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Paul Vaughan
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Initial commit of XOT 2.0 straight from the Zip file.
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‎ChangeLog

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‎JMolViewer/jmol.htm

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<head>
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<title>JMol Example</title>
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<script src="jmol/Jmol.js" type="text/javascript"></script>
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<script type="text/javascript">
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// ***** SET UP Jmol PARAMETERS & CONTROL BAR *****
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// file location
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var str = document.location.search.substr(1,document.location.search.length).replace(/%20/g," ");
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var modelFile = str.split(',')[0].split('xyz=')[1];
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var setUpInfo = "load " + modelFile + ";";
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// control bar?
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var controls = str.split(',')[2].split('controls=')[1];
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// spin
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var spin = str.split(',')[1].split('spin=')[1];
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if (spin == "true") {
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setUpInfo += " spin on;";
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spin = true;
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} else {
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spin = false;
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}
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// background colour
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var bgColour = str.split(',')[3].split('bgColour=')[1];
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if (bgColour != "Black" && bgColour != "Blue") {
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bgColour = "White";
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}
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setUpInfo += " background " + bgColour + ";";
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// display / initial appearance
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var initDisplay = str.split(',')[4].split('initLook=')[1];
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var currentDisplay = initDisplay;
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if (initDisplay == "CPK") {
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setUpInfo += " spacefill on; wireframe off; backbone on; cartoon off;";
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} else if (initDisplay == "Ball and Stick") {
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setUpInfo += " spacefill 25%; wireframe 35%; backbone on; cartoon off;";
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} else if (initDisplay == "Sticks") {
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setUpInfo += " spacefill off; wireframe 20%; backbone on; cartoon off;";
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} else if (initDisplay == "Wireframe") {
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setUpInfo += " spacefill off; wireframe on; backbone on; cartoon off;";
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} else if (initDisplay == "Cartoon") {
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setUpInfo += " spacefill off; wireframe off; backbone on; cartoon on;";
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} else if (initDisplay == "Backbone") {
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setUpInfo += " spacefill off; wireframe off; backbone 0.4; cartoon off;";
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}
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// model colours
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var initColour = str.split(',')[7].split('initColour=')[1];
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if (initColour == "Element") {
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setUpInfo += " color cpk;";
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} else if (initColour == "Amino Acid") {
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setUpInfo += " color amino;";
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} else if (initColour == "Chain") {
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setUpInfo += " color chain;";
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} else if (initColour == "Secondary Structure") {
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setUpInfo += " color structure;";
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} else { // default or not set
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if (initDisplay == "Cartoon") {
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setUpInfo += " color cartoon structure;";
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} else if (initDisplay == "Backbone") {
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setUpInfo += " color structure;";
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} else {
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setUpInfo += " color cpk;";
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}
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}
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var colourOpt = str.split(',')[12].split('colourOpt=')[1];
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// labels
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var labelOpt = str.split(',')[11].split('labelOpt=')[1];
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// surface
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var surfaceOpt = str.split(',')[10].split('surfaceOpt=')[1];
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setUpInfo += " set antialiasDisplay true;";
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// bespoke script stuff
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var initScript = str.split(',')[8].split('initScript=')[1];
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if (initScript != "undefined" && initScript != "" && initScript != "null") {
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setUpInfo += initScript;
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}
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var scriptOpt = str.split(',')[9].split('scriptOpt=')[1];
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// Jmol window size
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var windowW = Number(str.split(',')[13].split('width=')[1])-2;
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var windowH = Number(str.split(',')[14].split('height=')[1])-2;
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var modelW = windowW-4;
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var modelH = windowH-4;
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function setValues() {
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document.getElementById("spinCheck").checked = spin;
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var comboArray = new Array("displayCombo", "colourCombo", "labelCombo", "surfaceCombo");
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var valueArray = new Array(initDisplay, initColour, "None", "None");
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for (i=0; i<comboArray.length; i++) {
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var combo = document.getElementById(comboArray[i]);
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if (combo) {
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for (j=0; j<combo.options.length; j++) {
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if (combo.options[j].text == valueArray[i]) {
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combo.selectedIndex = j;
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break;
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}
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}
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}
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}
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}
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function displayChg() {
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var selected = document.getElementById("displayCombo").options[document.getElementById("displayCombo").selectedIndex].text;
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if (selected == "CPK") {
