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| - | <html>
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| - | <div id="Jmol_mainWrapper">
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| - | <div id="jmol_box"
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| - | style="margin:auto;width:550px;height:550px;border:solid 1px lightgray;padding: 0.5em;"
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| - | >
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| - |
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| - |
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| - | <script>
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| | | | |
| - | $(function() {
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| - | <script src="http://propka.ki.ku.dk/~jhjensen/Jmol.js" type="text/javascript"></script>
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| - | <script type="text/javascript">
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| - |
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| - |
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| - | jmolSetDocument(false);
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| - |
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| - | jmolInitialize("http://www.pdb.org/pdb/Viewers/jmol-12.0.41/",true);
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| - |
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| - | jmolSetCallback("loadStructCallback","myStructCallback");
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| - | jmolSetCallback("messageCallback", "myMessageCallback");
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| - | jmolSetCallback("pickCallback", "myPickCallback");
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| - |
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| - |
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| - | var jmol = jmolApplet(["100%","100%"], "script http://www1.rcsb.org/pdb/Viewers/jmol-12.0.41/customcolor.spt; load 'http://www1.rcsb.org/pdb/files/1XX1.pdb';set defaultStructureDSSP true; set measurementUnits ANGSTROMS; select all; spacefill off; wireframe off; backbone off; cartoon on; color cartoon structure; color structure; select ligand;wireframe 0.16;spacefill 0.5; color cpk ; select all; model 0;set antialiasDisplay true; ;save STATE state_1; ");
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| - |
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| - | $('#jmol_box').html(jmol);
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| - |
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| - | make_jmol_resizable();
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| - | });
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| - |
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| - |
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| - |
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| - |
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| - | </script>
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| - |
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| - | </div>
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| - |
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| - | Tip: right-mouse click on Jmol to get access to additional Jmol functionality.
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| - | <span id="jmol_box_resize_tip"></span>
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| - | </div>
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | </div>
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| - |
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| - | </div>
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| - |
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| - | <div class="b_body3">
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| - |
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| - |
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| - |
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| - | <div class="box_contentWrapper">
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| - |
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| - |
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| - |
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| - | <div id="Jmol_mainWrapper">
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| - |
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| - | <form name="Jmol_form" onsubmit="executeJmolScript(); return false;">
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| - | <input id="jmolScriptInput" type="text" name="inputjmol" size="60" class="textfield">
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| - |
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| - | <input value="Jmol Script" type="button" class="searchbutton" onclick="executeJmolScript(); return false;">
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| - | </form>
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| - |
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| - |
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| - | <table>
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| - |
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| - |
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| - | <tr>
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| - | <form name="Jmol_buttons">
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | <tr>
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| - | <td align="left" style="white-space: nowrap;">
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| - |
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| - | <b>Display</b>
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| - | </td>
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| - | <td align="left" style="white-space: nowrap;" >
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| - |
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| - | Style
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| - |
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| - | <select name="groupA" id="groupA">
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| - |
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| - | <option selected="selected">Cartoon</option>
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| - | <option >Backbone</option>
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| - | <option >CPK</option>
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| - | <option >Ball and Stick</option>
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| - | <option >Ligands</option>
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| - | <option >Ligands and Pocket</option>
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| - | </select>
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| - |
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| - |
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| - | Color
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| - |
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| - | <select name="group2" id="group2">
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| - | <option selected="selected">Secondary Structure</option>
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| - | <option >By Chain</option>
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| - | <option >Rainbow</option>
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| - | <option >By Element</option>
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| - | <option >By Amino Acid</option>
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| - | <option >Hydrophobicity</option>
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| - | </select>
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| - |
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| - | Surface
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| - |
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| - | <select name="group3" id="group3">
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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>
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| - |
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| - | </td>
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| - |
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| - |
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| - | </tr>
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | <tr>
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| - | <td align="left"><b>Toggle</b>
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| - | </td>
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| - | <td align="left" style="white-space: nowrap;" >
