[Molvis-list] Making Chime work fully in Firefox 2

[Eric Martz]

Because Protein Explorer will continue to depend on MDL Chime for an  
indeterminate period of time, and because there are so many excellent  
Chime sites that have not yet been ported to Jmol (listed at http:// 
molvisindex.org, some will likely never be ported), it is important  
to have a web browser that works well with MDL Chime and Protein  
Explorer. The best one is Firefox.

I have recently figured out how to work around a couple of Firefox 2  
bugs that affect MDL Chime (version 2.6 SP6, current since March  
2004). Incidentally, the auto-update in Firefox 1.5 (currently  
1.5.0.11) still doesn't update you to Firefox 2 (currently 2.0.0.3).  
Apparently Firefox 1.5.0.12 is forthcoming and will do so, after  
which 1.5 will no longer be supported. The following bugs and  
workarounds apply to both Firefox 1.5 and 2.

BUG 1. Once it occurs, this bug makes it impossible to develop  
MolSlides using a downloaded copy of Protein Explorer. It affects  
only the DOWNLOADED copy of Protein Explorer (PE), not PE on-line.  
However, using downloaded PE is crucial for serious MolSlide  
development. Although this bug does not affect the main molecular  
display in PE, instead of molecular views, you see blank black  
rectangles in MolSlides Manager, History, and Reset View. Also, once  
created, MolSlides that use Chime won't work from the local disk (tho  
they will work from a server).

This problem is induced in Firefox, after you download a PDB file  
from pdb.org. Chime is then permanently unable to display any PDB  
file from the local disk, when the PDB filename is specified in the  
src="filename.pdb" field of the embed tag. (It can still display PDB  
files loaded via a "load" command.) Firefox's Tools, Options,  
Content, File Types, Manage specifies how chemical/x-pdb MIMEs are to  
be handled, but is currently unable to correct this condition.

THE FIX: Close Firefox, then rename the file mimeTypes.rdf that you  
will find in

C:\Documents and Settings\[login_username]\Application Data\Mozilla 
\Firefox\Profiles\[xxxxxxxx].default

(where [xxxxxxxx] is a random alphanumeric string generated by Firefox).
For example, rename it to mimeTypes.old, which will be ignored by  
Firefox.

Deleting (or renaming) this file seems harmless, and is recommended  
on several websites that discuss this bug. Firefox creates a new  
default file when next started, and plugins such as Quicktime, Adobe  
PDF reader, Flash, and Java continue to work as before.

Here is a link that will induce this problem:
(WARNING: DON'T CLICK in Firefox on Windows unless you want to induce  
the problem!)
http://www.pdb.org/pdb/downloadFile.do? 
fileFormat=pdb&compression=NO&structureId=1D66

BUG 2. This one doesn't seem likely to affect most Chime websites,  
but does affect my PE/Chime troubleshooting pages. In Firefox, if you  
right click a link to a pdb file from a server that sends it with  
MIME chemical/x-pdb, and save it to disk, afterwards left clicking on  
that link fails to show the molecule. This is corrected by clearing  
the Firefox cache. (Tools, Clear Private Data). The problem seems to  
occur only if the PDB file on the server is not gzipped.

A link illustrating this problem:
http://www.umass.edu/microbio/chime/atp.pdb

---------------------------
I am in the process of documenting these workarounds for Protein  
Explorer.

Since Internet Explorer 7 does not work at all with Chime, and  
Internet Explorer 6 does not support all of Protein Explorer's  
functionality, it is particularly important that Firefox work well  
with Chime.

Netscape is now in use by no more than 1% of people coming to our  
websites (about 0.5% version 4 and 0.5% version 7). Netscape 8  
appears to be DOA. Mozilla appears to be retired in favor of Mozilla  
Firefox. Therefore, Firefox is the only widely used browser in the  
Gecko family.

Firefox 3 is now being developed. There is some evidence that the  
above two bugs may be fixed in Firefox 3 (not yet released), but it  
is hard to be sure because other new bugs affecting Chime have not  
yet been fixed.

Sincerely, -Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

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