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collagen.html
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<script type="text/javascript" src="jsmol/JSmol.min.js"></script>
<script type="text/javascript">
var Info = {
color: "#FFFFFF", // white background
height: 400,
width: "100%", // fill the JSMol box to its container's width
coverImage: "images/white.png",
deferApplet: true, // don't load until user clicks on JSMol box
deferUncover: true, // don't uncover until script fully executed
script: "script scripts/collagen1.txt",
use: "HTML5",
j2sPath: "jsmol/j2s",
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
disableInitialConsole: true,
debug: false,
};
// don't load any JSMol until the page itself has finished loading
$(document).ready(function(){
// prevent JSMol from taking entire page
Jmol.setDocument(0);
// create new JSMol instance with parameters defined in Info above
Jmol.getApplet("myJmol1", Info);
// reuse Info parameters for subsequent JSMol instances, changing
// only the script path
Info.script = "script scripts/collagen2.txt";
Jmol.getApplet("myJmol2", Info);
Info.script = "script scripts/collagen3.txt";
Jmol.getApplet("myJmol3", Info);
// put JSMol code into the correct containers (id=jsmolWindowN)
$("#jsmolWindow1").html(Jmol.getAppletHtml(myJmol1));
$("#jsmolWindow2").html(Jmol.getAppletHtml(myJmol2));
$("#jsmolWindow3").html(Jmol.getAppletHtml(myJmol3));
// give our JSMol containers breathing room above and below
$("#myJmol1_appletinfotablediv").css({
"margin-top": "10px",
"margin-right": "auto",
"margin-bottom": "10px",
"margin-left": "auto"
});
$("#myJmol2_appletinfotablediv").css({
"margin-top": "10px",
"margin-right": "auto",
"margin-bottom": "10px",
"margin-left": "auto"
});
$("#myJmol3_appletinfotablediv").css({
"margin-top": "10px",
"margin-right": "auto",
"margin-bottom": "10px",
"margin-left": "auto"
});
$("#resetBtn1").click(reset1);
$("#resetBtn2").click(reset2);
$("#resetBtn3").click(reset3);
$("#spinBox1").click(spin1);
$("#spinBox2").click(spin2);
$("#spinBox3").click(spin3);
});
function reset1(event){
Jmol.script(myJmol1, "script scripts/collagen1.txt")
};
function reset2(event){
Jmol.script(myJmol2, "script scripts/collagen2.txt")
};
function reset3(event){
Jmol.script(myJmol3, "script scripts/collagen3.txt")
};
function spin1(event){
if (event.target.checked){
Jmol.script(myJmol1, "set spin x 10; set spin y 10; spin on")
} else {
Jmol.script(myJmol1, "spin off")
};
};
function spin2(event){
if (event.target.checked){
Jmol.script(myJmol2, "set spin x 10; set spin y 10; spin on")
} else {
Jmol.script(myJmol2, "spin off")
};
};
function spin3(event){
if (event.target.checked){
Jmol.script(myJmol3, "set spin x 10; set spin y 10; spin on")
} else {
Jmol.script(myJmol3, "spin off")
};
};
// turn off the JSMol alert that binary file loading is limited
Jmol._alertNoBinary = false;
</script>
<!-- Page Title: Collagen -->
<h2>Introduction</h2>
<p>
This script shows the structure of collagen. (Based on
1cag.pdb, Bella et al. (1994) Science <strong>266
</strong>: 75-81)
</p>
<br>
<h2>Triple Helix</h2>
<p>
A classic collagen triple helix is shown here. The three helices are
<span style="color:red;">red</span>, <span style="color:gold;">yellow</span>
and <span style="color:green;">green</span>.
</p>
<!-- JSMol Window Container -->
<div id="jsmolWindow1"></div>
<!-- UI Control Box -->
<div style="text-align: center;">
<!-- give the button a right margin for spacing -->
<button type="button" id="resetBtn1" style="margin-right: 10px;">Reset</button>
<input type="checkbox" id="spinBox1"> Spin On/Off
</div>
<br>
<h2>Helix Stability</h2>
<p>
A special amino acid sequence makes the tight collagen triple helix
particularly stable. Every third amino acid is a glycine
(<span style="color:gold;">YELLOW</span>), and many of the remaining amino
acids are <span style="color:green;">proline</span> or
<span style="color:red;">hydroxyproline</span>.
</p>
<div id="jsmolWindow2"></div>
<div style="text-align: center; margin-top: 10px;">
<button type="button" id="resetBtn2" style="margin-right: 10px;">Reset</button>
<input type="checkbox" id="spinBox2"> Spin On/Off
</div>
<br>
<h2>Collagen 3</h2>
<p>
Notice how the glycine (<span style="color:gold;">YELLOW</span>) forms a
tiny elbow packed inside the helix, while the <span style="color:green;">
proline</span> and <span style="color:red;">hydroxyproline</span> smoothly
bend the chain back around the helix.
</p>
<div id="jsmolWindow3"></div>
<div style="text-align: center; margin-top: 10px;">
<button type="button" id="resetBtn3" style="margin-right: 10px;">Reset</button>
<input type="checkbox" id="spinBox3"> Spin On/Off
</div>