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, see Getting SPdbV.
Reminder: All accessory pages like Getting SPdbV will open in a second browser window; simply close the window to continue with the tutorial.
After installing the program, configure your web browser to use SPdbV as a helper application for files of MIME type chemical-x/pdb, with suffix .ent. For help with this task, see Configuring Netscape.
You will start learning about SPdbV by looking at the enzyme lysozyme in complex with the trisaccharide inhibitor tri-(N-acetylglucosamine) or tri-NAG (see a biochemistry text if you want to know more about lysozyme). Atomic coordinates for this model are contained in the Protein Data Bank file with code 1HEW. If you have the full set of files for SPdbV, you will find this file with the name 1HEW.pdb in the folder entitled hel. Otherwise, obtain this file from the Protein Data Bank using your web browser, and save a copy named 1HEW.pdb. For help with this task, see Getting PDB Files. (USM students can find the file in the folder PMLMAC.MACAPPS/Course Materials/BIOCHEM/SwissPdbViewer/hel)
For information about the contents of PDB files, see PDB File Contents, but this information may be more understandable to you later in the tutorial.
Double-click on the SwissPdbViewer icon to start the program. Click OK on any dialogs that appear, and click anywhere on the introduction screen to remove it.
File: Open PDB File ...
Find and open the file 1HEW.pdb. Click OK on
any dialogs that appear.
Go to Section 2 of the Tutorial.