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| - | <input type="checkbox" id="check41" name="toggleselection" />Selection
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| - |
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| - | <input type="checkbox" id="check42" name="togglehbonds" />H-Bonds
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| - |
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| - | <input type="checkbox" id="check46" name="toggledisulfide" />SS Bonds
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| - |
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| - | <input type="checkbox" id="check43" name="togglespin" />Rotation
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| - |
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| - | <input type="checkbox" id="check44" name="antialias" checked="checked"/>Antialias Display (nicer)
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| - |
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| - | <input type="checkbox" id="check45" name="backgroundWhite" checked="checked"/>Black Background
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| - | </td>
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| - |
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| - | </tr>
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | <tr><td></td>
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| - | <td align="left" style="white-space: nowrap;">
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| - |
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| - |
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| - | <input value="Reset Display" type="button" class="searchbutton" onclick="resetDisplay(); return false;">
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| - |
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| - | <input value="Export Image" type="button" class="searchbutton" onclick="executeJmolScript('write IMAGE 1XX1.jpg ;'); return false;">
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| - |
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | <input value="Slab" type="button" class="searchbutton" onclick="slab(); return false;">
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| - |
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| - |
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| - |
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| - |
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| - | </td></tr>
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| - |
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| - | </table>
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| - | </form>
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| - |
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| - | </div>
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| - |
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| - |
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| - |
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| - | <script>
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| - |
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| - | function resetDisplay(){
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| - | executeJmolScript('restore STATE state_1');
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| - | $("#asygroup").val('None');
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| - | $('#symmetry').val('None');
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| - | $('#groupA').val('Cartoon');
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| - | $('#group3').val('None');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - |
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| - | $('[input[name=toggleselection]').attr('checked',false);
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| - | $('[input[name=togglehbonds]').attr('checked',false);
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| - | $('[input[name=togglespin]').attr('checked',false);
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| - | $('[input[name=antialias]').attr('checked',true );
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| - | $('[input[name=backgroundWhite]').attr('checked',true );
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| - | $('[input[name=toggledisulfide]').attr('checked',false );
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| - |
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| - | }
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| - |
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| - |
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| - | $(document).ready(function(){
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| - |
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| - | var solventOff = " set solvent off; select solvent; spacefill off; wireframe off;";
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| - | var backbone = " backbone 0.3; spacefill off ; wireframe off; color structure; select ligand; wireframe 0.16;spacefill 0.5; color cpk;";
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| - |
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| - | $('#symmetry').change(function(){
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| - | var text = $(this).val();
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| - | if ( text == 'None') {
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| - | resetDisplay();
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| - |
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| - | } else if ( text == '3 unit cells a direction') {
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| - | var script = "save orientation 1;load \"\" 1 {455 655 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
| |
| - | } else if ( text == '3 unit cells b direction') {
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| - | var script = "save orientation 1;load \"\" 1 {545 565 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == '3 unit cells c direction') {
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| - | var script = "save orientation 1;load \"\" 1 {554 556 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == '3x3 unit cells ab plane') {
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| - | var script = "save orientation 1;load \"\" 1 {445 665 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == '3x3 unit cells bc plane') {
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| - | var script = "save orientation 1;load \"\" 1 {454 656 1};restore orientation 1; set unitcell 1;" + backbone +solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == '3x3 unit cells ac plane') {
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| - | var script = "save orientation 1;load \"\" 1 {544 566 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == '3x3x3 unit cells abc cube') {
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| - | var script = "save orientation 1;load \"\" 1 {444 666 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == 'Apply Crystal Symmetry (fill unit cell box)') {
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| - | var script = "save orientation 1;load \"\" 1 packed;restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == 'Apply Crystal Symmetry (translate chains)'){
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| - | var script = "save orientation 1;load \"\" {2 2 2} packed ;restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - |
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| - | } else if ( text == "Apply Crystal Symmetry (no translation)"){
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| - | var script = "save orientation 1;load \"\" 1 {555 555 0};restore orientation 1; set unitcell 1;" + backbone + solventOff;
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| - | executeJmolScript(script);
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| - | $('#groupA').val('Backbone');
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| - | $('#group2').val('Secondary Structure');
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| - | } else if (text == "None"){
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| - | resetDisplay();
| |
| - | } else if ( text == 'Show Unit Cell Outline'){
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| - | var script = "set unitcell 1;" ;
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| - | executeJmolScript(script);
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| - | //$("select[name='asygroup'] option[text=Show Cell]" ).attr("text", 'Hide Cell');
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| - |
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| - | } else if ( text == 'Hide Cell'){
