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!