Sandbox423: Difference between revisions
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:Start by finding a protein-drug complex with a known structure that interests your team (see assignment sheet instructions). Check the list below to see if another team has already chosen this protein. If not, start a new sandbox page (just try sandbox## in the search box to find an unused number) and add a link for your team/protein to our class list below (use editing button above (Ab) or follow my model). | :Start by finding a protein-drug complex with a known structure that interests your team (see assignment sheet instructions). Check the list below to see if another team has already chosen this protein. If not, start a new sandbox page (just try sandbox## in the search box to find an unused number) and add a link for your team/protein to our class list below (use editing button above (Ab) or follow my model). | ||
Copy the message at the top of this page into your sandbox page to "reserve" this sandbox for this course. | :Copy the message at the top of this page into your sandbox page to "reserve" this sandbox for this course. | ||
Find the pdb id for your protein-drug complex 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. | :Find the pdb id for your protein-drug complex 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 | ::Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load | ||
and display another structure. | and display another structure. | ||
{{STRUCTURE_1ema | PDB=1ema | SCENE= }} | {{STRUCTURE_1ema | PDB=1ema | SCENE= }} | ||
Revision as of 23:24, 16 March 2011
"This sandbox is in use until August 1, 2011 for UMass Chemistry 423. Others please do not edit this page. Thanks!'
L Thompson 3/16/11
Task #1 Due 3/30/11
- Start by finding a protein-drug complex with a known structure that interests your team (see assignment sheet instructions). Check the list below to see if another team has already chosen this protein. If not, start a new sandbox page (just try sandbox## in the search box to find an unused number) and add a link for your team/protein to our class list below (use editing button above (Ab) or follow my model).
- Copy the message at the top of this page into your sandbox page to "reserve" this sandbox for this course.
- Find the pdb id for your protein-drug complex 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: | , | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
