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jmol_demo.html
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jmol_demo.html
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<!doctype html>
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="content-type">
<title>Jmol Demo</title>
<!-- CSS stylesheets externalized -->
<link rel="stylesheet" href="./jquery/jquery-ui.css" type="text/css" charset="utf-8" />
<link rel="stylesheet" href="./jmol_demo.css" type="text/css" charset="utf-8"/>
</head>
<body>
<h1>Jmol Demo</h1>
<div id='commands'>
<ul><!-- The tab headers -->
<li><a href="#jcmd-1">Jmol 1</a></li>
<li><a href="#jcmd-2">Jmol 2</a></li>
<li><a href="#jcmd-3">Surfaces</a></li>
<li><a href="#jcmd-99">Jmol Info</a></li>
</ul>
<div id="jcmd-1"> <!-- Content of Tab Jmol 1 -->
<ul>
<li><div class="jmolscript">load mol/caffeine.mol;</div></li>
<li><div class="jmolscript">cpk 100%;</div></li>
<li><div class="jmolscript">cpk off; wireframe on;</div></li>
<li><div class="jmolscript">cpk 23%; wireframe 0.15;</div></li>
<li> </li>
<li><div class="jmolscript">calculate PARTIALCHARGE; label %.3P ;</div></li>
<li><div class="jmolscript">isosurface iso1 resolution 6 SOLVENT map MEP ;</div></li>
<li><div class="jmolscript">isosurface iso1 translucent ;</div></li>
<li><div class="jmolscript">isosurface iso1 off; labels off;</div></li>
<li> </li>
<li><div class="jmolscript">color atoms blue;</div></li>
<li><div class="jmolscript">load append "mol/caffeine.mol";</div></li>
<li><div class="jmolscript">frame 1.1;</div></li>
<li><div class="jmolscript">frame 2.1;</div></li>
<li><div class="jmolscript">frame all;</div></li>
<li><div class="jmolscript">select */2.1; rotate selected Y 20 molecular;</div></li>
<li><div class="jmolscript">axes 0.05</div></li>
<li> </li>
<li><div class="jmolscript">frame 2.1;</div></li>
<li><div class="jmolscript">set backgroundModel 1.1;</div></li>
<li><div class="jmolscript">select */2.1;</div></li>
<li> </li>
<li><div class="jmolscript">console;</div></li>
<li><div class="jmolscript">compare {*/1.1} {*/2.1}</div></li>
<li><div class="jmolscript">x=compare({*/1.1},{*/2.1},"stddev");print x</div></li>
<li> </li>
</ul>
</div>
<div id="jcmd-2"> <!-- Content of Tab Jmol 2 -->
<ul>
<li><div class="jmolscript">load "mol/AlF3NH3.cml"; label "%a - %i - %e"; </div></li>
<li><div class="jmolscript"></div></li>
<li><div class="jmolscript"></div></li>
<li><div class="jmolscript"></div></li>
<li><div class="jmolscript"></div></li>
<li><div class="jmolscript"></div></li>
<li><div class="jmolscript"></div></li>
<li><br/><br/><br/><br/><br/></li>
<li><div class="jmolscript">set allowRotateSelected TRUE</div></li>
<li><div class="jmolscript">mol_a = {*/1.1} ; mol_b = {*/2.1}</div></li>
</ul>
</div>
<div id="jcmd-3"> <!-- Content of Tab Jmol 3 -->
<ol>
<li>Load an example file:</li>
<li><div class="jmolscript">load "mol/methanol.log" ; frame 2</div></li>
<li> </li>
<li>Or load Browse local file:</li>
<li><div class="jmolscript">load "?" ; frame 2</div></li>
<li> </li>
<li>Display Electrostatic Potential or HOMO or LUMO mapped on molecular surface:</li>
<li><div class="jmolscript">isosurface id iso_mep molecular map mep #ESP</div></li>
<li><div class="jmolscript">isosurface id iso_homo molecular map mo homo</div></li>
<li><div class="jmolscript">isosurface id iso_lumo molecular map mo lumo</div></li>
<li> </li>
<li>Set Isosurface Tranlucent or Opaque:</li>
<li><div class="jmolscript">isosurface translucent 0.99 # translucent</div></li>
<li><div class="jmolscript">isosurface translucent 0.75</div></li>
<li><div class="jmolscript">isosurface translucent 0.5 </div></li>
<li><div class="jmolscript">isosurface translucent 0.25</div></li>
<li><div class="jmolscript">isosurface translucent 0.0 # opaque</div></li>
<li> </li>
<li>Download Image:</li>
<li><div class="jmolscript">write PNG "output.png?"</div></li>
<li><div class="jmolscript">write PNG 1000 1000 "output.png?"</div></li>
<li> </li>
<li>Delete Isosurface:</li>
<li><div class="jmolscript">isosurface delete</div></li>
<li> </li>
</ul>
</div>
<div id="jcmd-99"> <!-- Content of Tab Jmol Info -->
<div id="infodiv"></div>
</div>
</div>
<!-- DIV in which Jmol Applet will be placed -->
<div id='jmol_div'></div>
<!--
The performance of loading and displaying the page is better
if JavaScripts are loaded at the bottom of the page.
-->
<!-- Load Jmol javascript library and jQuery UI: -->
<script type="text/javascript" src="./jsmol/JSmol.min.js"></script>
<script type="text/javascript" src="./jquery/jquery-ui.js"></script>
<!-- calls to jQuery Jmol JSO -->
<script type="text/javascript" src="./jmol_demo.js"></script>
</body>
</html>