Please follow these steps to run the transmembrane protein prediction correctly:

Step 1 - Unzip the complete folder to a directory of your choice.
Step 2 - Open your cmd and navigate to the folder from step 1.
Step 3 - Run the MPF.py file with python version 3.5(lower versions are not supported!) and supply a pdb file as first argument.
Optional: To get an additional plot of the membrane planes and helices, add a "1" or "True" as additional argument.

Example:
python MPF.py 1bm1.pdb

or

python MPF.py 1bm1.pdb 1