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| - | var script = "set unitcell 0;" ;
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| - | executeJmolScript(script);
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| - | $("select[name='asygroup'] option[text=Hide Cell]" ).attr("text", 'Show Cell');
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| - |
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| - | }
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| - | });
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| - |
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| - |
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| - |
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| - |
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| - | $('#groupA').change(function() {
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| - | var text = $(this).val();
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| - |
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| - | if (text == 'Cartoon') {
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| - |
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| - | executeJmolScript("hide null; select all; spacefill off; wireframe off; backbone off;" +
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| - | " cartoon on; " +
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| - | " select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
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| - | " select *.FE; spacefill 0.7; color cpk ; " +
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| - | " select *.CU; spacefill 0.7; color cpk ; " +
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| - | " select *.ZN; spacefill 0.7; color cpk ; " +
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| - | " select all; ");
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| - | }
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| - | else if (text == 'Backbone') {
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| - |
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| - | executeJmolScript("hide null; select all; spacefill off; wireframe off; backbone 0.4;" +
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| - | " cartoon off; " +
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| - | " select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
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| - | " select *.FE; spacefill 0.7; color cpk ; " +
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| - | " select *.CU; spacefill 0.7; color cpk ; " +
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| - | " select *.ZN; spacefill 0.7; color cpk ; " +
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| - | " select all; ");
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| - |
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| - | } else if (text == 'CPK') {
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| - |
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| - | executeJmolScript("hide null; select all; spacefill off; wireframe off; backbone off;" +
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| - | " cartoon off; cpk on;" +
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| - | " select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
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| - | " select *.FE; spacefill 0.7; color cpk ; " +
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| - | " select *.CU; spacefill 0.7; color cpk ; " +
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| - | " select *.ZN; spacefill 0.7; color cpk ; " +
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| - | " select all; ");
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| - |
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| - | }
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| - | else if (text == 'Ligands') {
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| - | executeJmolScript("restrict ligand; cartoon off; wireframe on; display selected;"+
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| - | " select *.FE; spacefill 0.7; color cpk ; " +
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| - | " select *.CU; spacefill 0.7; color cpk ; " +
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| - | " select *.ZN; spacefill 0.7; color cpk ; " +
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| - | " select all; "
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| - | );
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| - | }
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| - |
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| - | else if (text == 'Ligands and Pocket') {
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| - | executeJmolScript(" select within (6.0,true, ligand); cartoon off; wireframe on; backbone off; display selected; " +
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| - | " select *.FE; spacefill 0.7; color cpk ; " +
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| - | " select *.CU; spacefill 0.7; color cpk ; " +
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| - | " select *.ZN; spacefill 0.7; color cpk ; " +
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| - | " select all; "
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| - | );
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| - | }
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| - | else if (text == 'Ball and Stick') {
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| - |
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| - | executeJmolScript("hide null; restrict not water; wireframe 0.2; spacefill 25%;" +
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| - | " cartoon off; backbone off; " +
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| - | " select ligand; wireframe 0.16; spacefill 0.5; color cpk; " +
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| - | " select *.FE; spacefill 0.7; color cpk ; " +
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| - | " select *.CU; spacefill 0.7; color cpk ; " +
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| - | " select *.ZN; spacefill 0.7; color cpk ; " +
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| - | " select all; ");
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| - |
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| - | }
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| - |
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| - |
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| - | });
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | $('#group2').change(function() {
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| - | var text = $(this).val();
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| - | if ( text == 'By Chain') {
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| - | executeJmolScript("hide null; select all;set defaultColors Jmol; color_by_chain(\"cartoon\"); color_by_chain(\"\"); select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
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| - | }
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| - | else if ( text == 'By Temperature') {
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| - | executeJmolScript("hide null; select all;spacefill off; wireframe off; backbone 0.4; cartoon off; set defaultColors Jmol; color relativeTemperature; color cartoon relateiveTemperature select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
| |
| - | }
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| - | else if ( text == 'Rainbow'){
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| - | executeJmolScript("hide null; select all; set defaultColors Jmol; color group; color cartoon group; select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
| |
| - | }
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| - | else if ( text == 'Secondary Structure'){
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| - | executeJmolScript("hide null; select all; set defaultColors Jmol; color structure; color cartoon structure;select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
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| - | }
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| - | else if ( text == 'By Element'){
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| - | executeJmolScript("hide null; select all; set defaultColors Jmol; color cpk; color cartoon cpk; select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
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| - | }
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| - | else if ( text == 'By Amino Acid'){
