You can now use TrOWL in Protégé 4.2. Simply download the TrOWl plug-in, unzip it, put it into the plugins folder of your Protégé. When you restart Protégé, TrOWL will appear as an option in the Reasoner menu. Use TrOWL plug-in with Protégé 4.1 has not be thoroughly tested but should be possible.
Currently TrOWL plug-in will compute class hierarchy, object property hierarchy, class assertions and object property relations in one go. We are working actively to support more different configurations and to support datatype properties.