motif.html

<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/motif1.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/motif2.txt";
        Jmol.getApplet("myJmol2", Info);
        Info.script = "script scripts/motif3.txt";
        Jmol.getApplet("myJmol3", Info);
        Info.script = "script scripts/motif4.txt";
        Jmol.getApplet("myJmol4", 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));
        $("#jsmolWindow4").html(Jmol.getAppletHtml(myJmol4));
        // 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"
        });
        $("#myJmol4_appletinfotablediv").css({
            "margin-top": "10px",
            "margin-right": "auto",
            "margin-bottom": "10px",
            "margin-left": "auto"
        });
        $("#resetBtn1").click(reset1);
        $("#resetBtn2").click(reset2);
        $("#resetBtn3").click(reset3);
        $("#resetBtn4").click(reset4);
        $("#spinBox1").click(spin1);
        $("#spinBox2").click(spin2);
        $("#spinBox3").click(spin3);
        $("#spinBox4").click(spin4);
    });

    function reset1(event){
        Jmol.script(myJmol1, "script scripts/motif1.txt")
    };

    function reset2(event){
        Jmol.script(myJmol2, "script scripts/motif2.txt")
    };

    function reset3(event){
        Jmol.script(myJmol3, "script scripts/motif3.txt")
    };

    function reset4(event){
        Jmol.script(myJmol4, "script scripts/motif4.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")
        };
    };

    function spin4(event){
        if (event.target.checked){
            Jmol.script(myJmol4, "set spin x 10; set spin y 10; spin on")
        } else {
            Jmol.script(myJmol4, "spin off")
        };
    };

    // turn off the JSMol alert that binary file loading is limited
    Jmol._alertNoBinary = false;
</script>

<!-- Page Title: Secondary Structure Motifs -->
<h2>Introduction</h2>
<p>
    Proteins have a limited number of structural motifs.
</p>
<br>

<h2>Motif 1</h2>
<p>
    This is a common secondary structure in proteins - the helix-loop-helix
    motif. (Based on 256B.pdb, (1981) J.Mol.Biol. <strong>148</strong>: 427-448)
</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>Motif 2</h2>
<p>
    This helix-loop-helix motif is called the "<strong>EF HAND</strong>" and
    represents the <span style="color:green;"><strong>CALCIUM</strong></span>-
    binding motif in many calcium-binding proteins. The calcium ion is bound to
    two Asp side chains and a Glu side chain. (based on 5CPV.pdb, Swain et al.
    (1989) J.Biol.Chem. <strong>264</strong>: 16620-16628)
</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>Motif 3</h2>
<p>
    This is a <strong>hairpin beta-sheet</strong> motif. Note that the
    &beta;-strands are <em> anti-parallel</em> (direction of the arrows).
</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>
<br>

<h2>Motif 4</h2>
<p>
    This is the <strong>beta-alpha-beta</strong> motif. Note that the
    &beta;-strands are <em> parallel</em> (direction of the arrows).
</p>
<div id="jsmolWindow4"></div>
<div style="text-align: center; margin-top: 10px;">
    <button type="button" id="resetBtn4" style="margin-right: 10px;">Reset</button>
    <input type="checkbox" id="spinBox4"> Spin On/Off
</div>