This could be taken care of with implementation of a driver program, but it's confusing to require "-pdb" in rinrus_trim2_pdb.py while requiring "-pdbfilename" in pymol_scripts.py for example.
Think the only remaining problems here are
Example 1.9: "-pdbfilename" instead of "-pdb"
example 5b: "-seed" instead of "-s"
Need to also change in the driver then should be done!
This could be taken care of with implementation of a driver program, but it's confusing to require "-pdb" in rinrus_trim2_pdb.py while requiring "-pdbfilename" in pymol_scripts.py for example.