atomium can be installed using pip:

$ pip3 install atomium

atomium is written for Python 3, and does not support Python 2.

If you get permission errors, try using sudo:

$ sudo pip3 install atomium


The repository for atomium, containing the most recent iteration, can be found here. To clone the atomium repository directly from there, use:

$ git clone git://


atomium requires requests for fetching structures from the RCSB, paramiko for fetching structures over SSH, msgpack for parsing .mmtf files, and valerius for dealing with sequences.


To test a local version of atomium, cd to the atomium directory and run:

$ python -m unittest discover tests

You can opt to only run unit tests or integration tests:

$ python -m unittest discover tests.unit $ python -m unittest discover tests.integration

You can run the ‘big test’ to get a random 1000 structures, parse them all, and report any problems:

$ python tests/

Finally, to perform speed profiles you can run:

$ python tests/time/

…which creates various profiles that SnakeViz can visualise.