A link has been going around among the Bioclipse developers lately. It links to a page in japanese using the Bioclipse scripting language (BSL). As my japanese is non-existing, I have had to depend on google translate to understand their text. Google translate actually seems to make a good job but the BSL code is even easier to understand. What the script does is taking the output from Metaprint2D and visualise it in 3d using Jmol.
This is just the sort of thing I was envisioning back in the days when we drew up the design for Bioclipse 2 with scripting (as can be found on some old dusty wiki page). The addition of a scripting language truly give the users the power to do things the developers of the program did not think of. What nice things can you do with BSL that we haven't thought of? :)