[phenixbb] Question regarding phenix.elbow

Pavel Afonine pafonine at lbl.gov
Tue Dec 2 00:07:46 PST 2008

Hi Young-Jin,

the command below should really work and the crash indicates a bug. 
Could you please send a PDB file so we can reproduce and fix this 
problem (please send it to my email address and not to the whole bb).

Meanwhile, you can use phenix.ready_set to add H atoms to your 
structure: both macromolecule and ligand. Example:

phenix.ready_set model.pdb

Please let us know if you still have problem with this or have other 


On 12/1/2008 6:53 AM, Young-Jin Cho wrote:
> 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
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