Dear Eric

You need to tell JSmol that the files are binary, and that's only through the 
filename. I know your problem, as I have had the same.
The only solution is to rename the files, I think (to .pdb.gz or .bin.pdb, for 
example). I had one case when I was using the extensions pdbz, molz, which 
I solved without renaming by extending the default list of binary extensions (I 
can provide details on that).

There is also the issue of having properly set the Info variable with its php 
parameter, which should point to the jmol.php file, best in your same server



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