Hi guys! I’m having trouble finding how to view the protein rotationally (as phil did in class). Can anyone clue me in on how to do this through the molecule of the month website? Thanks and see ya in class tmw!
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Weekly topics
Erin,
The trick is to go to a protein’s Protein Data Bank page and then view it under one of the Display Options. Usually you can follow one of Goodsell’s links when he refers explicitly to a PDB ID. For example, go to his hemoglobin page (fifth monthly entry in 2003). You will see links to the following PDB ID numbers: 1buw, 2hco, 1c7d, etc. Those are the ID’s of various hemoglobin structures deposited in the data bank over the years. Click on any of them to get to that proteins data page. Once there, choose one of the “Display Options” on the right to see the 3D model on your screen. Try Jmol since it works on most computers. You might prefer one of the other display options since they each render proteins in their own style. To rotate the molecule you usually have to press the shift key while moving the mouse (or something like that… I forget the actual commands; I do them naturally; the instructions for rotation, changing colors, etc., are always listed in obvious places.)
Note: The Molecule of the Month is a convenient route to the data pages, but certainly not the only route. You can get to a data page through the home page of the data bank (http://www.rcsb.org/pdb/home/home.do) where you can enter various search terms to find a protein’s data page. The most specific search term is the protein’s PDB ID, but you can also use english words such as “human hemoglobin” to find the protein you are looking for.