In particular I spent a lot of time porting the CE and FATCAT algorithms from C to Java and developing a new user interface. Check out the latest version at http://betastaging.rcsb.org/pdb/workbench/workbench.do . (E.g. try to align 4HHB chain A and 4HHB chain B ).
Having the algorithms in Java opens the door for a number of nice applications. It is now possible to launch the structure comparison application with a single mouse click using the Java Web Start technology.