When do you need the troubleshooting information below? When Protein Explorer deems your browser compatible, and tries to start (so you see 3 frames, one titled "FirstView"), but no molecule ever appears. Or when you have installed Chime, but no molecule appears at Chime-employing websites.

Protein Explorer: It is a common misconception that you can double-click on a PDB file to start Protein Explorer. There are several ways to tell Protein Explorer what molecule to load, all described on its FrontDoor; double-clicking a PDB file is not one of them. The instructions for starting a downloaded copy of Protein Explorer are at the download site and, although simple, must be followed if you are to succeed.

The information below is limited to Netscape 4.x. We hope to add information on Internet Explorer in the future. We have much less experience with IE (because it does not support LiveConnect, needed for most of our Chime projects). If you have information to contribute, please email it to emartz@microbio.umass.edu.

1. Verify that your browser is compatible. In Netscape, pull down the Help menu near the very top of your window (Macintosh: top right of your screen.) Select About Communicator. This displays the version number of the browser you are using. Here are points to consider:
   1. It is perfectly OK to have both Internet Explorer and Netscape installed on your computer. They do not interfere with each other, and can even be run simultaneously. (If you wish, you can use IE for your main browser, and Netscape only for Chime sites.) It is also OK to have multiple versions of Netscape installed (in different directories/folders).
   2. For best results, use the latest Netscape version 4.7x (4.78 at the time of this writing). If you have a version in the range 4.1 and 4.6, upgrade to 4.7x.
   3. Some computer labs can't support 4.7x and still use 4.08. Netscape 4.08 is also fine for almost all Chime sites. If you have a version number lower than 4.08, upgrade to 4.08 or 4.7x.
   4. Internet Explorer has only partial support for Chime -- some sites work with it (for example the Amino Acid Quizzer) but most don't (for example Protein Explorer). Internet Explorer is beyond the scope of this document (see italics notice near the top of this page).
   5. Netscape 6 does not work with Chime!

2. Is Chime really installed? (It is possible for the Chime installer to report 'successful completion' without installing Chime where you want it.)
   1. Functional test. In Netscape, go to this ATP molecule. Your window should turn black, the "MDL" frank should appear in the lower right of your window, and the ATP molecule should appear. If the molecule and MDL frank don't appear, Chime may not be installed. If a Non-Chime molecular image appears (molecule but no MDL frank at lower right), Chime is may be installed but disabled. In either case, read on.
   2. Acid test. Pull down Netscape's Help menu, and select About Plugins. If Chime is not in the list, it is not installed for this Netscape. (It may be installed for another browser on your computer, or another version of Netscape -- but not for the one you are using.)
   3. Is an obsolete version of Chime installed? Many Chime sites won't work with obsolete versions. In the list About Plugins (see previous step to get it), note the version of Chime. At the time of this writing (March 2001), either Chime 2.0.3 (Windows; Macintosh 2.0a) or Chime 2.6 work with all Chime sites. If you have an earlier version, download the installer for the current version from MDL.
   4. Fixing it. If Chime is not installed (does not appear in the list), most likely you failed to specify the browser you are now using during installation. Run the Chime installer again, being careful to specify the desired browser when asked.
      Macintosh: you will be given a list of "plugins" folders. You must select the one that belongs to Netscape Communicator. Otherwise, the installer puts Chime where Netscape can't find it, and reports "success".
   5. After installing Chime, you must exit/quit Netscape, then restart Netscape. Macintosh: be sure to Quit Netscape (not just close all the windows), so it is no longer listed in the Finder, before restarting it.

3. Is Chime installed but disabled?
   1. Examine the "About plugins" list carefully (see "Acid test" above to redisplay this list.) In the Chime section, look in the last column, "Enabled". If all rows say Enabled "Yes", Chime is enabled. In particular, if either of these rows are "No" (disabled!), most Chime sites won't work:
      application/x-spt | RASMol script | spt
      chemical/x-pdb | Brookhaven PDB | pdb,emb,embl
      For some Chime sites, other rows must be enabled (e.g. application/x-rasmol, xyz).
   2. Why would Chime be disabled? Some other applications may redirect critical MIME types such as pdb and spt to themselves. Examples are WebLab Viewer, and ChemDraw3D. In the process, they disable use of these MIME types for Chime. WebLab Viewer rarely uses PDB, so re-enabling Chime is unlikely to cause a problem for WebLab.
   3. Enabling Chime. Windows: Re-install Chime. The most recently installed application takes the MIME types it needs.
   4. Enabling Chime. Macintosh (Method I): You need to delete the pdb mime type from Netscape's preference file. This forces an initialization of the preference file upon restart of Netscape. Follow these steps after you start Netscape:
      1. In Netscape, pull down the Edit menu, and select Preferences.
      2. Open the Navigator category folder and select Applications.
      3. Select chemical/x-gaussian-cube and press the Delete button.
      4. Select chemical/x-mdl-tgf and press the Delete button.
      5. Select chemical/x-csm and press the Delete button.
      6. Select chemical/x-pdb and press the Delete button.
      7. Select application/x-spt and press the Delete button.
      8. Select the OK button to close the Preferences dialog.
      9. Exit Netscape.
      10. Restart Netscape.
      11. Be sure to give Netscape enough memory! (See below.)
      Now try the Chime site of interest again, or the Functional Test above.

   5. Enabling Chime. Macintosh (Method II -- Try this if method I failed!):
      1. In Finder, locate the file Macintosh HD:System:Preferences:Navigator.
      2. Delete this file.
      3. Shut down and reboot with extensions off (hold down Shift while booting).
      4. Reinstall Netscape.
      5. Reinstall Chime in Netscape.
      6. Be sure to give Netscape enough memory! (See below.)
    

4. Macintosh: Giving Netscape enough memory for Chime. (This is not a problem on Windows, provided your computer has at least 32 megabytes of RAM.) Quit from Netscape. Locate the Netscape Application file on your hard disk. Select it. Open Finder's File menu and select Get Info. The minimum size should be set to 15000k, and the preferred size should be set to 20000k. (If you can't change the memory settings, you didn't quit Netscape.) (By the way, you should have at least 32 MB of Ram on your Mac to load large images in Chime.) Restart Netscape.

5. Using Protein Explorer to diagnose the problem with another Chime site. Most Chime websites don't check your browser to make sure everything is set correctly, but Protein Explorer does. If you can get Chime to work at some sites, but not at others, try running Protein Explorer (www.proteinexplorer.org), and it will tell you automatically if something in your browser is not set correctly, and how to fix it. While all the settings required by Protein Explorer may not be needed at the problematic Chime site, this is a simple way to identify a possible incompatibility and learn how to fix it. (Protein Explorer requires Netscape 4.08 or later, with Chime 2 installed, with javascript, java, and cookies enabled.)

1. Version of operating system?
   Windows (right click on My Computer): 95, 98, NT, 2000, Me, etc.?
   Macintosh (watch message during booting): OS 8.6? 9.0? Etc.
2. Under About Communicator, what version is reported?
3. Version of Chime (see Acid Test above).
4. In About Plugins, under Chime, are all MIME types enabled?
5. Can you see the ATP molecule, and the MDL frank, when you go to ATP? If not, what do you see?
6. If you are having trouble with Protein Explorer, are you trying to use a downloaded copy, or use it on-line?
7. What is the URL of the Chime site that doesn't work?
8. At what exact point in this site does something fail?
9. What error messages, if any, do you get?
10. If you see "javascript error" in the status line, enter "javascript:" (with the colon at the end!) in the location slot, and copy the error message in your email.