[Molvis-list] Local PDB files don't display in Chime/Firefox

Eric Martz emartz at microbio.umass.edu
Sun Jul 23 20:44:31 EDT 2006

I have a vexing, persistent Chime/Firefox configuration problem that I hope 
someone can help me fix.


On one of my computers (but none of the others), local .pdb files fail to 
display in Chime in Firefox. This problem prevents 
local/developing/downloaded MolSlides from showing molecules. (Chime is 
invoked but remains blank and the MDL frank disappears). When you drag a 
.pdb file and drop it onto Firefox, Firefox shows an "Open or Save?" 
dialog, with Internet Explorer as the default "Open" application. If you 
try to tell that dialog to "Open in Firefox", you just get an endless 
sequence of such "Open or Save" dialogs. This problem does not prevent 
Chime from showing pdb files from on-line sources -- only pdb files on the 
local disk can't be displayed. Local pdb files dragged and dropped into 
Internet Explorer display in Chime just fine -- but IE doesn't work for 
MolSlide development.



I don't know why the problem arose on this one computer, but on none of my 
others. I have seen the same problem on a computer in the lab of a 
colleague, and again, the problem occurred only one of several computers 
there. The problem seems to be quite unusual, as I have only seen it twice 
among perhaps fifty computers in diverse labs in the USA and Japan.


The Windows "File Types" list specifies that PDB files are to be opened in 
Internet Explorer, both on computers without the problem and the one with 
the problem. The PDB setting under "File Types" appears to be identical on 
all computers. I have deleted this PDB entry and re-created it by 
installing Chime into IE, to no avail. I have also tried specifying here 
that Firefox should open PDB files, to no avail.


I had installed many different browsers on this computer. I uninstalled all 
of them (except IE which can't be uninstalled) to no avail.

Besides browsers, and burning CD's and DVD's, I have used this particular 
Windows XP SP2 installation very little.


I have uninstalled and reinstalled both Firefox (current version 
and Chime, in both orders, to no avail. Chime (file npchime.dll) remains 
behind in "Program Files\Mozilla Firefox\plugins", surviving uninstallation 
and reinstallation of Firefox. So I tried deleting the otherwise largely 
empty "Mozilla Firefox" directory tree after uninstalling, before 
reinstalling -- also to no avail.

When I speak of installing Chime, I mean both in Internet Explorer (where 
installation is automatic), and in Firefox, where I install Chime manually 
by copying the single file npchime.dll from the IE plugins directory to the 
Firefox plugins directory.


I have two Windows XP SP2 installations, one with the problem and one 
without. I compared the entire "Program Files\Mozilla Firefox" file trees 
looking for some configuration difference (notably in one of the 
configuration files such as all.js or firefox.js) but did not find 
anything. There were only a handful of differences and none seemed to be 
related to PDB files. This leads me to suspect that the problem is in the 
Windows Registry, because I don't know of any other configuration files 
that might be involved.


I have searched the Windows Registry for "pdb", "firefox", and "chemical" 
(as in "chemical/x-pdb") and deleted anything that looked suspicious. The 
problem computer still boots without complaint but the problem persists.

Next, I compared the entire exported registries from the problem computer, 
vs. another without the problem (both Windows XP SP2). There are two many 
differences to look at them all, but I looked at all the differences 
related to "pdb". I found four differences. I changed the registry in the 
problem computer to agree with the working computer regarding these four 
differences. Then, even after rebooting, and verifying that the changes 
"stuck", the problem remained.

Please let me know if you have any suggestions, or if you have seen this 
problem (with or without being able to fix it).

Sincerely, -Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
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