Team:UNICAMP-EMSE Brazil/test

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if($.browser.msie)
 
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doDebug = false;
 
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if (doDebug)
 
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debugDiv = document.createElement('div');
 
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var max_history_size = 30;
 
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var historyCounter  = 0;
 
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var historyArray    = new Array();
 
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var statusArray      = new Array();
 
-
var statusCounter    = -1;
 
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-
 
-
 
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-
function writeJmolStatus(status)
 
-
{
 
-
statusCounter ++;
 
-
debug(status);
 
-
var prev= status;
 
-
for (i=0; i < statusCounter-1;i++)
 
-
{
 
-
var tmp = statusArray[i];
 
-
statusArray[i] = prev;
 
-
prev = tmp;
 
-
}
 
-
statusArray[0] = status;
 
-
updateJmolStatus();
 
-
}
 
-
 
-
function updateJmolStatus()
 
-
{
 
-
var html="";
 
-
for (i=statusCounter-1;i>-1;i--)
 
-
{
 
-
html += statusArray[i] + "<br/>";
 
-
}
 
-
 
-
if ( statusCounter > max_history_size )
 
-
statusCounter = max_history_size;
 
-
 
-
$("ul#jmolStatus").html(html);
 
-
}
 
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-
 
-
 
-
 
-
function executeJmolScript(script)
 
-
{
 
-
if ( script == undefined)
 
-
{
 
-
script = $("input#jmolScriptInput").val();
 
-
$("input#jmolScriptInput").val('');
 
-
}
 
-
 
-
debug("executeJmolScript " + script);
 
-
 
-
var myscript = "try { " + script + " } catch (e) { prompt @e; }" ;
 
-
 
-
 
-
var msg = jmolScript(myscript);
 
-
   
 
-
 
-
writeJmolStatus("==");
 
-
var his = $("#history");
 
-
var elid = "historyAction" + historyCounter;
 
-
$(his).append('<li ><a href="#" id="'+elid+'_exec"><img src="/pdb/skins/web20/default/images/play.gif" /></a> <a href="#" id="'+elid+'">'+script+'</a></li>');
 
-
historyArray[elid] = script;
 
-
var historyAction = $("#"+elid);
 
-
var historyActionExec = $("#"+elid+"_exec");
 
-
 
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$(historyAction).attr('rev', elid);
 
-
$(historyActionExec).attr('rev', elid);
 
-
 
-
$(historyAction).click(function(e)
 
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{
 
-
var cmd = historyArray[this.rev];
 
-
$("input#jmolScriptInput").val(cmd);
 
-
});
 
-
 
-
 
-
$(historyActionExec).click(function(e)
 
-
{
 
-
var cmd = historyArray[this.rev];
 
-
$("input#jmolScriptInput").val(cmd);
 
-
executeJmolScript();
 
-
return false;
 
-
});
 
-
 
-
historyCounter += 1;
 
-
var objDiv = document.getElementById("Jmol_history");
 
-
objDiv.scrollTop = objDiv.scrollHeight;
 
-
}
 
-
 
-
function myStructCallback(a,b)
 
-
{
 
-
 
-
writeJmolStatus("successfully loaded " + b);
 
-
 
-
}
 
-
 
-
function myMessageCallback(a,b)
 
-
{
 
-
 
-
writeJmolStatus("jmol message: " + b);
 
-
 
-
}
 
-
 
-
function myPickCallback(a,b,atomIndex)
 
-
{
 
-
 
-
writeJmolStatus("picked " + b);
 
-
}
 
-
 
-
function debug(message)
 
-
{
 
-
if(doDebug)
 
-
{
 
-
var msg =  '<br/>'+(new Date()).getTime() +': ' + message;
 
-
debugDiv.innerHTML += msg;
 
-
}
 
-
}
 
-
 
-
// Making the jmol applet resizable
 
-
    function make_jmol_resizable() {
 
-
// There are some problems with older versions of IE
 
-
if(! $.browser.msie || ($.browser.version >= 8)) {
 
-
 
-
  $("#jmol_box").resizable();
 
-
}
 
-
};
 
-
 
-
$(function () {
 
-
if(! $.browser.msie || ($.browser.version >= 8)) {
 
-
  $("#jmol_box_resize_tip").html("<br/>You may also drag the right-bottom corner of the Jmol area to resize it.");
 
-
}
 
-
});
 
-
</script>
 
-
 
-
 
-
<link rel="stylesheet"    type="text/css"    href="/pdb/Viewers/jmol-12.0.41/jmol.css" />
 
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<table class="headerBox">
 
-
 
-
<tr>
 
-
 
-
<td class="leftCol">
 
-
 
-
<div id="se_structureTitle" class="lb_simple3"><div class="box_contentWrapper">
 
-
 
-
<span class="h3">Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D</span>
 
-
 
-
</div></div>
 
-
 
-
<div id="se_structureSubtitle" class="box_contentWrapper">
 
-
 
-
 
-
 
-
</div>
 
-
 
-
 
-
</td>
 
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<td class="rightCol leftCell">
 
-
 
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-
 
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<div id="se_rightColID">
 
-
 
-
<span id="se_pagetitle">1XX1</span>
 
-
 
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</div>
 
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<div class="webDisplay">
 
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<div id="se_rightColLinks">
 
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<div id="displayLink" class="se_rightColLink">
 
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<a href="" onclick="$('#se_downloadFiles').hide(); $('#se_displayFiles').slideToggle(); return false;" title="Display File">
 
-
 
-
<span class="iconSet-main icon-document">&nbsp;</span>
 
-
 
-
</a>
 
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<a href="" onclick="$('#se_downloadFiles').hide(); $('#se_displayFiles').slideToggle(); return false;" title="Display File">
 
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Display Files<span class="iconSet-int icon-arrowDown">&nbsp;</span>
 
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</a>
 
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<a href="" onclick="$('#se_displayFiles').slideUp(); return false;">close</a>
 
-
 
-
</div>
 
-
 
-
<div>
 
-
 
-
<!-- <a href="/pdb/explore/customStructureReportForm.do?exptype=misc">Custom Report</a> <br /> -->
 
