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 current versions of Mozilla Firefox or Netscape (4.X or 7.2; Netscape version 8 was problematic last time we checked in late 2006]).
• Windows ("Win32" = Win95/98/NT/2000/ME/XP or later) with Internet Explorer (IE) 5.5SP2 or later (6.0 SP1 is recommended). Internet Explorer 7 does not work with Chime!
• Intel Macintosh OS X: Use Windows in a virtual machine running within, and concurrently with, OS X. Here are instructions. (There is no Chime available for Intel Mac OS X.)
• Macintosh PPC (OS X: Classic environment is required for Chime; or OS 8.6 or OS 9.x): Netscape 4.7x-4.8x supports Chime and Protein Explorer (see PE-compatible browsers).

  • Not Safari: Chime is not available for native OS X, so it will not run in Safari.

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

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

Windows: Use Firefox 2 or later for Protein Explorer if you have a choice. While many capabilities of Protein Explorer work well in IE, several important ones doen't work in IE (see Browser Compatibility). Here are supported browser download links.

Trouble making MolSlides with downloaded PE? See this fix.

Internet Explorer (IE): 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).

Silicon Graphics Irix: Chime 0.9z is available (unsupported) for SGI, but Protein Explorer and most newer Chime websites require Chime 2.
Chime 2 is not available for any platforms other than Win32 and MacPPC. It is not available for Intel Mac (see above), linux or other flavors of unix. However, there are solutions for using Chime on linux.

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. See the list of Protein Explorer-compatible browsers. Older Chime sites often work best in Netscape 4.8.
   2. It is perfectly OK to have multiple browsers installed on your computer. They do not interfere with each other, and can even be run simultaneously. For example, on Windows, there is no way to remove Internet Explorer, but we recommend that you add Firefox 2.0 or later.

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.
      
      • Click this link to an ATP molecule: atp.pdb. 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 window turns black, but the MDL frank and the ATP molecule do not appear, and you are using Mozilla Firefox, clear the Mozilla Firefox cache (Tools, Clear Private Data), then try again. See details below.
      • If the molecule and MDL frank still 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 you are using Windows, and this test opens a file download dialog mentioning file atp.pbd (should be .pdb) and ChimeShimLibrary, you need to upgrade to Windows Chime 2.6 SP6 (or later).
   2. Freestanding SPT file 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.
      
      • Go to this simple embedded Chime page. It should display hemoglobin as shown at right. (This tests that Chime can obtain a PDB file specified in its embed tag "src=" parameter.)
      • If the molecule and MDL frank don't appear, Chime is either not installed, or not working properly.
   4. Firefox "About Plugins" test: Type about:plugins (no space after the colon!) in Firefox's web address slot (the upper left-most slot), and press Enter. This will display a list of all installed 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, but it is not installed in this one.)
      Internet Explorer regrettably lacks any "about:plugins" display.
   5. If Chime does not appear in the About Plugins list, here's what to do:

      • Firefox requires manual installation of Chime. Here are the manual installation instructions for Chime. You must quit Firefox and restart it after the installation to force Firefox to notice Chime.

      • Netscape 4 or Internet Explorer: Run the Chime installer again, being careful to specify the desired browser correctly when asked.

      • Macintosh PPC Classic: Run the Chime installer again, paying careful attention to each step. 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 your browser, then restart it. Macintosh PPC: be sure to Quit Netscape 4 (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 (May 2007) the current version is 2.6 SP6.
   • Chime version 2.6 SP6 (2.6 SP3 for Mac Classic) or later is recommended.
   • For Internet Explorer in Windows you must upgrade to Chime 2.6 SP6 or later!
   • If you need to update, here are instructions.

5. Is Chime installed but disabled?
   
   
   1. Why would Chime be disabled? Some other applications may redirect critical MIME types such as pdb and spt to themselves. Examples could be Accelrys (formerly WebLab) Viewer, or 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. Below are methods for fixing this.
      
      
   2. 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 PPC Classic (Method I) below. It always fixes this problem.

   3. 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).