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| - | executeJmolScript("hide null; select all; set defaultColors Jmol; color amino; color cartoon amino; select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
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| - | }
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| - | else if ( text == 'Hydrophobicity'){
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| - | executeJmolScript("hide null; set defaultColors Jmol; select hydrophobic; color red; color cartoon red; select not hydrophobic ; color blue ; color cartoon blue; select ligand;wireframe 0.16;spacefill 0.5; color cpk ;; select all; " );
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| - | }
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| - | });
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| - |
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| - |
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| - |
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| - | $('#group3').change(function() {
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| - |
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| - | var text = $(this).val();
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| - |
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| - | if ( text == 'None'){
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| - | executeJmolScript("isosurface off;");
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| - | }
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| - | else if ( text == 'Solvent Accessible'){
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| - | executeJmolScript("isosurface sasurface 1.2");
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| - | }
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| - | else if ( text == 'Solvent Excluded'){
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| - | executeJmolScript("isosurface solvent 1.2");
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| - | }
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| - | else if ( text == 'Cavities'){
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| - | executeJmolScript("isosurface cavity 1.2 10");
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| - | }
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| - |
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| - | });
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| - |
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| - |
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| - | $('[input[name=toggleselection]').click(function(){
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| - | if ( $('[input[name=toggleselection]').is(':checked') ) {
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| - | executeJmolScript("set display selected");
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| - | } else {
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| - | executeJmolScript("set display off");
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| - | }
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| - | });
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| - |
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| - | $('[input[name=togglehbonds]').click(function(){
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| - | if ( $('[input[name=togglehbonds]').is(':checked') ) {
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| - | executeJmolScript("calculate HBONDS {*} {*}; hbonds on; color hbonds magenta;");
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| - | } else {
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| - | executeJmolScript("hbonds off");
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| - | }
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| - | });
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| - |
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| - | $('[input[name=togglespin]').click(function(){
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| - | if ( $('[input[name=togglespin]').is(':checked') ) {
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| - | executeJmolScript("spin on; ");
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| - | } else {
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| - | executeJmolScript("spin off");
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| - | }
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| - | });
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| - |
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| - | $('[input[name=toggleasym]').click(function(){
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| - | if ( $('[input[name=toggleasym]').is(':checked') ) {
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| - | executeJmolScript("set unitcell on; ");
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| - | } else {
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| - | executeJmolScript("set unitcell off;");
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| - | }
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| - | });
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| - |
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| - | $('[input[name=antialias]').click(function(){
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| - | if ( $('[input[name=antialias]').is(':checked') ) {
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| - | executeJmolScript("set antialiasDisplay on; ");
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| - | } else {
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| - | executeJmolScript("set antialiasDisplay off;");
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| - | }
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| - | });
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| - |
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| - | $('[input[name=backgroundWhite]').click(function(){
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| - | if ( $('[input[name=backgroundWhite]').is(':checked') ) {
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| - | executeJmolScript("background black; ");
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| - | } else {
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| - | executeJmolScript("background white;");
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| - | }
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| - | });
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| - |
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| - |
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| - | $('[input[name=togglespin]').click(function(){
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| - | if ( $('[input[name=togglespin]').is(':checked') ) {
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| - | executeJmolScript("spin on; ");
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| - | } else {
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| - | executeJmolScript("spin off");
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| - | }
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| - | });
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| - |
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| - | $('[input[name=toggledisulfide]').click(function(){
| |
| - | if ( $('[input[name=toggledisulfide]').is(':checked') ) {
| |
| - | executeJmolScript("select {_S and connected({_S})} ; color yellow ; ssbonds on; set ssbonds backbone;");
| |
| - |
| |
| - | } else {
| |
| - | executeJmolScript("ssbonds off;");
| |
| - | }
| |
| - | });
| |
| - |
| |
| - |
| |
| - | $("input[name='group5']").click(function(){
| |
| - | if ($("input[name='group5']:checked").val() == 'packed') {
| |
| - | executeJmolScript("save orientation 1; load \"\" 1 packed; restore orientation 1; ");
| |
| - | } else if ($("input[name='group5']:checked").val() == 'unpacked') {
| |
| - | executeJmolScript("save orientation 1;load \"\" {1 1 1}; restore orientation 1; ");
| |
| - | } else if ($("input[name='group5']:checked").val() == 'unnorm'){
| |
| - | executeJmolScript("save orientation 1;load \"\" 1 {555 555 0};restore orientation 1","unnormalized cell");
| |
| - | }
| |
| - | });
| |
| - |
| |
| - | $("input[name='group6']").click(function(){
| |
| - | if ($("input[name='group6']:checked").val() == 'model1') {
| |
| - | executeJmolScript("model 1; set antialiasDisplay on;");
| |
| - | $('[input[name=antialias]').attr('checked',true)
| |
| - | } else if ($("input[name='group6']:checked").val() == 'modelAll') {
| |
| - | executeJmolScript("model 0; set antialiasDisplay off;");
| |
| - | $('[input[name=antialias]').attr('checked',false)
| |
| - | }
| |
| - | });
| |
| - |
| |
| - | });
| |
| - |
| |
| - | </script>
| |
| - |
| |
| - |
| |
| - |
| |
| - |
| |
| - | </html>
| |
"
