Tips & Techniques for using Protein Explorer (PE) Effectively.

Turn off rotation to increase responsiveness. The default rotation of the molecule consumes a large amount of computer resources. All operations will be much slower when rotation is on. It is recommended that you turn off rotation except when gazing tranfixed by the beauty of the (rotating) molecule.
Let the Explorer catch up before proceeding. Most problems with instability are induced by impatiently clicking buttons and links too rapidly. Never click over and over on the same item -- click once and wait at least five seconds to see what happens. Sometimes the browser needs to process thousands of lines of javascript before you see a response. If you change your mind, let the process finish before you close the window or click a different button. The and indicators will give you an impression of how long it takes PE to complete various tasks on your computer. However, this mechanism is not foolproof. If you rush ahead, clicking on links or buttons before PE has finished the previous task, it is possible to induce problems such as a permanent busy condition. If this happens, just close the window and start over -- but operate PE at a more relaxed pace.
In QuickViews, the pull-down menus (SELECT, DISPLAY, COLOR) won't perform the same operation twice in a row, unless the second time, you select (Repeat) near the top of each menu. For example, if you DISPLAY Spacefill, then select something else, then DISPLAY Spacefill again, nothing happens. Instead of the latter, pick DISPLAY (Repeat) and the new selection will be spacefilled. (This "feature" is not by design -- it is an annoying limitation of the HTML selection menu implementation.)
If the structure disappears or slides out of view when rotating, zoom down (click on the [-] button following [Zoom+]) and it will reappear. Keep the zoom lower when rotating.
With Macintoshes, do not attempt to resize the window running PE, or drag frame boundaries. Close PE and restart it in a window of the desired size. (This bug in Macintosh Netscape Communicator is beyond our control.) With Windows, after resizing PE's window or dragging the vertical frame boundary, if a permanent busy condition ensues (all buttons/commands ignored in the Comparator), click on the "Force Ready" link below the message window.
Be patient when loading large NMR PDB files. Most NMR PDB files are several megabytes in size. While loading, there will be a long period when Chime is blank and nothing seems to be happening. Be patient -- eventually the aligned conformers will appear.
Expand/reduce the command/message frame? If you are typing commands into the command-slot frequently, and if your screen is too small to see the entire message box, you may prefer to increase the size of the lower left frame. Just drag the top boundary of this frame up to give yourself more room, and you'll be able to see the entire message box. By dragging this frame boundary down, you can reduce the size of this area, which may sometimes be useful in QuickViews to expand the area for the middle help frame.
Windows: if clicks make beeps, tap the Alt key. In Windows, sometimes an Alert message appears in a box and then immediately gets put in the background before you even notice the box has appeared. When this happens, clicking on buttons or links will beep but otherwise be ignored, pending your pressing the "OK" button on the (invisible) alert message. To get the message back into the foreground, tap the Alt key once.