This is an example of the trajectory viewer with PDBID 1F39. Running inside the IPython notebook as a widget, many other options can be controled such as the color scheme, full screen, different representations, and more. This video shows an example of it running inside the notebook.
To use the trajectory widget in the notebook, start your IPython session with
from mdtraj.html import TrajectoryView, enable_notebook enable_notebook()
And then at the end of a cell, to render the viewer in the output space, use a