Visual Molecular Dynamics (VMD) has already been installed on the lab computers, but you can also install it on a personal computer from here for free.
ProDy is a plugin compatible with VMD.
To install ProDy on a computer with pip installed, use pip install -U ProDy.
Otherwise, instructions are available from
here.
To use ProDy, two Python dependencies are required (biopython and numpy).
If you have an Anaconda python installation, these can be installed with
conda install biopython and conda install numpy.
Otherwise, installing they can be installed the same way with pip.