A version of TrOWL tailored to Protege 4.1 beta has been released. You can download it from here. To install it, just copy it into the plugins folder in your Protege 4.1 installation. If you are using Protege on an Apple, you should right click on the application icon and select “Show contents”, you should be able to find the plugins folder in here.
A full release of TrOWL (version 0.6.0) supporting OWLAPI 3.1 will be released soon.