   4. Enabling Chime in Windows: Uninstall (Start, Settings, Control Panel, Add/Remove Programs) and then 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 for local PDB files in Windows Firefox:
      1. The Problem. Sometimes on Windows, Firefox gets configured so it works fine for on-line Chime websites, but won't display a PDB file from the local hard disk in Chime. Molecules won't display in downloaded (or locally created) MolSlides. PE's History and Reset View dialogs, and its MolSlide Manager show no molecular images (just blank black rectangles). Using a downloaded copy of Protein Explorer is recommended for creating MolSlides, and this problem blocks that creation process!
      2. The Cause. Downloading a PDB file from the Protein Data Bank often induces the above problem. This is due to bugs in the MIME type management within the Firefox 1.5 and 2 browsers, which we hope will be fixed when Firefox 3 is released.
      3. Diagnosis.
         • If you don't already have a PDB file on your local disk, download one. You can right-click on atp.pdb and Save Link As. The saved filename must end in ".pdb".
         • Drag the downloaded PDB file and drop it on a shortcut to Firefox, or into an open Firefox window. (Alternatively, in an open Firefox window, open the File menu, and select Open File, then open the PDB file from your local disk.)
         • Success: If the entire Firefox window turns black, and you see a wireframe display of the molecule (similar to at right), you do not have this problem, and this section does not apply to you.
         • Failure: If Firefox asks whether you wish to Open or Save the file, you do have this problem.
           (Changing the item on the Open pull-down menu will not fix this problem.
           Using Tools, Options, Content, File Types, Manage will not fix this problem.)

      4. How to Fix Firefox:
         1. Close all Firefox windows.
         2. Use Windows Search (Start, Search, Files or Folders) to find all files with the name mimeTypes.rdf. Limit the search to on disk drive C: only.
            Open the Advanced Options list, and
            • Uncheck "Search System Files".
            • Check "Search Hidden Files and Folders".
            • Check "Search Subfolders".
            • Check "Match Case".
            Start the search.
            Note that Windows Search is notoriously unreliable. Configuring the search exactly as above worked on four computers that we tested. Other variations did not.
            
            
         3. You are looking for the mimeTypes.rdf file in this filepath:
            C:\Documents and Settings\[your_login_name]\Application Data\Mozilla\Firefox\Profiles\[xxxxxxxx.default]
            (where xxxxxxxx is a random alphanumeric string generated by Firefox).
         4. Right-click the above file (make sure it is the one in the filepath above!) and select Rename. Change only the last three characters of the filename from rdf to old, so the name is now mimeTypes.old.
            This effectively hides the file from Firefox. Firefox will create a new default file. Our tests indicated that renaming this file not only restores proper Chime function, but does not interfere with other plugin MIME types. Notably, these plugins all worked correctly after renaming the file: Flash, Adobe PDF, QuickTime, Java.
         5. Start Firefox, and repeat the Diagnosis procedure above. If the problem is not fixed, make sure you renamed the file under the login name you are using.
         6. In the future, use Internet Explorer to download PDB files from the Protein Data Bank. This will avoid re-creating the problem in Firefox -- but if the problem happens again, simply follow the steps above again.
            
            Thanks to Shigehiro Nagashima (Osaka University, Japan) for help solving the above problem.
       
   6. Enabling Chime for an online PDB file that you downloaded in Windows Firefox:
      1. The Problem: In Windows Firefox, when you click on a direct link to a PDB file, such as this link to atp.pdb, the browser window turns black, but neither the MDL frank nor the molecule appear. This problem seems not very serious since it doesn't affect Protein Explorer (online or downloaded), nor any other Chime sites that we know of. However, it is certainly puzzling when it occurs, and the fix is easy!
      2. The Cause: In Windows Firefox, when you right click on a link to a PDB file (one that is not gzipped) and use Save Link As to download the PDB file, the above problem is created for only that one PDB file at the URL you clicked. This is the result of a bug in Firefox 2 that we hope will be fixed in Firefox 3.
      3. The Fix: Clear Firefox's cache: Tools, Clear Private Data.
       
   7. Enabling Chime in Macintosh PPC Classic (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.)

   8. Enabling Chime in Macintosh PPC Classic (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.
    
   
6. Critical Macintosh PPC-Specific Issues
   1. Giving Netscape 4.8 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 PPC 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 may fail 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.

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): 98, 98 Second Edition, NT, 2000, ME, XP SP1/SP2, Vista, etc.?
   Macintosh (watch message during booting): OS 8.6? 9.0? PPC with Classic under OSX? Intel OSX? Etc.
2. Macintosh PPC OSX with Classic: How much memory did you give to Netscape 4.8? (See above).
3. What browser are you using?
4. What is the version of your browser (including SP number for IE)? (Help, About).
5. Version of Chime? (Click on the MDL frank at the lower right in Chime, About).
6. Firefox: In About Plugins, under Chime, are all MIME types enabled?
7. For each of these tests, does it succeed or fail?
   • Freestanding PDB
   • Freestanding SPT
   • Embedded PDB
8. 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.
9. If Protein Explorer is not Chime site you are trying to get to work, what is the URL of that Chime site?
10. At what exact step does something fail?
11. What error messages, if any, do you get?
12. If you are using Firefox, open Tools, Error Console. Press Clear. Now reload the problematic Chime page. Copy any error messages into your email.