[phenixbb] Question regarding phenix.elbow

Nigel W Moriarty NWMoriarty at lbl.gov
Wed Dec 3 11:32:05 PST 2008


I have fixed this error and its will be in the next release.  Did you 
try ReadySet! as Pavel suggested?  I can provide a restraints so you can 
continue your refinement if you desire.



On 12/1/08 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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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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