-
 
-
<a href="/pdb/files/fasta.txt?structureIdList=1XX1" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: FASTA');">FASTA Sequence</a> <br />
 
-
 
-
<a href="/pdb/files/1XX1.pdb" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: PDB File');">PDB File</a> <br />
 
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<a href="/pdb/files/1XX1.pdb?headerOnly=YES" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: PDB File Header Only');">PDB File (Header)</a> <br />
 
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<a href="/pdb/files/1XX1.cif" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: mmCIF File');">mmCIF File</a> <br />
 
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<a href="/pdb/files/1XX1.cif?headerOnly=YES" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: mmCIF File Header Only');">mmCIF File (Header)</a> <br />
 
-
 
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<a href="/pdb/files/1XX1.xml" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: PDBML/XML File');">PDBML/XML File</a> <br />
 
-
 
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<a href="/pdb/files/1XX1-noatom.xml" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Display File', 'Display: PDBML/XML File Header Only');">PDBML/XML File (Header)</a> <br />
 
-
 
-
</div>
 
-
 
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</div>
 
-
 
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</div>
 
-
 
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<div id="downloadLink" class="se_rightColLink">
 
-
 
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<a href="" onclick="$('#se_displayFiles').hide(); $('#se_downloadFiles').slideToggle(); return false;" title="Download Files">
 
-
 
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<span class="iconSet-main icon-download">&nbsp;</span>
 
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</a>
 
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<a href="" onclick="$('#se_displayFiles').hide(); $('#se_downloadFiles').slideToggle(); return false;" title="Download Files">
 
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Download Files<span class="iconSet-int icon-arrowDown">&nbsp;</span>
 
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</a>
 
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<div id="se_downloadFiles" class="se_extrasMenu">
 
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<div id="se_downloadFilesClose" class="se_extrasMenuHeader">
 
-
 
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<a href="" onclick="$('#se_downloadFiles').slideUp(); return false;">close</a>
 
-
 
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</div>
 
-
 
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<div>
 
-
 
-
<a href="/pdb/download/downloadFile.do?fileFormat=FASTA&amp;compression=NO&amp;structureId=1XX1" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: FASTA');">FASTA Sequence</a><br />
 
-
 
-
<a href="/pdb/download/downloadFile.do?fileFormat=pdb&amp;compression=NO&amp;structureId=1XX1" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: PDB File');">PDB File (Text)</a> <br />
 
-
 
-
<a href="/pdb/files/1XX1.pdb.gz" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: PDB File GZ');">PDB File (gz)</a> <br />
 
-
 
-
<a href="/pdb/download/downloadFile.do?fileFormat=cif&amp;compression=NO&amp;structureId=1XX1" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: mmCIF File');">mmCIF File</a> <br />
 
-
 
-
<a href="/pdb/files/1XX1.cif.gz" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: mmCIF File GZ');">mmCIF File (gz)</a> <br />
 
-
 
-
<a href="/pdb/download/downloadFile.do?fileFormat=xml&amp;compression=NO&amp;structureId=1XX1" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: PDBML/XML File');">PDBML/XML File</a> <br />
 
-
 
-
<a href="/pdb/files/1XX1.xml.gz"  onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: PDBML/XML File GZ');">PDBML/XML File (gz)</a> <br />
 
-
 
-
 
-
<a href="/pdb/download/downloadFile.do?fileFormat=structfact&amp;structureId=1XX1" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Structure Factor');">Structure Factor (Text)</a> <br />
 
-
 
-
<a href="/pdb/files/r1XX1sf.ent.gz" onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Structure Factor GZ');">Structure Factor (gz)</a> <br />
 
-
 
-
 
-
<a href="/pdb/files/1XX1.pdb1.gz" title="Author and Software Generated by PISA" class="tooltip"  onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Biological Assembly');">Biological Assembly 1 (gz) (A+S)</a><br />
 
-
 
-
 
-
<a href="/pdb/files/1XX1.pdb2.gz" title="Author and Software Generated by PISA" class="tooltip"  onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Biological Assembly');">Biological Assembly 2 (gz) (A+S)</a><br />
 
-
 
-
 
-
<a href="/pdb/files/1XX1.pdb3.gz" title="Software Generated by PISA" class="tooltip"  onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Biological Assembly');">Biological Assembly 3 (gz) (S)</a><br />
 
-
 
-
 
-
<a href="/pdb/files/1XX1.pdb4.gz" title="Software Generated by PISA" class="tooltip"  onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Biological Assembly');">Biological Assembly 4 (gz) (S)</a><br />
 
-
 
-
 
-
<a href="/pdb/files/1XX1.pdb5.gz" title="Software Generated by PISA" class="tooltip"  onclick="pageTracker._trackEvent('Explorer Pages', 'Explorer Pages Download File', 'Download: Biological Assembly');">Biological Assembly 5 (gz) (S)</a><br />
 
-
 
-
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
<div id="shareLink" class="se_rightColLink">
 
-
 
-
<a href="" onclick="$('.hover_menu').slideToggle(); return false;" class="tabblutxt custom_button">
 
-
 
-
<span class="iconSet-main icon-addthis">&nbsp;</span>
 
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</a>
 
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<a href="" onclick="$('.hover_menu').slideToggle(); return false;" class="tabblutxt custom_button">
 
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Share this Page<span class="iconSet-int icon-arrowDown">&nbsp;</span>
 
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<a href="" onclick="$('.hover_menu').slideUp(); return false;">close</a>
 
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        <a class="addthis_button_email">Email</a>
 
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            <a class="addthis_button_delicious">Delicious</a>
 
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            <a class="addthis_button_stumbleupon">Stumble</a>
 
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            <a class="addthis_button_google">Google</a>
 
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-
       
 
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<a href="" onclick="return false;">Link this Page</a>
 
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</div>
 
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<div class="column2">
 
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<input type="text" name="shareURL" id="shareURL" value="" onfocus="this.select();" style="width: 188px"/>
 
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</div>
 
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<script type="text/javascript" language="Javascript">
 
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$(document).ready(function(){
 
