or "none"
}
$(document).ready(function() {
$("#appdiv").html(Jmol.getAppletHtml("jmolApplet0", Info))
})
var lastPrompt=0;
</script>
-->
</head>
<body class="body">
<header class="siteheader">
<div>
<span class="siteheader logo">
<a href="index.html"><img src="Images/header_logo.png" alt="Liu Group Logo"></a>
</span>
<ul>
<li><a href="index.html">HOME</a></li>
<li><a href="search.html">SEARCH</a></li>
<li><a href="about.html">ABOUT</a></li>
<li><a href="news.html">NEWS</a></li>
</ul>
</div>
<br>
</header>
<!--<script type="text/javascript">jmolInitialize("jsmol/JSmol.min.js")</script>-->
<main>
<h1>Here is a protein:</h1>
<h2>1AHO Visualization</h2>
<script src="https://3Dmol.org/build/3Dmol-min.js"></script>
<script src="https://3Dmol.org/build/3Dmol.ui-min.js"></script>
<div style="height: 400px; width: 400px; position: relative;" class='viewer_3Dmoljs' data-pdb='1AHO' data-backgroundcolor='0xffffff' data-style='stick' data-ui='true'></div>
<h2>8FLT Visualization</h2>
<script src="https://3Dmol.org/build/3Dmol-min.js"></script>
<script src="https://3Dmol.org/build/3Dmol.ui-min.js"></script>
<div style="height: 400px; width: 400px; position: relative;" class='viewer_3Dmoljs' data-pdb='8FLT' data-backgroundcolor='0xffffff' data-style='stick' data-ui='true'></div>
<!--
<script>
jmolApplet(400, "load 1aho.pdb", "0");
</script> arguments: size of window, file to load, applet window number (if you put another
window, number it "1")
-->
<!--look at Jmol documentation to find out what files Jmol accepts and is able to understand, then use
that type for the molecules you want to visualize-->
<br>
<p>Molecule visualized with 3Dmoljs<br>
Nicholas Rego and David Koes<br>
3Dmol.js: molecular visualization with WebGL<br>
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829</p>
</main>
<footer class="sitefooter">
<p>
Created by Liu Research Group at University of Florida
<hr>
<a href="https://liu.chem.ufl.edu/research/">Learn more about our research</a>
</p>
</footer>
</body>
</html>