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. Or when Chime-employing sites show the molecule, but the control buttons don't display the intended images (or don't work at all).

Starting Protein Explorer Correctly: 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.

This document covers, using these color cues, the following platform/browser combinations supported by MDL Chime and Protein Explorer:

• Windows ("Win32" = Win95/98/NT/2000/ME/XP or later) with Netscape (4.X, or 7.1 or later, or current versions of Firefox or Mozilla).
• Windows ("Win32" = Win95/98/NT/2000/ME/XP or later) with Internet Explorer 5.5SP2 or later (6.0 SP1 or later recommended).
• Macintosh PPC (OS 8.6, OS 9.x, OS X-classic environment only) with Netscape 4.7x-4.8x
  Macintosh PPC with Internet Explorer: NO CHIME AVAILABLE!

  Macintosh OS X: if Netscape suddenly disappears, or you get recurrent "Network errors", see solutions in the OS X section of Tips and Techniques.

  Macintosh G4 with >1 gigabyte of memory? See Mac-specific issues below.

  Windows: Use Netscape/Mozilla/Firefox for Protein Explorer if you have a choice. While the most-used capabilities of Protein Explorer work well in IE, one important feature doen't work in IE. Here are supported browser download links.

  Internet Explorer: If Chime appears to work (shows ATP) but Protein Explorer doesn't, try upgrading to Chime 2.6 SP6 or later.
  If clicking on ATP opens a file download dialog mentioning file atp.pbd (should be .pdb) and ChimeShimLibrary, you need to upgrade to Chime 2.6 SP6 (or later).

Windows 3.1: A compatible Chime 1.0 exists (unsupported) but Protein Explorer and most newer Chime websites require Chime 2.
Macintosh PPC with OS X: Chime is not available to work in the native OS X environment. However, Netscape 4.8 in the classic environment on OS X supports Chime and PE.
Macintosh 6800: Chime 1.0 exists (unsupported) for Mac 6800 (pre PPC), but Protein Explorer and most newer Chime websites require Chime 2.
Silicon Graphics Irix: Chime 0.9z is available (unsupported) for SGI, but Protein Explorer and most newer Chime websites require Chime 2.
A very simple viewer named FirstGlance in Chime, available at the Protein Data Bank, OCA PDB Browser, and PDB Lite, works with Chime 1 (or 0.9z).
Chime 2 is not available for any platforms other than Win32 and MacPPC. It is not available for linux or other flavors of unix. However, there are solutions for using Chime on these platforms.

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.

If you have information to contribute to this document, please email it to emartz@microbio.umass.edu.

1. Verify that your browser is compatible.
   1. Get your browser's version number.

      Chime is NOT available for Internet Explorer on the Macintosh PPC. For Macintosh PPC you must use Netscape.

      Netscape 4.8 or later (Windows or Macintosh PPC) or Netscape 7.1/Mozilla 1.0/Firefox 1.0 or later (Windows only): Pull down the Help menu near the very top of your window (Macintosh: top right of your screen.) Select About [Browser Name]. This displays the version number.

      Internet Explorer (Windows only): Pull down the Help menu near the very top of your window Select About Internet Explorer. Note both the "Version" number (top line) and the "Update Versions" SP (Service Pack) Number.

   2. Netscape 4.08 is also fine for most Chime sites. It works well with Protein Explorer in Windows (but not Macintosh PPC). Some computer labs can't support 4.7x/4.8x and still use 4.08. If you have a version number lower than 4.08, upgrade to 4.08 or better yet (if supportable at your site) 4.8 or 7.1.

   3. Internet Explorer: The only version guaranteed to work is 5.5SP2 or later, but 6.0 SP1 or later is recommended. Some earlier versions work (or work partially) with some versions of Chime on some websites. The number of possible combinations of versions is huge, and nobody has time to test all combinations thoroughly for all websites. To be safe, upgrade to 5.5SP2 or later. (In your present version of Internet Explorer, open the Tools menu, and select Windows Update).
      (In IE 5.5SP2 released summer 2001, Microsoft removed the partial "Netscape plugin" support that was present in 5.5SP1 and earlier. Chime is a Netscape plugin, so it wouldn't work at all in 5.5SP2. Thankfully, MDL then released Chime 2.6SP3 in fall 2001, able to work in IE 5.5SP2.)