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var script = document.createElement( 'script' );
 
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script.type = 'text/javascript';
 
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script.src = 'http://s7.addthis.com/js/250/addthis_widget.js#username=sdscpdb';
 
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$("body").append( script );
 
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});
 
-
 
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$('#shareURL').attr('value', window.location.href)
 
-
</script> 
 
-
 
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</div>
 
-
 
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</div>
 
-
 
-
</div>
 
-
 
-
<div class="clear"></div>
 
-
 
-
</td>
 
-
 
-
</tr>
 
-
 
-
</table>
 
-
 
-
<br />
 
-
 
-
 
-
 
-
 
-
 
-
<form id="biolselectform">
 
-
<select id="changebioldisplay">
 
-
 
-
 
-
<option value="--" id="default">-- Displaying Biological Assembly 1 --</option>
 
-
 
-
<option value="/pdb/explore/jmol.do?structureId=1XX1&opt=3" id="asym">
 
-
View Asymmetric Unit
 
-
</option>
 
-
 
-
 
-
<option value="/pdb/explore/jmol.do?structureId=1XX1&opt=3&bionumber=2">View Biological Assembly 2</option>
 
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<option value="/pdb/explore/jmol.do?structureId=1XX1&opt=3&bionumber=3">View Biological Assembly 3</option>
 
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<option value="/pdb/explore/jmol.do?structureId=1XX1&opt=3&bionumber=4">View Biological Assembly 4</option>
 
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<option value="/pdb/explore/jmol.do?structureId=1XX1&opt=3&bionumber=5">View Biological Assembly 5</option>
 
-
 
-
 
-
 
-
 
-
</select>
 
-
 
-
</form>
 
-
 
-
 
-
<br/>
 
-
Biological assembly 1 assigned by authors and generated by PISA (software)
 
-
<a id="image_help"
 
-
title="Biological Assembly Tutorial"
 
-
href="/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html#Anchor-BioUnit"
 
-
><span class="iconSet-main icon-help">&nbsp;</span></a>
 
-
 
-
<script type="text/javascript">
 
-
$("#changebioldisplay").change(function () {
 
-
   
 
-
    $("select#changebioldisplay option:selected").each(function () {
 
-
    if ( $(this).val() == "--")
 
-
    return false;
 
-
    window.location =$(this).val();
 
-
         
 
-
        });
 
-
   
 
-
  })
 
-
  .change();
 
-
</script>
 
-
 
-
<br/>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
<div>
 
-
 
-
<div class="db_head3">
 
-
 
-
 
-
<div class="box_header">
 
-
 
-
<b><a href="http://www.jmol.org"><img src="/pdb/Viewers/jmol-12.0.41/Jmol_icon_32.png" border="0"></a> Jmol Version 12.0.41</b>
 
-
 
-
</div>
 
-
 
-
 
-
 
-
</div>
 
-
 
-
 
-
 
-
<div class="w_body3">
 
-
 
-
 
-
 
-
<div class="box_contentWrapper">
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
<div id="Jmol_mainWrapper">
 
-
 
-
  <div id="jmol_box"
 
-
  style="margin:auto;width:550px;height:550px;border:solid 1px lightgray;padding: 0.5em;"
 
-
  >
 
-
 
-
 
 
-
<script>
 
-
 
-
$(function() {
 
-
 
-
 
-
jmolSetDocument(false);
 
-
 
-
jmolInitialize("/pdb/Viewers/jmol-12.0.41/",true);
 
-
 
-
jmolSetCallback("loadStructCallback","myStructCallback");
 
-
jmolSetCallback("messageCallback",  "myMessageCallback");
 
-
jmolSetCallback("pickCallback",      "myPickCallback");
 
-
 
-
 
-
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.pdb1.gz';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; ");
 
-
 
-
$('#jmol_box').html(jmol);
 
-
 
-
make_jmol_resizable();
 
-
});
 
-
 
-
 
-
 
-
 
-
</script>
 
-
 
-
  </div>
 
-
   
 
-
Tip: right-mouse click on Jmol to get access to additional Jmol functionality.
 
-
<span id="jmol_box_resize_tip"></span>
 
-
</div>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
<div class="b_body3">
 
-
 
-
 
-
 
-
<div class="box_contentWrapper">
 
-
 
-
 
-
 
-
<div id="Jmol_mainWrapper">
 
-
 
-
<form name="Jmol_form" onsubmit="executeJmolScript(); return false;">
 
-
<input id="jmolScriptInput" type="text" name="inputjmol"  size="60" class="textfield">
 
-
 
-
<input value="Jmol Script" type="button" class="searchbutton" onclick="executeJmolScript(); return false;">
 
-
</form>
 
-
 
-
 
-
<table>
 
-
 
-
 
-
<tr>
 
-
<form name="Jmol_buttons">
 
-
 
-
 
-
 
-
 
-
 
-
<tr>
 
-
<td align="left" style="white-space: nowrap;">
 
-
 
-
<b>Display</b>
 
-
</td>
 
-
<td align="left" style="white-space: nowrap;" >
 
-
 
-
Style
 
-
 
-
<select name="groupA" id="groupA">
 
-
 
-
<option selected="selected">Cartoon</option>
 
-
<option >Backbone</option>
 
-
<option >CPK</option>
 
-
<option >Ball and Stick</option>
 
-
<option >Ligands</option>
 
-
<option >Ligands and Pocket</option>
 
-
</select>
 
-
 
-
 
-
Color
 
-
 
-
<select name="group2" id="group2">
 
-
<option selected="selected">Secondary Structure</option>
 
-
<option >By Chain</option>
 
-
<option >Rainbow</option>
 
-
<option >By Element</option>
 
-
<option >By Amino Acid</option>
 
-
<option >Hydrophobicity</option>
 
-
</select>
 
-
 
-
Surface
 
-
 
-
<select  name="group3" id="group3">
 
-
<option selected="selected">None</option>
 
-
<option >Solvent Accessible</option>
 
-
<option >Solvent Excluded</option>
 
-
<option >Cavities</option>
 
-
</select>
 
-
 
-
</td>
 
-
 
-
 
-
</tr>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
<tr>
 
-
<td align="left"><b>Toggle</b>
 
-
</td>
 
-
<td align="left" style="white-space: nowrap;" >
 
-
<input type="checkbox" id="check41" name="toggleselection" />Selection
 
-
 
-
<input type="checkbox" id="check42" name="togglehbonds" />H-Bonds
 
-
 
-
<input type="checkbox" id="check46" name="toggledisulfide" />SS&nbsp;Bonds
 
-
 
-
<input type="checkbox" id="check43" name="togglespin" />Rotation
 
-
 
-
<input type="checkbox" id="check44" name="antialias" checked="checked"/>Antialias&nbsp;Display&nbsp;(nicer)
 
