Hi! My favorite way to do this is via pip. 1. First grab the pip installer from https://bootstrap.pypa.io/get-pip.py wget https://bootstrap.pypa.io/get-pip.py 2. Install pip in Chimera chimera --nogui --script get-pip.py 3. Call the newly installed pip to install your package, ie. scipy chimera --nogui --script `chimera --root`"/bin/pip install scipy" That's it!