def protein_only_and_noH(self, keep_ligands=None, force_rerun=False):
        """Isolate the receptor by stripping everything except protein and specified ligands.

        Args:
            keep_ligands (str, list): Ligand(s) to keep in PDB file
            force_rerun (bool): If method should be rerun even if output file exists

        """
        log.debug('{}: running protein receptor isolation...'.format(self.id))

        if not self.dockprep_path:
            return ValueError('Please run dockprep')

        receptor_mol2 = op.join(self.dock_dir, '{}_receptor.mol2'.format(self.id))
        receptor_noh = op.join(self.dock_dir, '{}_receptor_noH.pdb'.format(self.id))

        prly_com = op.join(self.dock_dir, "prly.com")

        if ssbio.utils.force_rerun(flag=force_rerun, outfile=receptor_noh):
            with open(prly_com, "w") as f:
                f.write('open {}\n'.format(self.dockprep_path))

                keep_str = 'delete ~protein'
                if keep_ligands:
                    keep_ligands = ssbio.utils.force_list(keep_ligands)
                    for res in keep_ligands:
                        keep_str += ' & ~:{} '.format(res)
                keep_str = keep_str.strip() + '\n'
                f.write(keep_str)

                f.write('write format mol2 0 {}\n'.format(receptor_mol2))
                f.write('delete element.H\n')
                f.write('write format pdb 0 {}\n'.format(receptor_noh))

            cmd = 'chimera --nogui {}'.format(prly_com)
            os.system(cmd)
            os.remove(prly_com)

        if ssbio.utils.is_non_zero_file(receptor_mol2) and ssbio.utils.is_non_zero_file(receptor_noh):
            self.receptormol2_path = receptor_mol2
            self.receptorpdb_path = receptor_noh
            log.debug('{}: successful receptor isolation (mol2)'.format(self.receptormol2_path))
            log.debug('{}: successful receptor isolation (pdb)'.format(self.receptorpdb_path))
        else:
            log.critical('{}: protein_only_and_noH failed to run on dockprep file'.format(self.dockprep_path))
Isolate the receptor by stripping everything except protein and specified ligands.

        Args:
            keep_ligands (str, list): Ligand(s) to keep in PDB file
            force_rerun (bool): If method should be rerun even if output file exists