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jmolScript("spacefill on; wireframe off; backbone on; cartoon off");
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} else if (selected == "Ball and Stick") {
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jmolScript("spacefill 25%; wireframe 35%; backbone on; cartoon off");
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} else if (selected == "Sticks") {
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jmolScript("spacefill off; wireframe 20%; backbone on; cartoon off");
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} else if (selected == "Wireframe") {
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jmolScript("spacefill off; wireframe on; backbone on; cartoon off");
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} else if (selected == "Backbone") {
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jmolScript("spacefill off; wireframe off; backbone 0.4; cartoon off");
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} else if (selected == "Cartoon") {
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jmolScript("spacefill off; wireframe off; backbone on; cartoon on");
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}
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currentDisplay = selected;
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colourChg();
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}
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function colourChg() {
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var selected;
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if (document.getElementById("colourCombo") == null) {
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selected = initColour;
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} else {
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selected = document.getElementById("colourCombo").options[document.getElementById("colourCombo").selectedIndex].text;
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}
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if (selected == "Element") {
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jmolScript("color cpk");
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} else if (selected == "Amino Acid") {
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jmolScript("color amino");
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} else if (selected == "Chain") {
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jmolScript("color chain");
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} else if (selected == "Secondary Structure") {
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jmolScript("color structure");
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} else { // default
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if (currentDisplay == "Cartoon") {
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jmolScript("color cartoon structure");
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} else if (currentDisplay == "Backbone") {
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jmolScript("color structure");
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} else {
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jmolScript("color cpk");
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}
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}
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}
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function labelChg() {
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var selected = document.getElementById("labelCombo").options[document.getElementById("labelCombo").selectedIndex].text;
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if (selected == "None") {
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jmolScript("label off");
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} else if (selected == "Element symbol") {
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jmolScript("label %e");
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} else if (selected == "Atom name") {
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jmolScript("label %a");
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} else if (selected == "Charged") {
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jmolScript("select carbon; label 'carbon'");
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}
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}
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function surfaceChg() {
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var selected = document.getElementById("surfaceCombo").options[document.getElementById("surfaceCombo").selectedIndex].text;
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if (selected == "Solvent accessible") {
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jmolScript("isosurface sasurface");
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} else if (selected == "Solvent excluded") {
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jmolScript("isosurface solvent");
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} else if (selected == "Cavities") {
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jmolScript("isosurface cavity");
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} else { // none
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jmolScript("isosurface off");
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}
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}
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function scriptChg() {
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var textArea = document.getElementById("scriptInput");
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if (textArea.value != "") {
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jmolScript(textArea.value);
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}
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}
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function spinChg() {
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var checkbox = document.getElementById("spinCheck");
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if (checkbox.checked == true) {
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jmolScript("spin on");
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} else {
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jmolScript("spin off");
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}
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}
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function resetBtn() {
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jmolScript(setUpInfo);
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if (scriptOpt == "true") {
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document.getElementById("scriptInput").value = "";
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}
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if (controls == "true") {
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setValues();
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}
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}
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function resize(newW, newH) {
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windowW = newW-2;
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windowH = newH-2;
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modelW = windowW-4;
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if (document.getElementById("controlBar") != null) {
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modelH = windowH-document.getElementById("controlBar").offsetHeight-4;
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} else {
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modelH = windowH-4;
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}
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jmolResizeApplet([modelW, modelH]);
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document.getElementById("holder").style.cssText = 'width: ' + windowW + 'px; height: ' + (windowH-11) + 'px;';
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}
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function init() {
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document.getElementById("holder").style.cssText = 'width: ' + windowW + 'px; height: ' + (windowH-11) + 'px;';
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// remove control bar elements not needed
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var remove = new Array();
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if (controls != "true" && scriptOpt != "true") {
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remove.push("controlBar");
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} else if (controls != "true" && scriptOpt == "true") {
