NOTE: Plan to work at least through section 4 of this tutorial without stopping. Thereafter, the end of any section is a convenient stopping point. Beyond section 6, you can take sections in any order.
ADVICE (no charge): Take time to PLAY with features of the program. Especially at the end of each section, you can play around without losing the continuity of the tutorial. By playing, by trying out various functions, you will discover additional features, and you will develop a personal style of using the program that will make it a more powerful tool in your hands.
If you do not already have access to the SwissPdbViewer program and accessory files, Get DeepView.
Reminder: All accessory pages, like Get DeepView, will open in a second browser window; simply close that window to continue with the tutorial.
You will start learning about DeepView by looking at the enzyme lysozyme in complex with the trisaccharide inhibitor tri-(N-acetylglucosamine) or tri-NAG. Atomic coordinates for this model are contained in the Protein Data Bank file with code 1HEW.
Go to the Protein Data Bank. Enter 1HEW in the search box at the top of the page and click Go. The 1HEW crystal structure page should now appear. At the right of the page, click on the Download Files dropdown menu and select PDB Format. Save the 1Hew.pdb file on your computer.
Start DeepView by double-clicking its icon. Click cancel on the Open dialog that appears.
File: Open PDB file... (remember the tutorial conventions: this is a menu command).
Find the 1HEW.pdb file you saved on your computer and click OK.
You model, in stick form, should appear.
You should now be looking at red, white, and blue stick model, on a black background. See if you can spot the inhibitor, which is composed of three chair-form rings of N-acetylglucose. It's not easy. Coming sections of the tutorial will show you how to highlight or single out specific features of a model and make them jump right out at you.
Go to Section 2 of the Tutorial.