INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/12_2022/8ear_27983.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 8ear_27983.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : I3P
  Using monomer library entry I3P as template

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

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

MoleculeClass :  C:42  N: 1  O: 8  P: 1 (CHEMICAL COMPONENTS format)
	140 atoms
	139 bonds
	270 angles
	381 dihedrals
	0 rings (groups, rings, atoms) 0 0
	3 chirals : S R S 

  Build ligand and use user provided restraints : PLX

  There is a tetra-coordinated nitrogen in your input.  You may need to add
  charge to the nitrogen thus:

ATOM  77320   N1PLX A2809     156.894 196.354 270.065  1.00119.36           N+1

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'