Before You Begin
Please ensure that PyMOL is in your
pymol or you can start PyMOL in server mode:
$ pymol -R #-cKRQ to run it without a GUI
pip install ipymol
You 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 display
This 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.