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Intro to Modeling/MW: 3D static models.
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Take a snapshot or two of your favorite views of this molecule.
Please submit a report of your work.
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<font face="Verdana, Arial, Helvetica, sans-serif" size="5" color="#FFFFFF"><strong>Intro to Modeling/MW:</strong> 3D static models.</font>
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<td><img src="motionMainIdea.png" width="98" height="58"></td>
<td><font face="Verdana, Arial, Helvetica, sans-serif" size="4">Another kind of computer model allows the user to explore and design virtual 3D objects. This kind of computer model can be used to design things like buildings or molecules. </font></td>
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<font face="Verdana, Arial, Helvetica, sans-serif" color="#5d6b86" size="5"><strong>A
Simple Model of a 3D Molecule</strong></font>
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<img width="18" height="6" src="rule.png">
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">A molecule is
a collection of atoms bonded together with covalent bonds. Below is a
simple model of water - H<sub>2</sub>O. As with <a href="script:page:0:message <t>dynamic = constantly changing</t>">dynamic</a>
models, 3D <a href="script:page:0:message <t>static = not changing</t>">static</a>
models also have two parts, a numerical description of the molecule (below
left), and a view of that data in some graphical format (below right).
Also, just like dynamic models, you can have different views of the model
data. Try using the different views to see several ways scientists view
molecules.</font>
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<div align="center"><font size="3" face="Verdana, Arial, Helvetica, sans-serif"><strong>WATER - A numerical description and graphical views. </strong></font>
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@<TRIPOS>MOLECULE
Water
3 2 0 0 0
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****
@<TRIPOS>ATOM
1 O1 0.0000 0.0645 0.0000 O.3 1 ABCD -0.3736
2 H2 0.7513 -0.5120 0.0000 H 1 ABCD 0.1868
3 H3 -0.7513 -0.5120 0.0000 H 1 ABCD 0.1868
@<TRIPOS>BOND
1 1 2 1
2 1 3 1
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<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Views
of Model Data</strong></font><br><br>
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<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:1:isosurface off; spacefill 0%; wireframe on;">
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wireframe
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<input name="radiobutton" type="radio" script="script:jmol:1:isosurface off; spacefill 20%; wireframe 0.15" value="radiobutton" checked="checked">
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ball and stick
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<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:1:isosurface off; spacefill 100%;">
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spacefill
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<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:1:isosurface delete color white resolution 6 solvent 1.2">
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molecular surface
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<p>
<font color="#660000">Drag your mouse over the molecule to rotate it.</font>
</p>
<p>
<font color="#660000">Shift-Drag to zoom in and out. </font>
</p>
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<img height="23" width="33" src="motionBullet.png">
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<font face="Verdana, Arial, Helvetica, sans-serif" color="#5d6b86" size="5"><strong>Viewing
proteins and flying through a molecule.</strong></font>
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<td colspan="2">
<img width="18" height="6" src="rule.png">
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">Sometimes more
abstract views are helpful for seeing the overall structure of more
complex molecules. Below is one of the simplest proteins. However, even
this simple protein is much more complex than water. To see the structure
more easily a "cartoon" view has been added which shows some basic
patterns of spirals, called alpha helices, and flat ribbons, called beta
sheets. Because proteins are long molecules that fold up, this one has
been colored using the colors of the rainbow <img width="115" height="17" src="rainbow.gif">
to allow you to follow the molecule from one end to the other. </font>
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<div align="center"><font size="3" face="Verdana, Arial, Helvetica, sans-serif"><strong>CRAMBIN - A small protein found in the seeds of Abyssinian cabbage. </strong></font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Views
of Model Data</strong></font><br><br>
</td>
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<td align="right">
<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:2:isosurface off; cartoons off; spacefill 0%; wireframe on;">
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wireframe
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<input name="radiobutton" type="radio" script="script:jmol:2:isosurface off; cartoons off; spacefill 20%; wireframe 0.15" value="radiobutton" checked="checked">
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ball and stick
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<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:2:isosurface off; cartoons off; spacefill 100%;">
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spacefill
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<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:2:isosurface off; spacefill 0%; wireframe off; cartoons on;">
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<strong>cartoon</strong>
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<input name="radiobutton" type="radio" value="radiobutton" script="script:jmol:2: isosurface on;">
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molecular surface
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<p>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif" color="#660000">Use
navigation mode to "fly" through molecules. When switching to navigation
mode, select "front" when asked. Then use the buttons which appear in
the upper left of the model to fly into the molecule. Using only the "+"
button you can fly straight in.</font><br><br>
</p>
<table cellpadding="0" border="0" cellspacing="0" width="100%">
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<td align="right">
<input name="checkbox" script_selected="script:jmol:2:set navigationMode true;set echo bottom center; color echo white; font echo 12 sansserif; echo if you use the keyboard for navigation|click on the molecule first;" type="checkbox" value="checkbox" script_deselected="script:jmol:2:set echo bottom off; set navigationMode false;">
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navigation mode
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<img height="23" width="33" src="motionBullet.png">
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<font face="Verdana, Arial, Helvetica, sans-serif" color="#5d6b86" size="5"><strong>Summary</strong></font>
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<img width="18" height="6" src="rule.png">
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">In this
activity we have only scratched the surface of computer modeling. Before
you leave this activity you should feel pretty confident about how to use
the tools and modify the models. You should also understand that you can
change model parameters to do "experiments" with the model.</font>
<p>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">Models are
used everywhere, from insuring the safety of the car you ride in, to
designing the next anti-cancer drug. However, computer models are not
perfect. Just check out the weather forecast to see a model that is
pretty good at telling you the weather over the next day or two, but not
so good at telling you the weather a week from now. Even with these
limitations we can learn enough from using models to make advances in
the many uses for which they have been applied. </font>
</p>
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Intro to Modeling/MW
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