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:
for Protein Explorer
if you have a choice.
Protein Explorer's support for
IE is much newer. While the most-used capabilities of Protein Explorer
work well in IE, a few special features don't work in IE or work better
in Netscape. For example, Protein Comparator and Animations work
poorly in IE.
Here are instructions on how to
If Chime appears to work
but Protein Explorer doesn't, see
Fixing a Script-Disabled Chime Installation in Internet Explorer
Windows 3.1: A compatible
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
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
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)
Internet Explorer 5.5SP2 or later (Win32 only),
If you have information to contribute to this document, please email
it to firstname.lastname@example.org.
Is Chime installed but disabled?
- Verify that your browser is compatible.
Get your browser's version number.
Chime is NOT available for
you must use
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.
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.
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.
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.
- 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
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.)
- 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).
- Is Chime really installed? (It is possible for the Chime installer
to report 'successful completion' without installing Chime where you want it.)
- Functional test. Go to this
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.
- Netscape "acid test":
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.
- 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".
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.
- Is an obsolete version of Chime installed?
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.
- Critical Macintosh-Specific Issues
(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
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.)
the way, you should have at least 32 MB of RAM on your Mac to load large
images in Chime.)
Giving Netscape enough memory for Chime.
- 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.
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.
- 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
FrontDoor, an error similar to this will be reported:
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.
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
For some Chime sites, other rows must be enabled (e.g.
chemical/x-pdb | Brookhaven PDB | pdb,emb,embl
- 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.
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
Internet Explorer with Scripts Disabled by IE's
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
- Does your computer have this problem?
The following simple diagnostic procedure will tell you.
- Start the
Amino Acid Quizzer (this link opens a new window so you can get
back to these instructions).
- 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.
- Enter 1 (or any number up to 141) in the slot (press Enter).
- 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).
- If no green amino acid appears, your IE installation has the
script-disabled condition, and will not work with Protein Explorer.
- 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.
- What does NOT fix this problem?
The following maneuvers that you might reasonably think would correct
the problem do NOT do so:
- Uninstalling and reinstalling Chime (regardless of how you do it).
- Upgrading IE to version 5.5 or 6.
- Reverting to an earlier version of IE (after upgrading).
- Re-installing IE (even after deleting all identifiable IE files).
- Start, Settings, Control Panel, Add/Remove Programs, Microsoft Internet
Explorer, Repair Internet Explorer.
- 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
- 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:
PROCEED AT YOUR OWN RISK. If you are not comfortable doing this
procedure, seek help from someone more familiar with the technical side
- Windows 98: Start,
Settings, Control Panel, Add/Remove Programs, then click the Startup
- Windows 2000: Start, Program, Accessories, System Tools,
In the Backup dialog select from the main menu Tools, then Create Emergency
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.)
- Start, Settings, Control Panel, Add/Remove Software.
- Uninstall Chime for IE, and if present, any other Chime installations
such as Chime for Netscape. All Chimes should be uninstalled.
- Start, Run, and enter "regedit" into the slot, then click OK. The
Registry Editor will open.
- 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.
- 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.
- Highlight the last entry, "Extension", and Edit, Delete, confirm
The following (or something similar) subsumed under Extension will
thereby be deleted. These keys appear to be responsible for the problem.
"Version"="2, 6, 0, 8"
@="Chemscape Chime 2.6 SP3"
- Close the Registry Editor (Registry, Exit, or simply click on the X at
the upper right corner).
- Install Chime into IE (and also in Netscape if you have it).
(download for Chime Installer.)
- Your IE should be fixed to work properly with Chime now.
Repeat the diagnostic test above to verify this.
- Enabling Chime in Macintosh (Method I):
This method is strongly recommended.
It almost always works. See also the
1 gigabyte memory problem.
- Make sure you have the Netscape 4.7x/4.8x installer available.
If not, download it.
- Make sure you have the Chime installer available.
If not, download it.
- In Finder, locate the file Macintosh
HD:System Folder:Preferences:Netscape Users:[Your User Name]:Netscape Preferences
- Drag the file Netscape Preferences into the trash, and empty the trash.
- Shut down and reboot with extensions off (hold down Shift while booting).
- Reinstall Netscape.
If forced to reboot, boot with extensions off (hold down Shift while booting).
- Reinstall Chime in Netscape.
- Reboot normally (extensions on).
- Be sure to give Netscape enough memory! (See below.)
- 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:
Now try the Chime site of interest again, or the Functional Test above.
- In Netscape, pull down the Edit menu, and select Preferences.
- Open the Navigator category folder and select Applications.
- Select chemical/x-gaussian-cube and press the Delete button.
- Select chemical/x-mdl-tgf and press the Delete button.
- Select chemical/x-csm and press the Delete button.
- Select chemical/x-pdb and press the Delete button.
- Select application/x-spt and press the Delete button.
- Delete any other MIME types you think you'll need.
- Select the OK button to close the Preferences dialog.
- Exit Netscape.
- Restart Netscape.
- Be sure to give Netscape enough memory!
If you completed all the applicable steps above, and Chime or Protein
Explorer still doesn't work, please contact
giving the following information:
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.
- Version of operating system?
(right click on My Computer, Properties): 95, 98, NT, 2000, Me, etc.?
Macintosh (watch message during booting): OS 8.6? 9.0? Etc.
How much memory do you have?
How much memory did you give to
Netscape? (See above).
- What browser are you using?
- What is the version of your browser (including SP for IE)?
- Version of Chime?
In About Plugins, under Chime, are all MIME types enabled?
- Can you see the ATP molecule, and the MDL frank, when you
If not, what do you see?
- 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.
- If Protein Explorer is not the problem,
what is the URL of the Chime site that doesn't work?
- At what exact step does something fail?
- What error messages, if any, do you get?
(with the colon at the end!) in the location slot, and copy the error
message in your email.
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;
Frieda Reichsman for critical reading and corrections.