I tried on the example, and I can't replicate the problem there. The odd thing is, our implementation did not change - upgrading to 5.4 causes the problem, reverting back to 5.3.8 fixes it. So there must be something about the configuration that is not acceptable to Marvin 5.4? Here is the html source of the page with the problem ....
=================================================================================
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" dir="" lang="en">
<head>
<title>MarvinSketch Key Generation</title>
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/popup/css/form.css' type='text/css' media='screen' />
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/popup/css/nav.css' type='text/css' media='screen' />
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/popup/css/popup.css' type='text/css' media='screen' />
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/common/css/tabs.css' type='text/css' media='screen' />
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/forms/css/newpassword.css' type='text/css' media='screen' />
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/common/css/print.css' type='text/css' media='print' />
<link rel='stylesheet' href='/wastatic/wacache3c59dc048e8850243be8079a5c74d079/themes/css/blue.css' type='text/css' media='screen' />
<script type="text/javascript">
//<![CDATA[
function addLoadEvent(func) {
var oldonload = window.onload;
if (typeof window.onload != 'function') {
try { window.onload = func; }
catch(err) {}
} else {
window.onload = function() {
oldonload();
func();
}
}
}
//]]>
</script>
<script type = 'text/javascript' src='http://www.dholyfield.dev.webassign.net/marvin-5.4.0/marvin.js?21'></ class="end-tag">script>
<script type='text/javascript' src='/wastatic/lib/js/mootools-1.2.4-core-yc.js'></script><script type='text/javascript' src='/wastatic/lib/js/mootools-1.2.2.2-more.js'></script>
<meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
<meta name="MSSmartTagsPreventParsing" content="TRUE" />
<meta http-equiv="expires" content="-1" />
<meta http-equiv= "pragma" content="no-cache" />
<meta name="robots" content="all" />
<meta name="description" content="" />
<script type="text/javascript">
//<![CDATA[
function getMarvinVal(mtype) {
var marvin, mol;
marvin = document.getElementById('mkey');
mol = document.getElementById('mol');
if(marvin && mol) {
mol.value = marvin.getMol(mtype).replace(/[\n\r\t]/g,'');
}
}
function getCxSmarts() {
var marvin, mol, cxopts, cxstr;
marvin = document.getElementById('mkey');
mol = document.getElementById('mol');
cxopts = document.getElementById('cxflags');
if(marvin && mol && cxopts) {
cxstr = 'cxsmarts';
if(cxopts.value != '') {
cxstr += ':' + cxopts.value;
try {
mol.value = marvin.getMol(cxstr).replace(/[\n\r\t]/g,'');
}
catch(err) {
mol.value = 'molConvert returned an error.';
}
}
}
}
function reloadMarvin() {
var frm = document.getElementById('MarvinSketchKey');
if(frm) {
frm.submit();
}
}
//]]>
</script>
<style type="text/css">
#top {
background: #336699;
}
</style>
</head>
<body>
<div id='webAssignShell'>
</div>
<div id='webAssign'>
<div id='popupWrap' class='container'>
<div id="top" class='container'>
<div id='topNav' class='container'>
<div id="left" class='container'>
<p>MarvinSketch Key Generation</p>
</div>
<div id="right" class='container'>
</div>
</div>
</div>
<div class='topNavBorder container'></div>
<div class='formWrap'>
<form method="post" id='MarvinSketchKey' name='MarvinSketchKey' action="marvin_key.html" enctype="x-www-form-urlencoded">
<div id='middle'>
<table width="95%" align="center"><tr valign="top"><td rowspan="2">
<applet codebase="http://www.dholyfield.dev.webassign.net/marvin-5.4.0" archive="appletlaunch.jar" code="chemaxon.marvin.applet.JMSketchLaunch" width="625" height="520" name="mkey" id="mkey" MAYSCRIPT>
<param name='scriptable' value='true'><param name='skin' value='javax.swing.plaf.metal.MetalLookAndFeel'><param name='autoscale' value='true'><param name='maxscale' value='42'><param name='scale' value='42'><param name='molbg' value='#c1d7e8'><param name='atomFont' value='Serif'><param name='undetachByX' value='false'><param name='menuconfig' value='http://www.dholyfield.dev.webassign.net/marvincustom/customization-pt.xml'><param name='shortcuts' value='http://www.dholyfield.dev.webassign.net/marvincustom/shortcuts-pt.xml'><param name='customizationEnabled' value='false'><param name='templateToolbarCustomizable' value='false'><param name='extraBonds' value='arom,wedge,either,any'><param name='atomNumbersVisible' value='false'><param name='bondLengthVisible' value='false'><param name='valenceErrorVisible' value='false'><param name='ezVisible' value='false'><param name='addRemoveHatomsEnabled' value='false'><param name='lonePairsAutoCalc' value='false'><param name='atomMappingVisible' value='true'><param name='lonePairsVisible' value='true'><param name='chiralitySupport' value='off'><param name='menubar' value='true'><param name='ttmpls0' value='*Generic*chemaxon/marvin/templates/generic.t'><param name='rendering' value='wireframe'><param name='atomSymbolsVisible' value='true'><param name='sketchCarbonVisibility' value='on'><param name='explicitH' value='true'><param name='implicitH' value='off'>
<strong>You must have Java and Javascript to view MarvinSketch</strong>
</applet>
<br>
<strong>Marvin Type:</strong><br><select name='mtype' id='mtype' onChange='reloadMarvin();'><option value='3D'>3D</option><option value='complete'>complete</option><option value='organic'>condensed</option><option value='lewis' selected>lewis</option><option value='mechanism'>mechanism</option><option value='mechanism_adv'>mechanism_adv</option><option value='reaction'>reaction</option><option value='reaction_adv'>reaction_adv</option><option value='resonance'>resonance</option><option value='skeleton'>skeleton</option><option value='skeleton_adv'>skeleton_adv</option><option value='spacefill'>spacefill</option>
<input type="button" name="getKey" value="Get Key" onClick="getMarvinVal('mrv')" />
</td>
<td width="100%" valign="top"><p><b>Instructions for Mechanism Questions</b><br />
Grading of mechanism questions is sensitive due to the way that Marvin
generates its XML representation (known as MRV). When creating a template/key
combination for a mechanism question, it is important to follow these
steps:</p>
<ol>
<li>Draw the template FIRST. Export MRV, copy/paste and save somewhere. Use
that for your $MARVIN_START value.</li>
<li>Modify the template as necessary to make it the key, i.e. 'answer'
it as if you were a student. Export MRV, copy/paste and use for your answer
key. It is important that you not move any of the template's structures
while doing so.</li>
</ol>
<p>If you need to edit these after the fact, be sure to copy in the MRV you
originally generated, or you may have to repeat both steps. You can paste
MRV directly into Marvin by copying it your clipboard, right-clicking anywhere
in Marvin and selecting 'paste'.<br />
<br />
</p></td></tr>
<tr valign="top">
<td valign="bottom"><textarea name="mol" id="mol" rows="13" cols="50"></textarea></td>
</tr>
</table>
</div>
</form>
</div>
</div>
</div>
</body>
</html>
=================================================================================
Let me know if you see anything obvious there. I can set you up with a link if you want to see the bug in action.
In our setup I can reproduce it 100% consistently, after 5.4 upgrade.
thanks
Danny Holyfield