Assuming your Anaconda Python is at the front of your path (type 'which ipython' to verify that it is using the Anaconda version). Here, Anaconda is installed in ~/anaconda
System Commands are preceded with ">"
Python Commands are preceded with ">>"
If you download the Pyrosetta Binaries, unzip them, source the SetPyrosettaEnvironment.sh and run ipython while using Ananconda's version of Ipython, you may see the following error: