[phenixbb] Question regarding phenix.elbow

Young-Jin Cho yjcho at brandeis.edu
Mon Dec 1 06:53:56 PST 2008

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>
  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
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB
  File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String
  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.


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