INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/12_2022/5tv4_8469.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 5tv4_8469.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for PA1
  Running eLBOW on PA1.cif

MoleculeClass :  C: 6  N: 1  O: 5 (CHEMICAL COMPONENTS format)
	25 atoms
	25 bonds
	44 angles
	69 dihedrals
	1 rings (groups, rings, atoms) 1 6
	5 chirals : S R R S R 

  Build ligand and use user provided restraints : PA1

  Build ligand and use monomer library to name atoms : GMH
  Using monomer library entry GMH as template

  Build ligand and use monomer library to name atoms : FTT
  Using monomer library entry FTT as template

  More than 20 percent of the atoms are missing for MYR
  as compared to the Monomer Library

  More than 20 percent of the atoms are missing for MYR
  as compared to the Chemical Components

  More than 20 percent of the atoms are missing for DAO
  as compared to the Monomer Library

  More than 20 percent of the atoms are missing for DAO
  as compared to the Chemical Components

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

MoleculeClass :  C: 8  O: 8 (CHEMICAL COMPONENTS format)
	29 atoms
	29 bonds
	51 angles
	81 dihedrals
	1 rings (groups, rings, atoms) 1 6
	5 chirals : R R R R R 

  Build ligand and use user provided restraints : KDO
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'