To fix this, please give Protein Explorer permission to open new windows.

Why to you have this problem? The usual reason for this problem is use of software designed to stop websites from "popping-up" new windows to display advertisements. Such ad-blocking software may need to be disabled in order to use Protein Explorer, or it may have an option to give permission to certain websites to open new windows. In the latter case, if you are using Protein Explorer from, for example, molvis.sdsc.edu, give permission for all websites in the domain sdsc.edu to pop open new windows.

Netscape 4.8 does not have a built-in blocker for pop-up windows, but Internet Explorer 6.0 SP2 (on Windows XP) does have! Other generic software that we know about that can block popup windows includes AdSubtract, the Google Toolbar, PopSwat, Popup Dummy, PopUp Stopper, StopZilla, and many more!

How do you find the blocking software? If you don't know what software is blocking popups, here are some ideas to help you find it.

• Windows: carefully inspect the browser window in which Protein Explore fails to start. Many pop-up blockers alert you about what they are doing, sometimes with a message or icon that appears near the top or bottom of the browser window. In Internet Explorer in Windows XP, an alert may appear, and also an Information Bar appears that enables you to give permission for the current website to open pop-ups.
• Windows: carefully inspect everything in your task bar at the lower right. Most popup blockers have an icon there to access their settings.
• Windows: carefully inspect everything on your Start, Programs menu.
• Windows or Macintosh: find all files with "block" or "pop" in their names.
• Windows, Control Panel, Add/Remove Software: inspect the list of installed software.
• Windows: Ctrl-Alt-Del to open the Task Manager. Look for running processes with suspicious names.