Sandbox3
From Proteopedia
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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). | :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). | ||
'''Chem490a Sandbox pages:''' | '''Chem490a Sandbox pages:''' | ||
| - | [[Sandbox4]] [[sandbox5]] [[sandbox7]] [[sandbox8]] [[sandbox9]] [[sandbox10]] | + | [[Sandbox4]] [[sandbox5]] [[sandbox7]] [[sandbox8]] [[sandbox9]] [[sandbox10]] [[sandbox11]] |
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). | 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). | ||
Revision as of 16:01, 3 March 2009
This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!
L Thompson 3/1/09
- 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).
Chem490a Sandbox pages: Sandbox4 sandbox5 sandbox7 sandbox8 sandbox9 sandbox10 sandbox11
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).
Give "credit" for all your entries: add your name (like mine above) and also the source of anything that you got from another source.
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.
Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load and display another structure.
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| 1ema, resolution 1.90Å () | |||||||||
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| Non-Standard Residues: | , | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Wow -- you can start exploring your structure now!
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. Example: (L Thompson) The 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.
