Troubleshooting Chime and Protein Explorer
Here are downloading links for the Chime Installer and for Netscape 4.8x.

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 2 and Protein Explorer:

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, the classic environment on OS X supports Chime.
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. (Protein Explorer requires Netscape 4.08 or later (Win32/MacPPC) or Internet Explorer 5.5SP2 or later (Win32 only), with Chime 2 installed, with javascript, java, and cookies enabled.)

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


Troubleshooting Steps
  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 (Windows or Macintosh PPC): 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.

      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: 4.8x, the latest version in the 4.8 series, will give best results. The 4.7 series also works fine as far as we know. If you have a version in the range 4.1 and 4.6, upgrade to 4.8x. Here are instructions for finding the 4.8x "Communicator" browers at Netscape's site.
        Version 6 does not work with Chime. Why Netscape released version 6 without plugin support is a mystery. Whether or when they will fix it is unknown.
    3. Netscape 4.08 is also fine for most Chime sites. It works well with Protein Explorer. 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) 4.8x.

    4. Internet Explorer: The only version guaranteed to work is 5.5SP2 or later. 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.)

    5. 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. 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. 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 favor of another molecular visualization software package. In either case, read on.
    2. Netscape "acid test": Pull down the Help menu, and select About Plugins. If Chime is not in the list, it is not installed for this version. (It may be installed for another browser on your computer, or another version of Netscape -- but not for the one you are using.)
        Internet Explorer regrettably lacks any "About Plugins" display.
    3. 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".
    4. 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 an obsolete version of Chime installed? While displaying the ATP molecule, click on MDL (at the lower right), then "About..". Note Chime's version number. At the time of this writing (January 2002) the current version is 2.6 SP3. 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, 2.6SP1, 2.6SP2. Good versions are 2.0.3, 2.0a, and 2.6SP3. 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.  

  4. 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.

  5. 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: 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).

    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 (here is a link to download the Chime installer). 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.
      • After re-installing Chime, your Netscape should be ready to go -- but your Internet Explorer installation could still possibly be damaged so as to be unable to work with Protein Explorer. Use the diagnostic test in the next step to find out, and fix it if necessary.
       
    5. Fixing Windows Internet Explorer with Scripts Disabled by IE's Plugin Management: Some installations of IE that display ATP correctly nevertheless fail to process commands from the browser to Chime correctly, and Protein Explorer (as well as some other Chime sites) will not operate.
      1. Does your computer have this problem? The following simple diagnostic procedure will tell you.
        1. Start the Amino Acid Quizzer (this link opens a new window so you can get back to these instructions).
        2. Click on the big link "Amino Acid Quizzer!", after which you should see a molecule on the left and a form slot on the right.
        3. Enter 1 (or any number up to 141) in the slot (press Enter).
        4. If one amino acid turns green, zooms in, and ends up in ball and stick, your IE/Chime is working properly (and will support Protein Explorer).
        5. If no green amino acid appears, your IE installation has the script-disabled condition, and will not work with Protein Explorer.
      2. What causes this problem? The problem arises only when the very first installation of Chime is directed to Netscape only (specifying that Chime not be installed in IE), and when the IE version is 5.0. The problem is due to a peculiarity in IE's plugin management, and is known to occur for all versions of the Chime Installer 2.0 through 2.6SP3. MDL reports that IE attempts to grab the plugin from Netscape, leaving a nonfunctional entry in the Windows registry. I first identified this problem and reported it to MDL in April, 2002. MDL expects that changes in the Installer for Chime 2.6 SP4 (not yet available at the time of this writing) will prevent this in the future.
      3. What does NOT fix this problem? The following maneuvers that you might reasonably think would correct the problem do NOT do so:
        1. Uninstalling and reinstalling Chime (regardless of how you do it).
        2. Upgrading IE to version 5.5 or 6.
        3. Reverting to an earlier version of IE (after upgrading).
        4. Re-installing IE (even after deleting all identifiable IE files).
        5. Start, Settings, Control Panel, Add/Remove Programs, Microsoft Internet Explorer, Repair Internet Explorer.
      4. How to Fix the Damage to IE:
        MDL plans to release Chime 2.6 SP4 soon, and the installer with this new version is supposed to fix this problem automatically. Until that happens, here is another solution to this frustrating problem.

        1. Caution: this procedure involves editing the Windows Registry, and though unlikely if the procedure is followed carefully, could possibly render your computer unbootable. Backup critical files first, and be sure you have a bootable rescue diskette:
          • Windows 98: Start, Settings, Control Panel, Add/Remove Programs, then click the Startup Disk tab.
          • Windows 2000: Start, Program, Accessories, System Tools, Backup. In the Backup dialog select from the main menu Tools, then Create Emergency Repair Disk. Put an empty diskette into A. Check the Also backup registry checkbox, and then OK. (To restore a "dead" registry, you have to start-up the PC from the Win2000 CD-ROM, and follow the instructions.)
          PROCEED AT YOUR OWN RISK. If you are not comfortable doing this procedure, seek help from someone more familiar with the technical side of Windows.
        2. Start, Settings, Control Panel, Add/Remove Software.
        3. Uninstall Chime for IE, and if present, any other Chime installations such as Chime for Netscape. All Chimes should be uninstalled.
        4. Start, Run, and enter "regedit" into the slot, then click OK. The Registry Editor will open.
        5. In the Registry Editor, click Help, Help Topics, Restore the Registry. Right click the help text that appears and print it, just in case. I have never had to do this, but better safe than sorry.
        6. In the Registry Editor, click the [+] next to each of the following in the hierarchy of keys. Each click will open the keys encompassed by the parent key, enabling you to find the next key to open.
          HKEY_LOCAL_MACHINE
            Software
              Microsoft
                Internet Explorer
                  Plugins
                    Extension
          
        7. Highlight the last entry, "Extension", and Edit, Delete, confirm deletion. The following (or something similar) subsumed under Extension will thereby be deleted. These keys appear to be responsible for the problem.
              "Content Type"="chemical/x-pdb"
              "Version"="2, 6, 0, 8"
              @="Chemscape Chime 2.6 SP3"
              "Location"="C:\\NAVIGATO\\PROGRAM\\PLUGINS\\npchime.dll"
          
        8. Close the Registry Editor (Registry, Exit, or simply click on the X at the upper right corner).
        9. Install Chime into IE (and also in Netscape if you have it). (download for Chime Installer.)
        10. Your IE should be fixed to work properly with Chime now. Repeat the diagnostic test above to verify this.
       
    6. Enabling Chime in Macintosh (Method I): This method is strongly recommended. 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 below.)
    7. 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.

If you completed all the applicable steps above, and Chime or Protein Explorer still doesn't work, please contact emartz@microbio.umass.edu giving the following information:
  1. Version of operating system?
    Windows: (right click on My Computer, Properties): 95, 98, NT, 2000, Me, etc.?
    Macintosh (watch message during booting): OS 8.6? 9.0? 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 for IE)?
  6. Version of Chime?
  7. Netscape: In About Plugins, under Chime, are all MIME types enabled?
  8. Can you see the ATP molecule, and the MDL frank, when you go to ATP? If not, what do you see?
  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.
The most common reason (and most frustrating to you and me) that I can't help is that I was not given sufficient detail about the problem you're having. Give me step by step, click by click details, with error messages verbatim.


Thanks to Franklin Adler of MDL for information on re-enabling Chime 2 on the Macintosh; to Jean Holt of MDL for much support and advice; to Tim Driscoll for Macintosh advice; and to Frieda Reichsman for critical reading and corrections.