-
 
-
<input type="checkbox" id="check45" name="backgroundWhite" checked="checked"/>Black&nbsp;Background
 
-
</td>
 
-
 
-
</tr>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
<tr><td></td>
 
-
<td align="left" style="white-space: nowrap;">
 
-
 
-
 
-
<input value="Reset Display" type="button" class="searchbutton" onclick="resetDisplay(); return false;">
 
-
 
-
<input value="Export Image" type="button" class="searchbutton" onclick="executeJmolScript('write IMAGE 1XX1.jpg ;'); return false;">
 
-
 
-
 
-
 
-
 
-
 
-
 
-
<input value="Slab" type="button" class="searchbutton" onclick="slab(); return false;">
 
-
 
-
 
-
 
-
 
-
</td></tr>
 
-
 
-
</table>
 
-
</form>
 
-
 
-
</div>
 
-
 
-
 
-
 
-
<script>
 
-
 
-
function resetDisplay(){
 
-
executeJmolScript('restore STATE state_1');
 
-
$("#asygroup").val('None');
 
-
$('#symmetry').val('None');
 
-
$('#groupA').val('Cartoon');
 
-
$('#group3').val('None');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
 
-
$('[input[name=toggleselection]').attr('checked',false);
 
-
$('[input[name=togglehbonds]').attr('checked',false);
 
-
$('[input[name=togglespin]').attr('checked',false);
 
-
$('[input[name=antialias]').attr('checked',true );
 
-
$('[input[name=backgroundWhite]').attr('checked',true );
 
-
$('[input[name=toggledisulfide]').attr('checked',false );
 
-
 
-
}
 
-
 
-
 
-
$(document).ready(function(){
 
-
 
-
var solventOff = " set solvent off; select solvent; spacefill off; wireframe off;";
 
-
var backbone = " backbone 0.3; spacefill off ; wireframe off; color structure; select ligand; wireframe 0.16;spacefill 0.5; color cpk;";
 
-
 
-
$('#symmetry').change(function(){
 
-
var text = $(this).val();
 
-
if ( text == 'None') {
 
-
resetDisplay();
 
-
 
-
} else if ( text == '3 unit cells a direction') {
 
-
var script = "save orientation 1;load \"\" 1 {455 655 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
} else if ( text == '3 unit cells b direction') {
 
-
var script = "save orientation 1;load \"\" 1 {545 565 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
}  else if ( text == '3 unit cells c direction') {
 
-
var script = "save orientation 1;load \"\" 1 {554 556 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
}  else if ( text == '3x3 unit cells ab plane') {
 
-
var script = "save orientation 1;load \"\" 1 {445 665 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
}  else if ( text == '3x3 unit cells bc plane') {
 
-
var script = "save orientation 1;load \"\" 1 {454 656 1};restore orientation 1; set unitcell 1;" + backbone +solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
}  else if ( text == '3x3 unit cells ac plane') {
 
-
var script = "save orientation 1;load \"\" 1 {544 566 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
}  else if ( text == '3x3x3 unit cells abc cube') {
 
-
var script = "save orientation 1;load \"\" 1 {444 666 1};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
} else if ( text == 'Apply Crystal Symmetry (fill unit cell box)') {
 
-
var script = "save orientation 1;load \"\" 1 packed;restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
} else if ( text == 'Apply Crystal Symmetry (translate chains)'){
 
-
var script = "save orientation 1;load \"\" {2 2 2} packed ;restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
 
-
} else if ( text == "Apply Crystal Symmetry (no translation)"){
 
-
var script = "save orientation 1;load \"\" 1 {555 555 0};restore orientation 1; set unitcell 1;" + backbone + solventOff;
 
-
executeJmolScript(script);
 
-
$('#groupA').val('Backbone');
 
-
$('#group2').val('Secondary Structure');
 
-
} else if (text == "None"){
 
-
resetDisplay();
 
-
} else if ( text == 'Show Unit Cell Outline'){
 
-
var script = "set unitcell 1;" ;
 
-
executeJmolScript(script);
 
-
//$("select[name='asygroup'] option[text=Show Cell]"  ).attr("text", 'Hide Cell');
 
-
 
-
} else if ( text == 'Hide Cell'){
 
-
var script = "set unitcell 0;" ;
 
-
executeJmolScript(script);
 
-
$("select[name='asygroup'] option[text=Hide Cell]"  ).attr("text", 'Show Cell');
 
-
 
-
}
 
-
});
 
-
 
-
 
-
 
-
 
-
$('#groupA').change(function() {
 
-
var text =  $(this).val();
 
-
 
-
  if (text == 'Cartoon') {
 
-
 
-
    executeJmolScript("hide null; select all;  spacefill off; wireframe off; backbone off;" +
 
-
" cartoon on; " +
 
-
" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
 
-
" select *.FE; spacefill 0.7; color cpk ; " +
 
-
" select *.CU; spacefill 0.7; color cpk ; " +
 
-
" select *.ZN; spacefill 0.7; color cpk ; " +
 
-
" select all; ");
 
-
    }
 
-
    else if (text == 'Backbone') {
 
-
   
 
-
    executeJmolScript("hide null; select all; spacefill off; wireframe off; backbone 0.4;" +
 
