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
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 questions. Cheers, Pavel. 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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
YoungJin 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. Thanks Nigel 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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- 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 : [email protected] Web : CCI.LBL.gov
Thanks Nigel.
Pavel's suggestions worked. thanks again for your mail.
Best,
YoungJin
----- Original Message -----
From: "Nigel W Moriarty"
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- 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 : [email protected] Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Nigel W Moriarty -
Pavel Afonine -
Young-Jin Cho