This page provides a series of examples, tutorials and recipes for using MSMBuilder.
Each subsection is a notebook. To open these notebooks in a “live” IPython session and execute the documentation interactively, you need to download the repository and start the IPython notebook.
If you installed MSMBuilder from source, you will need to navigate to path-to-msmbuilder/examples. The notebook files for these examples and the notebooks are available in the top level examples folder on github as well. In the directory with the notebook files, start an IPython notebook server:
$ ipython notebook