Installation on MacOS and Linux

Install Anaconda

Download the Python 3.7 Anaconda installer and install Anaconda.

Install Git

The Git version control system is used to download respositories from Github.

To check if you have git installed, type the following line on your terminal:

git --version

Download and install Git

Create a Conda Environment for mmtf-pyspark

A conda environment is a directory that contains a specific collection of conda packages that you have installed. If you change one environment, your other environments are not affected. You can easily activate or deactivate environments, which is how you switch between them.

git clone

cd mmtf-pyspark

conda env create -f binder/environment.yml

Activate the Conda Environment

conda activate mmtf-pyspark

Test the Installation


If the metadata for 1AQ1 are printed, you have successfully installed mmtf-pyspark.

Launch Jupyter Notebook

jupyter notebook

In Jupyter Notebook, open DataAnalysisExample.ipynb and run it.

Notebooks that demonstrate the use of the mmtf-pypark API are available in the demos directory.

Deactivate the Conda Environment

conda deactivate

Actvate the environment again if you want to use mmtf-pyspark.

Remove the Conda Environment

To permanently remove the environment type:

conda remove -n mmtf-pyspark --all

Download Hadoop Sequence Files

The entire PDB can be downloaded as an MMTF Hadoop sequence file and environmental variables can be set by running the following command

curl -o
. ./

The default download location is in the user’s home directory. The specify another directory, use the -o flag:

curl -o