[phenixbb] Question regarding phenix.elbow

[Young-Jin Cho]

Hi
I would like to know how I can add H atoms to my ligand, ADP in the protein complex.
I was trying to add H atoms to one of my ligand, ADP.
When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h",
it went on but failed with the following error message:
Traceback (most recent call last):
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module>
    run()
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run
    molecule = post_process(molecule, options)
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process
    options,
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager
    pre_opt))
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB
    original_order=original_order,
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String
    self.AdjustHydrogenNames()
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames
    if test_name[3]==" ": test_name[3]="0"
TypeError: 'str' object does not support item assignment

FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names.

By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine.

Thanks in advance for your help.

Best,
YoungJin