A. How.

Overall, and for most molecules and features, PE works quite well in IE.
This is thanks in part to Paul Pillot and Jean-Philippe Demers, who volunteered a great deal of their time in 2001 prior to the first IE-compatible release of PE in December 2001.
(MDL Chime does not support Macintosh IE, and therefore neither can PE.)

However, there are a few molecules or features where PE's operation in IE is less satisfactory. Therefore we recommend that you use the free Netscape (or Mozilla or Firefox) browser for PE when feasable.
(The only cases we know of where this is not feasable are in companies, institutions, or teaching computer labs where the support policies forbid the installation of Netscape.) Netscape does not interfere with Windows IE (they can be run concurrently). Here are the problems that I am aware of that PE has in IE:

1. Netscape supports PE's Features of the Molecule page in all modes of use, while IE not only requires a separate data file (in addition to the PDB file), but even then displays Features of the Molecule in only a limited set of modes of use. (Details.)

2. While neither browser, in combination with Chime, is crash-proof, IE seems more susceptible to freezing/crashing than does Netscape. This is more common when multiple sessions of PE (or windows containg Chime) are running concurrently, and more common on some Windows 98 systems. After running animations from the NMR Models/Animation page, closing the windows often causes IE to crash, and sometimes freezes Windows 98, requiring a reboot. Limited testing suggests that when IE crashes in Windows 2000 or XP, reboots are not required.

3. Beginning with Chime 2.6 SP4, the version can be detected in IE. However, IE cannot detect the version of MDL Chime installed, if it is version 2.6 SP3 or earlier. Threfore, if (to avoid the minor inconvenience of upgrading) you wish to use an older version of Chime for PE in IE, you will occasionally be asked to designate the Chime version manually. Netscape can detect all versions of MDL Chime automatically.

4. Some important operations that work smoothly in Netscape are slower or fail completely in IE, at least intermittantly. These include:
   • The Sequences and Seq3D displays for sequences longer than about 5,000 residues. For example, 1FPY, 1PMA, and 1G3I each contains between 5,000 and 6,000 residues, and each sometimes stalls PE's Sequences display indefinitely in IE, whereas in Netscape, PE displays these sequences in under 12 seconds. PE can display sequences of PDB files with under 4,000 residues in IE, e.g. 1FJF, (3,900 residues).
   • Animation of large ensembles of models often fail to display in IE, but always works in Netscape. For example, animation of the NMR ensemble 1JSA usually fails to display in IE.

5. In IE, if two or more windows are opened containing Chime, when the second Chime-containing window is closed, you may get a Plugin Error alert. Rarely, this may crash the IE browser, or even require a reboot. If you use the Quit link to close a PE session, the error is prevented, while if you click on the "x" button at the upper right of the window to close the session, the error occurs. This problem does not exist in Netscape.

6. When attempting to load a new molecule, IE fails to indicate the real progress (if any) in receiving the PDB file data. You just sit there in the dark, waiting and hoping. Netscape shows the count of bytes (or percentage of the file) received, so you can tell if data have stopped arriving from the server (or never started arriving), close PE, and try another source for the PDB file.

7. Some additional potentially confusing idiosyncracies of IE are mentioned in Tips & Tricks for Using PE Effectively.

8. Advanced users who create command scripts for use in PE's Project Folders will find lots of problems.

The MDL Chime plugin gave me a tremendous head-start in constructing Protein Explorer. Without Chime, an order of magnitude more time and resources would have been needed to construct a PE-like tool. PE is therefore absolutely dependent on Chime.

Chime is provided free by MDL Information Systems, Inc., but its development has been slow, and MDL has refused access to the Chime source code by either the academic community or companies interested in enhancing Chime. Despite the problems this causes (e.g. inability to fix some bugs in Chime that would be easy to fix), I have chosen to build Protein Explorer upon Chime because it is still very advantageous.

Chime was designed as a "Netscape plugin" at a time (1995) when Netscape had invented the plugin, and was by far the predominant browser in general use. By 2002, Netscape use has fallen to less than 10%, due largely to Microsoft's policy of bundling IE with Windows, and placing an unremovable shortcut to IE on the desktop. (These policies have led to some of the continuing anti-trust suits against Microsoft.)

MDL has made continuing efforts to enable Chime to work in IE. However, probably because Chime was designed to work in Netscape, its operation in IE is not quite as good and there are numerous serious bugs. Microsoft never implemented more than partial plugin support in IE, and they removed even that in IE 5.5 SP2 in mid-2001. Much credit is due MDL for making, within months, timely and crucial changes in Chime 2.6 SP3 that enabled Chime to continue to work in IE 5.5 and 6.

Literally months of full-time effort have been expended to make PE work well in IE (see implementation). Despite this, some of the remaining problems PE has in IE are probably due to the fact that PE was first implemented in Netscape (1998-2001), and later adapted to work in IE. Perhaps changes in design of some of the javascript that is the core of PE could solve some of these problems, but other priorities seem higher. Other problems PE has in IE reside within Chime and so are inaccessible to me.