IPyMOL allows you to control PyMOL sessions via IPython. This tool is ideal for situations where you'd like to present your work neatly in a Jupyter Notebook or conveniently prototype PyMOL scripts.
Please ensure that PyMOL is in your $PATH as pymol or you can start PyMOL in server mode:
$ pymol -R #-cKRQ to run it without a GUIpip install ipymolYou can fire up an IPython or IPython Notebook session and start using IPyMOL. For example:
from ipymol import viewer as pymol
pymol.fetch('3odu') # Fetch PDB
pymol.show_as('cartoon') # Show as cartoon
pymol.bg_color('white') # Set background color to white
pymol.display() # Show current displayThis series of commands will define a variable pymol of class MolViewer, which can pass commands to PyMOL, and then create an image of PDBID:3odu in your IPython session.
Additional commands can be invoked via pymol.do("[ENTER YOUR COMMAND HERE]").
Here's an example notebook with more information.
Enjoy!