Generates the PyMOL session for the scaffold, model, and design structures.
            Returns this session and the script which generated it.

def generate_pymol_session(self, bonsai_pdb_content, cutting_pdb_content, bonsai_label = 'Bonsai', cutting_label = 'Cutting', pymol_executable = 'pymol', settings = {}):
        ''' Generates the PyMOL session for the scaffold, model, and design structures.
            Returns this session and the script which generated it.'''
        if not pymol_load_failed:
            b = BatchBuilder(pymol_executable = pymol_executable)

            loop_residues = set()
            for l in cutting_pdb_content.split('\n'):
                if l.startswith('ATOM  ') and l[12:16] == ' C  ':
                    loop_residues.add(l[21:27])
            loop_residues = sorted(loop_residues)

            structures_list = [
                (bonsai_label, bonsai_pdb_content, set()),
                (cutting_label, cutting_pdb_content, loop_residues),
            ]
            settings['Main'] = bonsai_label
            settings['Loop'] = cutting_label
            PSE_files = b.run(LoopRemovalBuilder, [PDBContainer.from_content_triple(structures_list)], settings = settings)
            return PSE_files[0], b.PSE_scripts[0]