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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/simple.htm
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197
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/simple.htm
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<!DOCTYPE html>
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<html>
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<head>
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<script type="text/javascript" src="JSmol.min.js"></script>
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<script type="text/javascript">
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// 1/21/2013 10:54:15 PM -- adds image handling
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var jmolApplet0; // set up in HTML table, below
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// logic is set by indicating order of USE -- default is HTML5 for this test page, though
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var use = "HTML5" // JAVA HTML5 WEBGL IMAGE are all otions
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var s = document.location.search;
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// Developers: The _debugCode flag is checked in j2s/core/core.z.js,
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// and, if TRUE, skips loading the core methods, forcing those
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// to be read from their individual directories. Set this
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// true if you want to do some code debugging by inserting
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// System.out.println, document.title, or alert commands
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// anywhere in the Java or Jmol code.
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Jmol._debugCode = (s.indexOf("debugcode") >= 0);
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jmol_isReady = function(applet) {
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Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
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}
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var xxxx = document.location.search
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if (xxxx.indexOf("_USE=") > 0)xxxx = xxxx.substring(0, xxxx.indexOf("_USE=") - 1);
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if (xxxx.length == 5 || xxxx.length == 0) {
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xxxx = (xxxx + "?1crn").substring(1,5)
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script = 'h2oOn=true;set animframecallback "jmolscript:if (!selectionHalos) {select model=_modelNumber}";'
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+'set errorCallback "myCallback";'
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+'set defaultloadscript "isDssp = false;set defaultVDW babel;if(!h2oOn){display !water}";'
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+'set zoomlarge false;set echo top left;echo loading XXXX...;refresh;'
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+'load "http://www.rcsb.org/pdb/files/XXXX.pdb";set echo top center;echo XXXX;'
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+'spacefill off;wireframe off;cartoons on;color structure;'
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script = script.replace(/XXXX/g, xxxx)
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} else {
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script = unescape(xxxx.substring(1))
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}
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var Info = {
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width: 450,
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height: 450,
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debug: false,
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color: "white",
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addSelectionOptions: false,
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serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
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use: "HTML5",
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j2sPath: "j2s",
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readyFunction: jmol_isReady,
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script: script,
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//jarPath: "java",
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//jarFile: (useSignedApplet ? "JmolAppletSigned.jar" : "JmolApplet.jar"),
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//isSigned: useSignedApplet,
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//disableJ2SLoadMonitor: true,
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disableInitialConsole: true
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//defaultModel: "$dopamine",
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//console: "none", // default will be jmolApplet0_infodiv
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}
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Models = []
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template = "xid='%1';load =%1|%2 (%1)"
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function addModel(xxxx, text) {
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Models.push(template.replace(/\%1/g, xxxx).replace(/%2/g, text).split("|"))
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}
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addModel("1crn", "small")
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addModel("1blu","Fe/S")
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addModel("1bna","b-DNA")
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addModel("1d66","transcription")
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// these are conveniences that mimic behavior of Jmol.js
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function jmolCheckbox(script1, script0,text,ischecked) {Jmol.jmolCheckbox(jmolApplet0,script1, script0, text, ischecked)}
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function jmolButton(script, text) {Jmol.jmolButton(jmolApplet0, script,text)}
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function jmolHtml(s) { document.write(s) };
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function jmolBr() { jmolHtml("<br />") }
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function jmolMenu(a) {Jmol.jmolMenu(jmolApplet0, a)}
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</script>
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</head>
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<body>
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<center>
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<table><tr>
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<td>
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<i>set platformSpeed...</i>
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<br>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 8')">8</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 7')">7</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 6')">6</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 5')">5</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 4')">4</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 3')">3</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 2')">2</a>
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<a href="javascript:Jmol.script(jmolApplet0, 'set platformSpeed 1')">1</a>
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</td>
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<td align=center>
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<script type="text/javascript">
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jmolApplet0 = Jmol.getApplet("jmolApplet0", Info)
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</script>
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</td><td>
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<form><!-- (FORM tag is important to automatically set checkbox off when page reloads) -->
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<script type="text/javascript">
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Jmol.setButtonCss(null,"style='width:160px'")
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Jmol.setMenuCss(null,"style='width:160px'")
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jmolButton("if (!xid) { xid = '1crn'};var x = prompt('Enter a four-digit PDB ID',xid);if (!x) { quit }; xid = x; load @{'=' + x}","Load PDB by ID")
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jmolBr()
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jmolCheckbox("set pdbAddHydrogens TRUE","set pdbAddHydrogens FALSE","with hydrogens",false)
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jmolBr()
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jmolCheckbox("set defaultLoadFilter 'biomolecule 1'","set defaultLoadFilter ''","biomolecule 1",false)
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jmolBr()
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jmolHtml("Examples:")
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jmolBr()
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jmolMenu(Models)
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jmolBr()
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jmolButton("if (!molname) { molname = 'tylenol'};var x = prompt('Enter the name or identifier (SMILES, InChI, CAS) of a molecule',molname);if (!x) { quit }; molname = x; load @{'$' + molname}","Load MOL by NAME")
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jmolBr()
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jmolButton("load ?","Load URL")
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jmolBr()
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jmolButton("load file://?","Load FILE")
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jmolBr()
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jmolButton("script ?.spt","Load SCRIPT")
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jmolBr()
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jmolBr()
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jmolCheckbox("h2oOn=true;display *","h2oOn=false;display !water","display water",true)
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jmolBr()
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jmolBr()
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jmolButton("write FILE ?","Save FILE")
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jmolBr()
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jmolButton("write IMAGE ?.jpg","Save JPG")
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jmolBr()
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jmolButton("write IMAGE ?.png","Save PNG")
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jmolBr()
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jmolButton("write ?.jmol","Save Jmol")
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jmolBr()
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jmolButton("write PNGJ ?.png","Save PNG+Jmol")
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jmolBr()
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jmolButton("write STATE ?.spt","Save STATE")
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jmolBr()
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</script>
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</form>
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</td></tr>
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<tr>
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<td></td>
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<td align=center>
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<script type="text/javascript">
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jmolBr()
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Jmol.setButtonCss(null,"style='width:120px'")
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jmolButton("color cpk")
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jmolButton("color group")
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jmolButton("color amino")
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jmolButton("color structure")
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jmolBr()
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jmolButton("trace only")
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jmolButton("cartoon only")
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jmolButton("backbone only")
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jmolButton("spacefill only;spacefill 23%;wireframe 0.15","ball&stick")
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jmolBr()
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Jmol.setButtonCss(null,"style='width:60px'")
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jmolButton("Model")
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Jmol.setButtonCss(null,"style='width:50px'")
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jmolButton("model; if (!isDssp) { save structure s1; isDssp = true; calculate structure DSSP;cartoons only;color structure}", "DSSP")
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Jmol.setButtonCss(null,"style='width:50px'")
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jmolButton("model; if (isDssp) { restore structure s1; isDssp = false; cartoons only;color structure}", "Auth")
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Jmol.setButtonCss(null,"style='width:160px'")
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jmolButton("Ramachandran relative")
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jmolButton("Quaternion difference")
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jmolBr()
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Jmol.setButtonCss(null,"style='width:100px'")
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jmolButton("console")
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Jmol.jmolCommandInput(jmolApplet0)
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</script>
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</td></tr></table>
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</body>
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</html>
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