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IPyMOL

IPyMOL allows you to control PyMOL <https://www.pymol.org>_ sessions via IPython. This tool is ideal for situations where you'd like to present your work neatly in a Jupyter Notebook <https://jupyter.org/>_ or conveniently prototype PyMOL scripts.

Before You Begin

Please ensure that PyMOL is in your $PATH as pymol or you can start PyMOL in server mode:

.. code:: shell

$ pymol -R #-cKRQ to run it without a GUI

Installation

.. code:: shell

pip install ipymol

Example Usage

You can fire up an IPython or IPython Notebook session and start using IPyMOL. For example:

.. code:: python

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 <https://nbviewer.org/github/cxhernandez/iPyMol/blob/master/examples/Example1.ipynb>_ with more information.

Enjoy!