-
" cartoon off; " +
 
-
" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
 
-
" select *.FE; spacefill 0.7; color cpk ; " +
 
-
" select *.CU; spacefill 0.7; color cpk ; " +
 
-
" select *.ZN; spacefill 0.7; color cpk ; " +
 
-
" select all; ");
 
-
   
 
-
    } else if (text == 'CPK') {
 
-
   
 
-
    executeJmolScript("hide null; select all; spacefill off; wireframe off; backbone off;" +
 
-
" cartoon off; cpk on;" +
 
-
" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
 
-
" select *.FE; spacefill 0.7; color cpk ; " +
 
-
" select *.CU; spacefill 0.7; color cpk ; " +
 
-
" select *.ZN; spacefill 0.7; color cpk ; " +
 
-
" select all; ");
 
-
   
 
-
    }
 
-
    else if (text == 'Ligands') {
 
-
    executeJmolScript("restrict ligand; cartoon off; wireframe on;  display selected;"+
 
-
    " select *.FE; spacefill 0.7; color cpk ; " +
 
-
" select *.CU; spacefill 0.7; color cpk ; " +
 
-
" select *.ZN; spacefill 0.7; color cpk ; " +
 
-
" select all; "
 
-
    );
 
-
    }
 
-
 
-
    else if (text == 'Ligands and Pocket') {
 
-
    executeJmolScript(" select within (6.0,true, ligand); cartoon off; wireframe on; backbone off; display selected; " +
 
-
    " select *.FE; spacefill 0.7; color cpk ; " +
 
-
" select *.CU; spacefill 0.7; color cpk ; " +
 
-
" select *.ZN; spacefill 0.7; color cpk ; " +
 
-
" select all; "
 
-
    );
 
-
    }
 
-
    else if (text == 'Ball and Stick') {
 
-
   
 
-
    executeJmolScript("hide null; restrict not water;  wireframe 0.2; spacefill 25%;" +
 
-
" cartoon off; backbone off; " +
 
-
" select ligand; wireframe 0.16; spacefill 0.5; color cpk; " +
 
-
" select *.FE; spacefill 0.7; color cpk ; " +
 
-
" select *.CU; spacefill 0.7; color cpk ; " +
 
-
" select *.ZN; spacefill 0.7; color cpk ; " +
 
-
" select all; ");
 
-
   
 
-
    }
 
-
 
-
 
 
-
});
 
-
 
-
 
-
 
-
 
-
 
-
$('#group2').change(function() {
 
-
var text =  $(this).val();
 
-
if ( text == 'By Chain') {
 
-
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; " );
 
-
}
 
-
else if ( text == 'By Temperature') {
 
-
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; " );
 
-
}
 
-
else if ( text == 'Rainbow'){
 
-
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; " );
 
-
}
 
-
else if ( text == 'Secondary Structure'){
 
-
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; " );
 
-
}
 
-
else if ( text == 'By Element'){
 
-
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; " );
 
-
}
 
-
else if ( text == 'By Amino Acid'){
 
-
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; " );
 
-
}
 
-
else if ( text == 'Hydrophobicity'){
 
-
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; " );
 
-
}
 
-
});
 
-
 
-
 
-
 
-
$('#group3').change(function() {
 
-
 
-
var text =  $(this).val();
 
-
 
-
if ( text == 'None'){
 
-
executeJmolScript("isosurface off;");
 
-
}
 
-
else if ( text == 'Solvent Accessible'){
 
-
executeJmolScript("isosurface sasurface 1.2");
 
-
}
 
-
else if ( text == 'Solvent Excluded'){
 
-
executeJmolScript("isosurface solvent 1.2");
 
-
}
 
-
else if ( text == 'Cavities'){
 
-
executeJmolScript("isosurface cavity 1.2 10");
 
-
}
 
-
 
-
});
 
-
 
-
 
-
$('[input[name=toggleselection]').click(function(){
 
-
if ( $('[input[name=toggleselection]').is(':checked') ) {
 
-
executeJmolScript("set display selected");
 
-
} else {
 
-
executeJmolScript("set display off");
 
-
}
 
-
});
 
-
 
-
$('[input[name=togglehbonds]').click(function(){
 
-
if ( $('[input[name=togglehbonds]').is(':checked') ) {
 
-
executeJmolScript("calculate HBONDS {*} {*}; hbonds on; color hbonds magenta;");
 
-
} else {
 
-
executeJmolScript("hbonds off");
 
-
}
 
-
});
 
-
 
-
$('[input[name=togglespin]').click(function(){
 
-
if ( $('[input[name=togglespin]').is(':checked') ) {
 
-
executeJmolScript("spin on; ");
 
-
} else {
 
-
executeJmolScript("spin off");
 
-
}
 
-
});
 
-
 
-
$('[input[name=toggleasym]').click(function(){
 
-
if ( $('[input[name=toggleasym]').is(':checked') ) {
 
-
executeJmolScript("set unitcell on; ");
 
-
} else {
 
-
executeJmolScript("set unitcell off;");
 
-
}
 
-
});
 
-
 
-
$('[input[name=antialias]').click(function(){
 
-
if ( $('[input[name=antialias]').is(':checked') ) {
 
-
executeJmolScript("set antialiasDisplay on; ");
 
-
} else {
 
-
executeJmolScript("set antialiasDisplay off;");
 
-
}
 
-
});
 
-
 
-
$('[input[name=backgroundWhite]').click(function(){
 
-
if ( $('[input[name=backgroundWhite]').is(':checked') ) {
 
-
executeJmolScript("background black; ");
 
-
} else {
 
-
executeJmolScript("background white;");
 
-
}
 
-
});
 
-
 
-
 
-
$('[input[name=togglespin]').click(function(){
 
-
if ( $('[input[name=togglespin]').is(':checked') ) {
 
-
executeJmolScript("spin on; ");
 
-
} else {
 
-
executeJmolScript("spin off");
 
-
}
 
-
});
 
-
 
-
$('[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>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
<div class="lb_body3">
 
-
 
-
 
-
 
-
<div class="box_contentWrapper">
 
-
 
-
 
-
 
-
<script type="text/javascript">
 
-
$(function() {
 
-
$("#Jmol_tabs").tabs();
 
