UTF-8
Intermolecular Attractions: Your Immune System
240233207
1
1
1
org.concord.modeler.text.LineIcon750.03010105<html>
<head>
</head>
<body>
<strong><font face="Verdana, Arial, Helvetica, sans-serif" color="#FFFFFF" size="5">Intermolecular
Attractions:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" color="#FFFFFF" size="5">
Your Immune System</font>
</body>
</html>
-59a2d4
1
1
1
org.concord.modeler.text.LineIcon750.0105101015<html>
<head>
</head>
<body marginheight="5">
<table border="0" cellpadding="0" cellspacing="0">
<tr>
<td>
<img height="58" width="98" src="chargeMainIdea.png">
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Your
immune system works by making molecules called <strong>antibodies</strong>
that stick to other "bad" molecules in your system. These bad
molecules are called <strong>antigens</strong> and might be a toxin
produced by a microbe or a molecule on the surface of a bacteria or
virus. Intermolecular attractions are the binding force used to link
antibody with antigen. </font>
</td>
</tr>
</table>
</body>
</html>
-15235a
1
1
1
5.0
org.concord.modeler.PageTextBox
750.0
30.0
<html>
<head>
</head>
<body background="subHeadingBackground.png">
<table border="0" cellpadding="0" cellspacing="0">
<tr>
<td>
<img height="23" width="33" src="chargeBullet.png">
</td>
<td>
<strong><font face="Verdana, Arial, Helvetica, sans-serif" color="#a65d2c" size="5">3D
Exploration of Bound Antibody & Antigen</font></strong>
</td>
</tr>
<tr>
<td colspan="2">
<img height="6" width="18" src="rule.png">
</td>
</tr>
</table>
</body>
</html>
false
1
org.concord.modeler.PageMolecularViewer
falsefalsefalse1EAP.pdb.gzpage8$0.jms430.0
380.0
Lowered Bevel
org.concord.modeler.PageTextBox
310.0
380.0
<html>
<head>
</head>
<body>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">To the left,
part of an antibody (green) is shown bound to an antigen (white). As you
learned earlier, how well two molecules stick to each other can be related
to how well the shapes of the molecules fit together.</font><br>
<ul>
<li>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">Use the
controls below to explore how well the antibody and antigen fit
together.</font>
</li>
<li>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">You can
also drag or shift-drag the molecule to change the view.</font>
</li>
<li>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">Then </font><strong><font face="Verdana, Arial, Helvetica, sans-serif" color="#990000" size="4">take
a snapshot that shows the excellent fit between antibody and antigen</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" color="#990000" size="4">.</font><br>
</li>
</ul>
<table border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td>
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Antibody:</font></strong>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input script_selected="script:jmol:1:select *A; color atoms opaque" type="checkbox" script_deselected="script:jmol:1:select *A; color atoms translucent" name="checkbox" value="checkbox" checked="checked">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">1st half </font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input script_selected="script:jmol:1:select *B; color atoms opaque" type="checkbox" script_deselected="script:jmol:1:select *B; color atoms translucent" name="checkbox2" value="checkbox" checked="checked">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">2nd half </font>
</td>
</tr>
<tr>
<td>
 
</td>
<td valign="top">
<input script="script:jmol:1:select *A; spacefill 20%; wireframe 0.15;" type="radio" name="RadioGroup1" id="RadioGroup1_0" value="radio">
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">ball &
stick</font>
</td>
<td valign="top">
<input script="script:jmol:1:select *B; spacefill 20%; wireframe 0.15;" type="radio" name="RadioGroup2" id="RadioGroup2_0" value="radio">
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">ball &
stick</font>
</td>
</tr>
<tr>
<td>
 
</td>
<td valign="top">
<input script="script:jmol:1:select *A; spacefill 100%;" type="radio" name="RadioGroup1" id="RadioGroup1_1" value="radio" checked="checked">
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">spacefilled<br><br></font>
</td>
<td valign="top">
<input script="script:jmol:1:select *B; spacefill 100%;" type="radio" name="RadioGroup2" id="RadioGroup2_1" value="radio" checked="checked">
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">spacefilled</font><br><br>
</td>
</tr>
<tr>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><strong>Antigen:</strong></font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input script="script:jmol:1:select HEP; spacefill 100%;" type="radio" name="radiobutton" value="radiobutton" checked="checked">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">spacefilled
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input script="script:jmol:1:select HEP; spacefill 25%; wireframe 0.2;" type="radio" name="radiobutton" value="radiobutton">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">ball &
stick </font>
</td>
</tr>
</table>
</body>
</html>
false
1
org.concord.modeler.PageButton
Take a snapshot
false
org.concord.modeler.PageMolecularViewer
0
Take a snapshot
org.concord.modeler.PageTextBox
330.0
15.0
<html>
<head>
</head>
<body>
</body>
</html>
false
1
1
1
org.concord.modeler.PageTextBox
750.0
30.0
<html>
<head>
</head>
<body background="subHeadingBackground.png">
<table border="0" cellpadding="0" cellspacing="0">
<tr>
<td>
<img height="23" width="33" src="chargeBullet.png">
</td>
<td>
<strong><font face="Verdana, Arial, Helvetica, sans-serif" color="#a65d2c" size="5">Design
Your Own Antibody</font></strong>
</td>
</tr>
<tr>
<td colspan="2">
<img height="6" width="18" src="rule.png">
</td>
</tr>
</table>
</body>
</html>
false
1
org.concord.modeler.PageTextBox
750.0
80.0
<html>
<head>
</head>
<body>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">The attraction
between antibody and antigen often utilizes both types of intermolecular
attractions: dipole-dipole and London dispersion.<strong> Your job is to
design an antibody</strong> that will form the strongest attraction to the
antigen below. To do this you will <strong>select the shape of the
antibody, add charge, dock the antigen to your antibody, and then take a
snapshot</strong> of your work. </font>
</body>
</html>
false
1
org.concord.mw2d.activity.AtomContainer
page8$0.mmlfalsetrue
org.concord.modeler.PageTextBox
390.0
385.0
<html>
<head>
</head>
<body marginwidth="10" marginheight="10">
<map name="Map">
<area shape="rect" href="script:mw:1:load antibodyDesign1.mml;" coords="5,7,111,73"></area>
<area shape="rect" href="script:mw:1:load antibodyDesign3.mml;" coords="129,5,231,73"></area>
<area shape="rect" href="script:mw:1:load antibodyDesign2.mml;" coords="143,82,222,137"></area>
<area shape="rect" href="script:mw:1:load antibodyDesign4.mml;" coords="14,87,112,139"></area>
</map>
<div align="center">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Design
Your Antibody</font> </strong>
</div>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">- <strong>Select
a the initial molecule shape</strong> for the antibody by clicking on
one of these images:</font>
</p>
<p align="center">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><img src="antibodyChoice.gif" height="147" width="240" border="0" usemap="#Map">
</font>
</p>
<p>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">- <strong>Add
charge</strong> to the antibody by using the charge tools <img src="addPositiveCharge.gif" height="15" width="15">
and <img src="addNegativeCharge.gif" height="15" width="15"> in the
toolbar. To charge part of the antibody, select the appropriate charge
tool and then click on the atoms you want to charge.<br>- <strong>Run
the model, click on the green star, and "dock" the antigen to your
antibody</strong>.<br>- <strong>Take a snapshot</strong> of your best
creation. </font>
</p>
</body>
</html>
-141617
Raised Bevel
1
15.0
org.concord.modeler.PageTextBox
104.0
20.0
<html>
<head>
</head>
<body>
</body>
</html>
false
org.concord.modeler.PageButton
Take a snapshot
14360
false
org.concord.mw2d.models.MolecularModel
0
Take a snapshot
org.concord.modeler.PageTextBox
510.0
60.0
<html>
<head>
</head>
<body>
<table border="0">
<tr>
<td valign="middle">
<img height="14" width="50" src="pointer.gif">
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Take a
snapshot of your best antibody. If you have time, try using another
shape. What would be the second best design for an antibody that
will attract strongly to the antigen?</font>
</td>
</tr>
</table>
</body>
</html>
false
1
8.0
org.concord.modeler.ImageQuestion371325<html>
<head>
<link href="chemStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="question">
<p class="question">
Image of the 3D anitibody/antigen from top of page:
</p>
</body>
</html>
false
Line
org.concord.modeler.ImageQuestion371325<html>
<head>
<link href="chemStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="question">
<p class="question">
Image of the anitbody you just designed:
</p>
</body>
</html>
false
Line
1
org.concord.modeler.PageTextBox
750.0
32.0
<html>
<head>
</head>
<body marginwidth="0" background="navBarBottomBackground.jpg" marginheight="0">
<table width="100%" cellpadding="0" border="0" cellspacing="0" id="Table_01">
<tr>
<td colspan="2">
<img src="navBarBottomColorBar.gif" height="6" width="14">
</td>
</tr>
<tr>
<td>
<img src="navBarBottomLeftMargin.jpg" height="26" width="8">
<a href="page7.cml"><font><img src="prev.jpg" height="26" width="60" border="0">
</font></a><font><a href="page9.cml"><img src="next.jpg" height="26" width="59" border="0">
</a></font>
</td>
<td align="right">
<img src="page.jpg" height="26" width="54">
<a href="index.cml"><font><img src="index.jpg" height="26" width="46" border="0">
</font></a><font><a href="page1.cml"><img src="page1.jpg" height="26" width="28" border="0">
</a><a href="page2.cml"><img src="page2.jpg" height="26" width="28" border="0">
</a><a href="page3.cml"><img src="page3.jpg" height="26" width="28" border="0">
</a><a href="page4.cml"><img src="page4.jpg" height="26" width="29" border="0">
</a><a href="page5.cml"><img src="page5.jpg" height="26" width="28" border="0">
</a><a href="page6.cml"><img src="page6.jpg" height="26" width="28" border="0">
</a><a href="page7.cml"><img src="page7.jpg" height="26" width="28" border="0">
</a><a href="page8.cml"><img src="page8Selected.jpg" height="26" width="29" border="0">
</a><a href="page9.cml"><img src="page9.jpg" height="26" width="28" border="0">
</a><a href="page10.cml"><img src="page10.jpg" height="26" width="25" border="0">
</a></font><img src="navBarBottomRightMargin.jpg" height="26" width="7">
</td>
</tr>
</table>
</body>
</html>
false
1
10