Sandbox3

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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!'''
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#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 (not sure yet how to do this easily...). If so, join their page. If not, start a new sandbox page.
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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 of the pdb id for your protein in the Protein Data Bank. Use this code to find the Proteopedia entry: this is the "automatically seeded entry". Copy this into your sandbox as a starting point.
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I looked for the earliest GFP structure I could find in the protein data bank and found 1ema. I searched Proteopedia for 1ema, clicked "edit page" button at the top, and then copied the contents below.
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{{Seed}}
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[[Image:1ema.png|left|200px]]
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<!--
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The line below this paragraph, containing "STRUCTURE_1ema", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_1ema| PDB=1ema | SCENE= }}
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===GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA===
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<!--
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The line below this paragraph, {{ABSTRACT_PUBMED_8703075}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 8703075 is the PubMed ID number.
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-->
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{{ABSTRACT_PUBMED_8703075}}
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==About this Structure==
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1EMA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. The June 2003 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Green Fluorescent Protein (GFP)'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2003_6 10.2210/rcsb_pdb/mom_2003_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EMA OCA].
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==Reference==
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<ref group="xtra">PMID:8703075</ref><references group="xtra"/>
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[[Category: Aequorea victoria]]
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[[Category: Ormo, M.]]
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[[Category: Remington, S J.]]
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[[Category: Autocatalytic]]
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[[Category: Beta-barrel]]
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[[Category: Bioluminescense fluorescent protein]]
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[[Category: Fluorophore]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:53:56 2009''
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==This is a placeholder==
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This is a placeholder text to help you get started in
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placing a Jmol applet on your page. At any time, click
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"Show Preview" at the bottom of this page to see how it goes.
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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_3cin | PDB=3cin | SCENE= }}
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Current revision

  1. REDIRECTSandbox 3
Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox3"
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