IPyMOL allows you to control PyMOL sessions via IPython.
Before You Begin
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 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.start() # Start PyMOL RPC server
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.
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