Sandbox3
From Proteopedia
| Line 45: | Line 45: | ||
[[http://meta.wikimedia.org/wiki/Cheatsheet Wikimedia cheat sheet]] | [[http://meta.wikimedia.org/wiki/Cheatsheet Wikimedia cheat sheet]] | ||
| - | [[http://en.wikipedia.org/wiki/How_to_edit General help with Wiki editing]] | + | [[http://en.wikipedia.org/wiki/How_to_edit General help with Wiki editing]], plus more [[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Text examples]] |
| + | |||
| + | Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites. | ||
Revision as of 22:01, 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.
| |||||||||
| 1ema, resolution 1.90Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Non-Standard Residues: | , | ||||||||
| |||||||||
| |||||||||
| 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.
Student projects:
Jamal Salah & Vishwa Shah- deoxyhemoglobin (sandbox4)
Elli Schmidt - HRas p21 (sandbox5)
Marissa McGarry - (sandbox8)
Tami Allen - Human Beta-Secretase (sandbox9)
Brendan Jones - Myosin 2 motor domain (sandbox10)
K Sniffen - ?? (sandbox11)
Help Editing
Hint: Ctl-click or right-click on links below and select "Open Link in New Window"
[General help with Wiki editing], plus more [Wiki Text examples]
Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites.