-
});
 
-
</script>
 
-
 
-
 
-
<div id="Jmol_tabs">
 
-
<ul>
 
-
<li><a href="#Jmol_annotations">Annotations</a></li>
 
-
<li><a href="#Jmol_history">History</a></li>
 
-
<li><a href="#Jmol_console">Console</a></li>
 
-
<li><a href="#Jmol_help">Help</a></li>
 
-
</ul>
 
-
 
-
<div id="Jmol_annotations" >
 
-
 
-
<div id="annotations"></div>
 
-
 
-
</div>
 
-
 
-
 
-
<div id="Jmol_history" class="Jmol_interface">
 
-
 
-
<div id="history"></div>
 
-
 
-
</div>
 
-
 
-
<div id="Jmol_console" class="Jmol_interface">
 
-
 
-
<ul id="jmolStatus"></ul>
 
-
 
-
</div>
 
-
 
-
<div id="Jmol_help" class="Jmol_interface">
 
-
 
-
<div id="help-container">
 
-
 
-
<ul id="help">
 
-
 
-
<li>
 
-
 
-
<a href="http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/scripting/molmast.htm#II" target="_blank">
 
-
 
-
Introduction to Jmol scripting tutorial <span class="iconSet-main icon-external" title="Link out to Jmol scripting tutorial">&nbsp;</span>
 
-
</a>
 
-
 
-
</li>
 
-
 
-
 
-
<li>
 
-
       
 
-
        Scripting quickstart: <a href="http://wiki.jmol.org/index.php/Rendering" target="_blank">rendering options
 
-
        <span class="iconSet-main icon-external" title="Link out to Jmol rendering options">&nbsp;</span></a> -
 
-
       
 
-
        <a href="http://wiki.jmol.org/index.php/Selecting" target="_blank">selecting atoms
 
-
        <span class="iconSet-main icon-external" title="Link out to Jmol selecting atoms">&nbsp;</span></a>
 
-
       
 
-
       
 
-
        </li>
 
-
 
-
<li>
 
-
       
 
-
        <a href="http://jmol.sourceforge.net/docs/" target="_blank">
 
-
 
-
Jmol Documentation
 
-
<span class="iconSet-main icon-external" title="Link out to Jmol selecting atoms">&nbsp;
 
-
</a>
 
-
 
-
</li>
 
-
 
-
<li>
 
-
 
-
<a href="http://jmol.sourceforge.net/docs/surface/">
 
-
 
-
Surfaces in Jmol
 
-
<span class="iconSet-main icon-external" title="Link out to Jmol selecting atoms">&nbsp;
 
-
</a>
 
-
 
-
</li>
 
-
 
-
</ul>
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
 
-
<div class="lb_foot3">
 
-
 
-
&nbsp;
 
-
 
-
</div>
 
-
 
-
 
-
 
-
The applet on this page is Jmol, an open source Java viewer for chemical structures in 3D: <a href="http://www.jmol.org">http://www.jmol.org</a>
 
-
 
-
 
-
 
-
<script type="text/javascript">
 
-
 
-
var DPHelp  = "<div id=&quot;dpHelp&quot; width=&quot;300&quot;><b>DP domain assignment</b><br/>Click on label to display all domains in 3D<br/><hr/>Reference:<br/><b>Protein domain decomposition using a graph-theoretic approach.</b><br/>Xu Y., Xu D., Gabow H.N., Gabow H.<br/>Bioinformatics 2000 Dec<br/>PMID: 11159328</div>";
 
-
var PDPHelp  = "<div id=&quot;pdpHelp&quot; width=&quot;300&quot;><b>PDP domain assignment</b><br/>Click on label to display all domains in 3D<br/><hr/>Reference:<br/><b>PDP: protein domain parser.</b><br/>Alexandrov N., Shindyalov I.<br/>Bioinformatics 2003 Feb<br/>PMID: 12584135</div>";
 
-
var SCOPHelp = "<div id=&quot;scopHelp&quot; width=&quot;300&quot;><b>SCOP domain assignment</b><br/>Click on label to display all domains in 3D<br/><hr/>Reference:<br/><b>Data growth and its impact on the SCOP database: new developments</b><br/>Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner,  Tim J. P. Hubbard, Cyrus Chothia and Alexey G. Murzin </b><br/>Nucleic Acids Research, 2008, Vol. 36, Database issue D419-D425<br/>PMID: 18000004</div>";
 
-
 
-
      $(document).ready(function(){
 
-
 
-
      loadAnnotations();
 
-
 
-
  });
 
-
 
-
      var annotationData = new Array();
 
-
     
 
-
      function  loadAnnotations() {
 
-
 
-
      $.getJSON("jmol.do?structureId=1XX1&json=true&bionumber=1", function(json){
 
-
 
-
  annotationData = new Array();
 
-
  annotationData = json;  
 
-
 
-
  $("#annotations").append("<table class=\"plain\" id=\"AnnotationTable\"></table>");
 
-
  $("#annotations").append("<div class=\"se_spacer\">&nbsp;</div>");
 
-
  $("#AnnotationTable").append("<tr id=\"legend\"><td><h3>Domain Assignment</h3>(click to display in Jmol)</td><td><h3>Classification</h3></td><td><h3>Location</h3></td><td><h3>Name</h3></td><td><h3>Link Out</h3></tr>");
 
-
  var scopSize = annotationData.scop.size;
 
-
  if ( scopSize > 0 )
 
-
  showScop(annotationData.scop);
 
-
 
-
  var dpSize = annotationData.dp.size;
 
-
  if ( dpSize > 0 )
 
-
  showDomainFragment(annotationData.dp,"DP");
 
-
 
-
  var pdpSize = annotationData.pdp.size;
 
-
  if ( pdpSize > 0 )
 
-
  showDomainFragment(annotationData.pdp,"PDP");
 
-
 
 
-
  if ( annotationData.protmod != undefined) {
 
-
 
 
-
  var protModSize = annotationData.protmod.size;
 
-
  if ( protModSize > 0)
 
-
  showProtModData(annotationData.protmod);
 