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remove.push("normalControls");
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} else if (controls == "true" && scriptOpt != "true") {
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remove.push("scriptHolder");
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}
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if (controls == "true") {
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if (colourOpt != "true") {
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remove.push("colourHolder");
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}
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if (surfaceOpt != "true") {
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remove.push("surfaceHolder");
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}
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if (labelOpt != "true") {
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remove.push("labelHolder");
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}
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if (str.split(',')[6].split('backOpt=')[1] == "false") {
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remove.push("backbone");
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}
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if (str.split(',')[5].split('cartoonOpt=')[1] == "false") {
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remove.push("cartoon");
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}
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}
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for (i=0; i<remove.length; i++) {
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var tag = document.getElementById(remove[i]);
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tag.parentNode.removeChild(tag);
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}
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// set init values
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if (controls == "true") {
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setValues();
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}
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// resize so no scrolling
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if (controls == "true" || scriptOpt == "true" || controls == true) {
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modelH = windowH-document.getElementById("controlBar").offsetHeight-4;
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jmolResizeApplet([modelW, modelH]);
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}
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}
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</script>
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<style type="text/css">
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<!--
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select, button, input {
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font-size: 11px;
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}
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.model {
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border: solid 2px white;
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background-color: white;
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text-align: center;
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}
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.controlBar {
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border: solid 2px white;
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background-color: #E6E6E6;
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padding-top: 10px;
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padding-bottom: 5px;
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}
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.block {
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display:inline-block;
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padding-left: 10px;
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padding-bottom: 5px;
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}​
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-->
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</style>
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</head>
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<body style="margin:0; width:100%; height:100%; min-height:100%; background-color:#D6E0EC; font-family:Verdana, sans-serif; font-size:11px; overflow:hidden" onload="init();">
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<div name="holder" id="holder">
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<div class="model">
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<script type="text/javascript">
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jmolInitialize("jmol");
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jmolSetAppletColor(bgColour);
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jmolApplet([modelW, modelH], setUpInfo);
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</script>
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</div>
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<div class="controlBar" id="controlBar">
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<span id="normalControls">
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<label id="displayHolder" class="block">Display: <select name="displayCombo" id="displayCombo" onchange="displayChg();">
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<option>CPK</option>
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<option>Ball and Stick</option>
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<option>Sticks</option>
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<option>Wireframe</option>
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<option id="backbone">Backbone</option>
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<option id="cartoon">Cartoon</option>
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</select></label>
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<label id="colourHolder" class="block">Colour: <select name="colourCombo" id="colourCombo" onchange="colourChg();">
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<option>Default</option>
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<option>Element</option>
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<option>Amino Acid</option>
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<option>Chain</option>
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<option>Secondary Structure</option>
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</select></label>
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<label id="surfaceHolder" class="block">Surface: <select name="surfaceCombo" id="surfaceCombo" onchange="surfaceChg();">
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<option selected="selected">None</option>
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<option>Solvent accessible</option>
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<option>Solvent excluded</option>
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<option>Cavities</option>
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</select></label>
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<label id="labelHolder" class="block">Labels: <select name="labelCombo" id="labelCombo" onchange="labelChg();">
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<option selected="selected">None</option>
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<option>Element symbol</option>
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<option>Atom name</option>
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<option>Charged</option>
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</select></label>
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<label id="spinHolder" class="block">Spin: <input type="checkbox" name="spinCheck" id="spinCheck" onclick="spinChg();" checked="false" /></label>
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</span>
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<label id="scriptHolder" class="block"><input type="text" name="scriptInput" id="scriptInput" /><button onclick="scriptChg();">Apply script</button></label>
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<span class="block">
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<button onclick="resetBtn();">Reset</button>
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</span>
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</div>
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</div>
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</body>

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