I am trying to modify the apply function of a protocol and then use that protocol in RosettaScripts. I was able to modify the function and successfully compile the new protocol, but when I call the protocol in RosettaScripts, it seems to use the version of the protocol from before I modified it. I can successfully call the modified function from a freestanding pilot app, but the compiler does not seem to be properly incorporating the new version into the RosettaScripts framework. Currently, I have just tried compiling using the “scons” and “scons bin” commands. Is there something else I can do to make sure all updated protocols are included in RosettaScripts?