-
      }
 
-
 
 
-
    });
 
-
   
 
-
      }
 
-
 
-
      function showAllDomainFragments(name){
 
-
         
 
-
  var data;
 
-
  if ( name == "DP" )
 
-
  data = annotationData.dp;
 
-
  else
 
-
  data = annotationData.pdp;
 
-
 
 
-
  var jmolScript = "set ChainCaseSensitive; ";
 
-
  for ( var i = 0 ; i< data.size ; i++ ) {
 
-
var domain = data.domains[i];
 
-
jmolScript += " select "+ domain.jmolRange +"; color "+ domain.color+"; cartoon off; backbone 0.6 ; ";
 
-
  }
 
-
 
-
  executeJmolScript(jmolScript);
 
-
 
 
-
 
 
-
  }
 
-
     
 
-
  function showAllScop(){
 
-
  var scop = annotationData.scop;
 
-
  var jmolScript = "set ChainCaseSensitive; ";
 
-
  for ( var i = 0 ; i< scop.size ; i++ ) {
 
-
var domain = scop.domains[i];
 
-
jmolScript += " select "+ domain.jmolRange +"; color "+ domain.color+"; cartoon off; backbone 0.6 ; ";
 
-
  }
 
-
 
-
  executeJmolScript(jmolScript);
 
-
 
 
-
 
 
-
  }
 
-
 
 
-
 
-
 
 
-
  function showDomainFragment(df,name){
 
-
 
-
  var lb = '<br/>';     
 
-
  var ref = '<b>' +df.reference.title + '</b>' + lb + df.reference.authors + lb + df.reference.journal + ' (' + df.reference.volume + ') '+ df.reference.issue + ',' + df.reference.pages + ' (' + df.reference.pubYear+')';       
 
-
   
 
-
 
 
-
 
-
$("#AnnotationTable").append("<tr class=\"subheader1\" id=\""+name+"Header\"><td colspan=\"5\" id=\""+name+"Legend\"></td></tr>");
 
-
$("#"+name+"Legend" ).append("<h4><a href=\"javascript:showAllDomainFragments('"+name+"');\" >"+name+"</a>" +
 
-
    " <a href=\"javascript:showAllDomainFragments('"+name+"');\" title=\""+ref+"\" " +
 
-
    " class=\"mantooltip\"><span class=\"iconSet-main icon-info\">&nbsp;</span></a></h4>");
 
-
$(".mantooltip").tipTip({maxWidth: "auto"});
 
-
 
-
var pos = 0;
 
-
for ( var i = 0 ; i< df.size ; i++ ) {
 
-
 
-
var domain = df.domains[i];
 
-
 
-
var dname = domain.name;
 
-
 
-
if ( pos == 0 )
 
-
$("#AnnotationTable").append("<tr class=\"queryWhite\" id=\""+name+"Row"+ i + "\">");
 
-
else
 
-
$("#AnnotationTable").append("<tr class=\"queryBlue\" id=\""+name+"Row"+ i + "\">");
 
-
 
-
$("#"+name+"Row"+i).append("<td id=\""+name+"Cell"+ i + "\"></td>");
 
-
 
-
$("#"+name+"Cell"+i).append("<a href=\"javascript:executeJmolScript('set ChainCaseSensitive; select "+
 
-
domain.jmolRange +"; color "+ domain.color+"; cartoon off; backbone 0.6; set display selected ;'); \" "+
 
-
 
-
">" +
 
-
dname+"</a>");
 
-
 
-
$("#"+name+"Row"+i).append("<td></td>");
 
-
$("#"+name+"Row"+i).append("<td>" + domain.range + "</td><td>" + dname + "</td>");
 
-
$("#"+name+"Row"+i).append("<td></td>");
 
-
 
-
        pos = pos + 1;
 
-
        if  ( pos > 1)
 
-
        pos = 0;
 
-
}
 
-
  }
 
-
 
 
-
  function showProtModData(protmods){
 
-
 
-
  var ref = "Protein Modifications";
 
-
 
 
-
  $("#AnnotationTable").append("<tr class=\"subheader1\" id=\"protModHeader\"><td colspan=\"5\" id=\"protModLegend\"></td></tr>");
 
-
    $("#protModLegend").append("<h4><a href=\"javascript:showAllProtMod();\">Protein Modifications</a>"+
 
-
    " <a href=\"javascript:showAllProtMod();\" title=\"" + ref +"\" " +
 
-
    " class=\"mantooltip\"><span class=\"iconSet-main icon-info\">&nbsp;</span></a></h4>");
 
-
   
 
-
 
-
  var pos = 0;
 
-
for ( var i = 0 ; i< protmods.size ; i++ ) {
 
-
 
-
var protmod = protmods.domains[i];
 
-
 
-
var id = protmod.id;
 
-
var name = protmod.description;
 
-
var classification = protmod.description;
 
-
var description = protmod.description;
 
-
var range = protmod.range;
 
-
var tip = description;
 
-
 
-
if ( pos == 0 )
 
-
$("#AnnotationTable").append("<tr class=\"queryWhite\" id=\"protModRow"+ i + "\">");
 
-
else
 
-
$("#AnnotationTable").append("<tr class=\"queryBlue\" id=\"protModRow"+ i + "\">");
 
-
 
-
$("#protModRow"+i).append("<td id=\"protModCell"+ i + "\"></td>");
 
-
 
-
$("#protModCell"+i).append("<a href=\"javascript:executeJmolScript('set ChainCaseSensitive; select "+
 
-
protmod.jmolRange +"; color cpk; cartoon off; wireframe 0.6; set display selected ;'); \" "+
 
-
" title=\"" +
 
-
tip +
 
-
"\" class=\"mantooltip\"" +
 
-
">" +
 
-
id+"</a>");
 
-
 
-
 
-
$("#protModRow"+i).append("<td>" +  description + "</td>");
 
-
$("#protModRow"+i).append("<td>" + range + "</td><td>&nbsp;</td><td>&nbsp;</td>");
 
-
 
-
}
 
-
   
 
-
  }
 
-
 
 
-
      function showScop(scop){
 
-
 
-
var lb = '<br/>';     
 
