This tool performs automated filtering based on predefined residue categories (e.g., water, ions, ligands, cofactors). While common functional components are retained according to user selection, we strongly recommend visually inspecting the cleaned structure using PyMOL or other molecular visualization tools. Manual inspection ensures that biologically relevant entities—such as catalytic metal ions, active-site ligands, or bound cofactors—are not inadvertently removed prior to downstream modeling or simulation.