   4. 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. It is also OK to have multiple versions of Netscape installed (in different directories/folders). Unfortunately, IE versions 5.5 and later don't allow earlier versions of IE to remain available (unless you uninstall the later version).

2. Disable Pop Blockers/Swatters! PE needs to open many windows in order to work. If you have pop-up window blocking software enabled, PE cannot work, unless you give it special permission to open windows, or disable your blocking software. The symptom of a pop-swatter is that when you try to start PE, it hangs at the page about popup blockers, which displays possible solutions.

3. Is Chime really installed? (It is possible for the Chime installer to report 'successful completion' without installing Chime where you want it.)
   1. Freestanding PDB file test.
      • This test works in all compatible browsers except Netscape 7 (for which go to the Embedded PDB test).
      • 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 in a wireframe display as shown at right. (This tests that MIME chemical/x-pdb is working.)
      • If the molecule and MDL frank don't appear, Chime is either not installed, or not working properly.
      • If a Non-Chime molecular image appears (molecule but no MDL frank at lower right), Chime is may be installed but disabled in favor of another molecular visualization software package. In either case, read on.
      • If this test opens a file download dialog mentioning file atp.pbd (should be .pdb) and ChimeShimLibrary, you need to upgrade to Chime 2.6 SP6 (or later).
   2. Freestanding SPT file test.
      • This test works in all compatible browsers except Netscape 7 (for which go to the Embedded PDB test).
      • Go to Chime script atp.spt. Your window should turn black, the "MDL" frank should appear in the lower right of your window, and the ATP molecule should appear in a spacefill display as shown at right. (This tests that MIME chemical/x-spt is working.)
      • If the molecule and MDL frank don't appear, Chime is either not installed, or not working properly.
   3. Embedded PDB file test.
      • This test is provided only for Netscape 7 where the above two tests fail.
      • Go to this simple embedded Chime page. It should display hemoglobin as shown at right.
      • If the molecule and MDL frank don't appear, Chime is either not installed, or not working properly.
   4. Netscape/Mozilla/Firefox "About Plugins" test: Pull down the Help menu, and select About Plugins. If Chime is not in the list, it is not installed in this browser. (It may be installed for another browser on your computer, or another version of Netscape -- but not for the one you tested.)
      Internet Explorer regrettably lacks any "About Plugins" display.
   5. 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.

      • Netscape 7/Mozilla/Firefox require manual installation.

      • Netscape 4 or Internet Explorer: 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".

   6. 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.

4. Is an obsolete version of Chime installed? While Chime is visible (in one of the tests above), click on MDL (at the lower right), then "About..". Note Chime's version number. At the time of this writing (January 2005) the current version is 2.6 SP6. Chime version 2.6 SP6 (SP3 for Mac) or later is recommended.

   For Internet Explorer in Windows you must upgrade to Chime 2.6 SP6 or later!

   Whether you need to upgrade depends partly on which browser you are using and what Chime sites you wish to use. The following versions have known problems and should be upgraded regardless: any version "1" or earlier ("0.9"), any 2 "beta" version, 2.0, 2.0.1, 2.0.2, 2.6, 2.6 with SP1-5. Good versions are 2.0.3, 2.0a, and 2.6SP6. Protein Explorer checks the version of Chime you have installed and will refuse to proceed if it is too old. (The oldest Protein Explorer-compatible Chime version depends on which browser you are using.) If you need to update, download the installer for the current version from www.mdlchime.com.  

5. Critical Macintosh-Specific Issues
   1. 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 have 64 MB or more of RAM, use even higher settings. (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.

   2. Macintosh G4 1 Gig Memory Problem The following problem and solutions were reported in January 2002 thanks to Michael Morales, Peter Walter, and James W. Caras. Chime 2.6SP3 fails to work on Macintosh G4's with >= 1 gigabyte of memory when running OS 9.2. There are two solutions. First, you can run OS X, and Chime will work properly in the Classic environment. Second, you can physically remove some of your hardware memory.