-
var ref = '<b>' +scop.reference.title + '</b>' + lb + scop.reference.authors + lb + scop.reference.journal + ' (' + scop.reference.volume + ') '+ scop.reference.issue + ',' + scop.reference.pages + ' (' + scop.reference.pubYear+')';       
 
-
   
 
-
    $("#AnnotationTable").append("<tr class=\"subheader1\" id=\"scopHeader\"><td colspan=\"5\" id=\"scopLegend\"></td></tr>");
 
-
    $("#scopLegend").append("<h4><a href=\"javascript:showAllScop();\">SCOP</a>"+
 
-
    " <a href=\"javascript:showAllScop();\" title=\"" + ref +"\" " +
 
-
    " class=\"mantooltip\"><span class=\"iconSet-main icon-info\">&nbsp;</span></a></h4>");
 
-
   
 
-
 
-
    var pos = 0;
 
-
for ( var i = 0 ; i< scop.size ; i++ ) {
 
-
 
-
var domain = scop.domains[i];
 
-
 
-
var name = domain.domainDescription;
 
-
 
-
var tip = "<div style=&quot;width: 300px;&quot;>" +
 
-
"<table><tr><td>Class</td><td>" + domain.classDescription + " </td></tr>"+
 
-
"<tr><td>Fold</td><td>" + domain.foldDescription + " </td></tr>"+
 
-
"<tr><td>Superfamily</td><td>" + domain.superfamDescription + " </td></tr>"+
 
-
"<tr><td>Family</td><td>" + domain.familyDescription + " </td></tr>"+
 
-
"<tr><td>Protein</td><td>" + domain.domainDescription + " </td></tr>"+
 
-
"<tr><td>Species</td><td>" + domain.speciesDescription + " </td></tr>"+
 
-
"</table></div>";
 
-
 
-
if ( pos == 0 )
 
-
$("#AnnotationTable").append("<tr class=\"queryWhite\" id=\"scopRow"+ i + "\">");
 
-
else
 
-
$("#AnnotationTable").append("<tr class=\"queryBlue\" id=\"scopRow"+ i + "\">");
 
-
$("#scopRow"+i).append("<td id=\"scopCell"+ i + "\"></td>");
 
-
 
-
$("#scopCell"+i).append("<a href=\"javascript:executeJmolScript('set ChainCaseSensitive; select "+
 
-
domain.jmolRange +"; color "+ domain.color+"; cartoon off; backbone 0.6; set display selected ;'); \" "+
 
-
" title=\"" +
 
-
tip +
 
-
"\" class=\"mantooltip\"" +
 
-
">" +
 
-
name+"</a>");
 
-
 
-
 
-
$("#scopRow"+i).append("<td>" +  domain.familyDots + "</td>");
 
-
$("#scopRow"+i).append("<td>" + domain.range + "</td><td>" + domain.name + "</td>");
 
-
$("#scopRow"+i).append("<td><a href=\"http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid="+ domain.species+ "\" target=\"_new\">in SCOP <span class=\"iconSet-main icon-external\" title=\"Link Out to SCOP\">&nbsp;</span></a></td>");
 
-
pos = pos + 1;
 
-
        if  ( pos > 1)
 
-
        pos = 0;
 
-
}
 
-
$(".mantooltip").tipTip({maxWidth: "auto"});
 
-
 
-
      }
 
-
 
-
  function slab(){
 
-
 
-
  var script = "slab on; ";
 
-
 
 
-
  var step=5;
 
-
  var inc = 0.2;
 
-
  var v =1;
 
-
  while ( v >0 && v < 100 ) {
 
-
  v += step*inc;
 
-
  script += " slab " +v +"; delay 1; ";  
 
-
  }
 
-
 
-
 
 
-
  executeJmolScript(script);
 
-
  }
 
-
   
 
-
 
 
-
</script>
 
-
 
-
 
-
 
-
 
-
 
-
</div>
 
-
 
-
</td>
 
-
 
-
</tr>
 
-
 
-
</table>
 
-
 
-
</div>
 
-
 
-
<div id="footer" class="footer">
 
-
 
-
The RCSB PDB is managed by two members of the <a href="http://home.rcsb.org" target="_blank">RCSB</a>: <br />
 
-
 
-
<a target="_blank" href="http://www.rutgers.edu">Rutgers</a> and <a target="_blank" href="http://www.ucsd.edu/">UCSD</a>, and is funded by <a target="_blank" href="http://www.nsf.gov">NSF</a>,
 
-
<a target="_blank" href="http://www.nigms.nih.gov/">NIGMS</a>, <a target="_blank" href="http://www.science.doe.gov">DOE</a>,<a target="_blank" href="http://www.nlm.nih.gov/"> NLM</a>,
 
-
<a target="_blank" href="http://www.nci.nih.gov/"> NCI</a>, 
 
-
<a target="_blank" href="http://www.ninds.nih.gov/">NINDS</a>, and <a target="_blank" href="http://www2.niddk.nih.gov/">NIDDK</a>.
 
-
 
-
<br />
 
-
 
-
</div>
 
-
 
-
<div id="footer_copywrite" class="copyright">
 
-
 
-
<a target="_blank" href="http://home.rcsb.org/">&copy; RCSB Protein Data Bank</a>
 
-
 
-
</div>
 
-
 
-
</td></tr></table>
 
-
 
-
 
-
 
-
 
 
-
 
-
<script type="text/javascript">
 
-
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
 
-
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
 
-
</script>
 
-
<script type="text/javascript">
 
-
var pageTracker = _gat._getTracker("UA-3923365-3");
 
-
pageTracker._initData();
 
-
pageTracker._trackPageview();
 
-
</script>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
<script type="text/javascript" language="Javascript" src="/pdb/common/lib/awstats_misc_tracker.js"></script>
 
-
 
-
 
-
 
-
 
-
</body>
 
-
 
-
</html>
 

Latest revision as of 14:08, 14 September 2011

Retrieved from "http://2011.igem.org/Team:UNICAMP-EMSE_Brazil/test"