ocramz/ipymol

Control PyMOL sessions via IPython

IPyMOL

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.

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

Installation

pip install ipymol

Example Usage

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.do('fetch 3odu; as cartoon; bg white')
pymol.show()

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. Any additional commands can be invoked via pymol.do("[ENTER YOUR COMMAND HERE]").

Here's an additional example.

Enjoy!