>  java net ConnectException Connection timed out

This is different. Maybe the server is down today. Try accessing it in your 
browser
http://cactus.nci.nih.gov/chemical/structure


> assuming they do connect to different sources of SMILES translations.

On the other hand yes, there was a change in the default server used by Jmol 
for retrieving 
smiles. You can configure that via a Jmol variable.
http://wiki.jmol.org/index.php/File_formats/Chemical_Structure


> Other instances of jmol applets work fine.

I understand you mean those that do not access smiles servers



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