Basic Tutorial For DeepView

1. Getting Started

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 (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.

Let's use DeepView's file import function to get this model.

Start DeepView by double-clicking its icon. Click cancel on the Open dialog that appears.

Linux: Start DeepView, either by typing out the full path name to the supplied wrapper shell script at the shell prompt in an xterm, $ /usr/local/spdbv/SPDBV/bin/ or use the menu or icon facility provided by your window manager/desktop environment.

File: Import (remember the tutorial conventions: this is a menu command)
The Import dialog box appears. Enter the Protein Data Bank ID code 1HEW (upper or lower case is OK) in the Name box. Then press return, or click the button "PDB File" under "Grab from SERVER:" (NOT under "Grab from disk".) The model, in stick form, should appear.

You can also obtain this file from the Protein Data Bank using your web browser by following these instructions:.

  1. Click here to open a new window for the PDB Home Page. You may wish to add this site to your menu of bookmarks or favorites.
  2. Slide the PDB window aside so that you can read these instructions and carry them out in the PDB window.
  3. A search box with a Site Search button is near the top of the screen, in the middle. Make sure that "PDB ID or Keyword" is turned on (button to left of box), and type 1HEW (the first character is the number one) in the box. Then click the Site Search button. The Structure page for 1HEW appears.
  4. At the left side of the page, click Display Molecule to reveal a drop-down list, and then click Swiss-PDB Viewer.
  5. Your browser should download the file, perhaps asking you where to save it.
  6. Start DeepView. The Open dialog appears. Find your downloaded file, select it, and click the Open button.

Linux: PDB files (compressed/uncompressed) may be downloaded using Netscape under Linux by holding down the Shift key while left-clicking the file link. Downloaded files are saved in your home directory, by default. The 'Pick App' functionality may be achieved by opening up the 'Edit -> Preferences -> Navigator-> Applications ' menu in Netscape and associating the .pdb/.ent file ending with the executable DeepView program.

For full instructions about using the Protein Data Bank, click Help under the menu list on the left.

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.

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.

Next Section: 2. Windows and Help

To The Molecular Level