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| '''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!'''
| | #REDIRECT[[Sandbox 3]] |
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| L Thompson 3/1/09
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| :Start by finding a protein with a known structure that interests you (see assignment sheet instructions). Determine whether anyone else in the class has already started a sandbox page for your protein (see list below). If so, join their page. If not, start a new sandbox page (you can use any unused ones listed below, or search for available numbers) and add a link to your page to our class list below (use editing button above (Ab) or follow my model).
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| '''Chem490a Sandbox pages:'''
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| [[Sandbox4]] [[sandbox5]] [[sandbox7]] [[sandbox8]] [[sandbox9]] [[sandbox10]] | |
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| Copy the message at the top into your sandbox page to "reserve" this sandbox for this course (others can still edit it but there is a way to go back -- not sure how yet).
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| Give "credit" for all your entries: add your name (like mine above) and also the source of anything that you got from another source.
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| Look for the pdb id for your protein in the Protein Data Bank. I looked for the earliest GFP structure I could find in the protein data bank and found 1ema, then followed the directions below to pull up a rotating GFP on this page.
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| Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
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| and display another structure.
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| {{STRUCTURE_1ema | PDB=1ema | SCENE= }}
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| Wow -- you can start exploring your structure now!
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| Task#1 (Due Wed 3/4 in the workshop). Describe the overall structure of your protein in words and make a "greenlink" illustration to go along with your description. Use the scene authoring tools and watch video 7 for instructions.
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| Example: (L Thompson)
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| The <scene name='Sandbox3/Secondary_structure/1'>overall structure</scene> of green fluorescent protein is an 11-stranded beta barrel (yellow) surrounding a central helix (pink). The chromophore is part of the central helix. Information from [[1ema]].
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