INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x80_22088/12_2022/6x80_22088.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 6x80_22088.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for P8E
  Running eLBOW on P8E.cif

  group index 6
change? False

ChiralClass
	Atom  O2 (17) xyz:(-0.626, -1.813, -0.260)     
	Atom  C2 ( 8) xyz:( 0.750, -1.814, -0.266)    S ring index: 1
	Atom  O6 (12) xyz:( 1.222, -0.623, -1.004)      ring index: 1
	Atom  C1 ( 9) xyz:( 1.240, -3.050, -0.965)     
	Atom  C3 ( 7) xyz:( 1.250, -1.829,  1.186)      ring index: 1

	not correct chiralisation

MoleculeClass :  C: 9  N: 2  O: 6 (CHEMICAL COMPONENTS format)
	34 atoms
	34 bonds
	61 angles
	96 dihedrals
	1 rings (groups, rings, atoms) 1 6
	6 chirals : S S S S S S 

  Build ligand and use user provided restraints : P8E
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 1108, in <module>
    run(args)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 882, in run
    random_seed=working_params.ready_set.run_options.random_seed,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 266, in run_though_all_the_options
    None),
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2487, in run
    hydrogens=hydrogens,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2027, in elbow_on_pdb_file
    line.name = atom.atom_name_in_input
AttributeError: AtomClass instance has no attribute 'atom_name_in_input'