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*Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.
*Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.
*For full credit, your slides must include at least 2 animations.


*Additional work beyond the minimum required may earn extra credit.
*Additional work beyond the minimum required may earn extra credit.
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Show side-by-side <font color='e000e0'><b>two snapshots</b></font> comparing the asymmetric unit with the biological unit. The ''Cartoon'' representation in FirstGlance is best for these snapshots. Make sure to label which is which.
Show side-by-side <font color='e000e0'><b>two snapshots</b></font> comparing the asymmetric unit with the biological unit. The ''Cartoon'' representation in FirstGlance is best for these snapshots. Make sure to label which is which.


===Section 9: Animation from Polyview-3D===
===Section 9 - Contacts/Non-covalent Bonds===
Minimal steps to make an animation:
<!--
#Use the Firefox browser. (Initial orientation, Set by Jmol does not work in Safari.)-->
#Go to [http://polyview.cchmc.org/polyview3d.html Polyview-3D].
#Enter your PDB code in the PDB ID slot near the top. (If the slot is not visible, open the section ''Source of Structural Data''.)
#Change "Type of request" from "Single slide" to "Animation". It is under the ''Image Settings'' section near the bottom.
#Click any "Preview" link.<font color='gray'>
#Optional: If you want to modify the orientation or zoom of the molecule, click on ''View by Jmol / Set orientation'' under ''Quick links'' at the upper left of the page. Use the mouse to rotate and zoom in Jmol. Then click the ''Set and close'' button.
#Optional: If you want to change the colors, hide portions of the molecule, emphasize certain residues, etc. feel free to try out these options in the form, using ''Preview'' to check your results.</font>
#In the "Animation Settings" section at the bottom of the page, set Delay to 10/100.
#Change "Angle step" to 5 degrees.
#Check "Rocking".
#Change "angle range" for rocking to 30 degrees.
#Click "Submit".
 
The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. <font color="gray">Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why. </font>
 
<!--In Powerpoint, animations move only when the slides are projected (full-screen).
 
'''Method 1:''' When your Polyview-3D job is done, you will see the animation in the web browser. Simply drag the animation directly from the Polyview-3D web page and drop it into a  slide. If the result does not animate when you project the slide, try the following method.
 
'''Method 2:''': -->
 
After your animation is completed and appears in the PolyView-3D web page:
#Right-click (Mac: control-click, or trackpad 2-finger click) on the animation in the Polyview-3D web page, and select Save Image As ...
#Save the image to the Desktop.
#Drag the image file (filename ending in .gif) from the Desktop and drop it into a slide.
#In Google Slides, the animation should move immediately.
 
<!--http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt-->
<span style="font-size:140%;background:#c0ffc0;">[https://docs.google.com/presentation/d/1PAzssvqDRBKFIl9DWvWpXXxM--gtIIdT0p8fMCXfE10/edit?usp=sharing Examples of Slides with Polyview-3D Animations]</span> (These slides are only to show you what is possible. These are not in your assignment.)
 
 
----
 
===Section 10 - Contacts/Non-covalent Bonds===
Example: [http://firstglance.jmol.org/fg.htm?mol=4d7b 4d7b].
Example: [http://firstglance.jmol.org/fg.htm?mol=4d7b 4d7b].
#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance.
#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance.
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Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing '''exactly one hydrogen bond'''. Be sure to identify the two entities (amino acids, nucleotides, ligand) by name, chain, and sequence number.  I need enough detail to be able to reproduce what you are reporting.
Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing '''exactly one hydrogen bond'''. Be sure to identify the two entities (amino acids, nucleotides, ligand) by name, chain, and sequence number.  I need enough detail to be able to reproduce what you are reporting.


===Section 11 - How Structure Supports Function===
===Section 10 - How Structure Supports Function===
Write a brief description ''in your own words'' (avoid plagiarism!) of how the structure of this protein supports its function. Doing some online research will strengthen your description.
Write a brief description ''in your own words'' (avoid plagiarism!) of how the structure of this protein supports its function. Doing some online research will strengthen your description.


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Your description should be at least 75 words. More work, if well done, will earn more credit.
Your description should be at least 75 words. More work, if well done, will earn more credit.


Section 11 in the [https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time.
Section 10 in the [https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time.


==VII. See Also==
==VII. See Also==
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