6. Is Chime installed but disabled?
   1. On Macintosh PPC the symptom of this is that PE attempts to start, and you get 3 frames, but you never see a molecule, and there is a javascript error reported in the status line at the bottom of the window. If you enter "javascript:" into the Location slot at the FrontDoor, an error similar to this will be reported: Javascript error:
      top-fr_chime.document.form_chime.chime_graphics01 has no properties If you have this problem, go directly to Enabling Chime in Macintosh (Method I) below. It always fixes this problem.

   2. Netscape/Mozilla/Firefox: Examine the "About plugins" list carefully (see About Plugins 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).

   3. 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.

   4. Enabling Chime in Windows: Re-install Chime. The most recently installed application takes the MIME types it needs.
      • Before re-installing Chime, exit/quit Netscape and Internet Explorer. After running the installer, the browser will become aware of Chime when you restart it.
       
   5. Enabling Chime in Macintosh (Method I): This method is strongly recommended whenever Chime fails to work properly. It almost always works. See also the 1 gigabyte memory problem.
      1. Make sure you have the Netscape 4.7x/4.8x installer available. If not, download it.
      2. Make sure you have the Chime installer available. If not, download it.
      3. In Finder, locate the file Macintosh HD:System Folder:Preferences:Netscape Users:[Your User Name]:Netscape Preferences
      4. Drag the file Netscape Preferences into the trash, and empty the trash.
      5. Shut down and reboot with extensions off (hold down Shift while booting).
      6. Reinstall Netscape. If forced to reboot, boot with extensions off (hold down Shift while booting).
      7. Reinstall Chime in Netscape.
      8. Reboot normally (extensions on).
      9. Be sure to give Netscape enough memory! (See above.)

   6. Enabling Chime in Macintosh (Method II): This method is not recommended because it often fails, in contrast to Method I above that usually solves the problem. It is listed here for completeness.

      Delete the relevant MIME types 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. Delete any other MIME types you think you'll need.
      9. Select the OK button to close the Preferences dialog.
      10. Exit Netscape.
      11. Restart Netscape.
      12. Be sure to give Netscape enough memory! (See above.)
      Now try the Chime site of interest again, or the Functional Test above.

7. Troubleshooting PE's Startup Process

   PE uses a complicated process to start up. Should it fail to start properly, a mechanism is provided to help diagnose where the problem is. On the FrontDoor, look for the section Custom Startup Options for PE (at the bottom of the middle gray column). Check the checkbox Start PE step by step (for troubleshooting). Now use a Quick-Start link and record where the startup process fails to proceed.

   The checked status of this checkbox will be remembered (with a cookie) only for the duration of the browser session. New browser sessions will always leave this checkbox unchecked. This is in contrast to the other startup options, which, once set, are remembered indefinitely.

1. Version of operating system?
   Windows: (right click on My Computer, Properties): 95, 98, NT, 2000, Me, XP SP1/SP2, etc.?
   Macintosh (watch message during booting): OS 8.6? 9.0? Classic under OSX? Etc.
2. Macintosh: How much memory do you have?
3. Macintosh: How much memory did you give to Netscape? (See above).
4. What browser are you using?
5. What is the version of your browser (including SP number for IE)?
6. Version of Chime?
7. Netscape/Mozilla/Firefox: In About Plugins, under Chime, are all MIME types enabled?
8. For each of these tests, does it succeed or fail?
   • Freestanding PDB
   • Freestanding SPT
   • Embedded PDB
9. If you are having trouble with Protein Explorer, are you trying to use a downloaded copy, or use it on-line? To be sure, look in the Location slot near the top of your FrontDoor window. Does it begin "http" (on-line) or "file" (downloaded copy)? Paste the entire URL from the FrontDoor location slot into your email, please.
10. If Protein Explorer is not the problem, what is the URL of the Chime site that doesn't work?
11. At what exact step does something fail?
12. What error messages, if any, do you get?
13. If you see "javascript error" in Netscape's status line, enter "javascript:" (with the colon at the end!) in the location slot, and copy the error message in your email.