model_file_name = None Model file name to use as input for obtaining a complete model
action = *model_completion capping The type of hydrogen addition requested. Model completion will complete side-chains and terminii. Capping with add enough hydrogens to create a stable molecule for QM convergence.
keep_alt_loc = True Retain alt loc. This is not a useful option and not tested well.
skip_validation = False Don't perform the validation of the charge after finalisation.
calculate_charge = False Will calculate total charge of molecule.
Q|Refinement