Support/Jupyter
Running JSmol in Jupyter notebooks
The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text.
JSmol may be implemented in a Jupyter Notebook through Jupyter Notebook Extensions, which blend javascript with the notebook environment. One extension is jupyter-jsmol by Adam Fekete. Jupyter-jsmol provides a python wrapper to the JSmol widget.
Installation
Jupyter-jsmol can be installed with pip in your notebook virtual environment. (Note the use of the underscore in the pip package)
pip install jupyter_jsmol
Old versions of Jupyter Notebooks require you to enable the extension:
jupyter nbextension enable --py [--sys-prefix|--user|--system] jupyter_jsmol
If you use JupyterLab you'll have to install the extension:
jupyter labextension install @jupyter-widgets/jupyterlab-manager
Examples
There are several examples on the jupyter-jsmol github
Wayne Decatur has setup a Binder container to demonstrate usage
ChemCompute has jupyter-jsmol preinstalled in its Jupyter notebooks. ChemCompute is a free website for students to run Computational Chemistry jobs. Through ChemCompute's Jupyter Notebook you can run a calculation with Psi4 and view the output in JSmol.
- Go to ChemCompute and login or register at the top right. You can likely login with your institutional login.
- Access an example Jupyter Notebook
