Opened 19 months ago

Closed 19 months ago

#14879 closed defect (fixed)

Better handling of conflicting defattr registration

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.6.3-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-GFP_Heat_Map/ChimeraX_Sessions/attr_test1.cxs" format
> session

Log from Wed Apr 3 00:16:48 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/1_Cytoplasm_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/1_Cytoplasm_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
20771 messages similar to the above omitted  
  
Chain information for 1_Cytoplasm_rebuilt.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
G H K L O P | No description available  
J N R | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/2_Inner_ring_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/2_Inner_ring_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
233583 messages similar to the above omitted  
  
Chain information for 2_Inner_ring_rebuilt.pdb #2  
---  
Chain | Description  
A E I M Q U | No description available  
B F J N R V | No description available  
C G K O S W | No description available  
D H L P T X | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/3_Membrane_ring_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/3_Membrane_ring_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
42629 messages similar to the above omitted  
  
Chain information for 3_Membrane_ring_rebuilt.pdb #3  
---  
Chain | Description  
A F K P U Z | No description available  
B G L Q V a | No description available  
E J O T Y d | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/4_Mlps.pdb"

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/5_Nic96complex_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/5_Nic96complex_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
107139 messages similar to the above omitted  
  
Chain information for 5_Nic96complex_rebuilt.pdb #5  
---  
Chain | Description  
A E I M Q U Y c g k o s | No description available  
B F J N R V Z d h l p t | No description available  
C G K O S W a e i m q u | No description available  
D H L P T X b f j n r v | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/6_Nucleoplasm_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/6_Nucleoplasm_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
6029 messages similar to the above omitted  
  
Chain information for 6_Nucleoplasm_rebuilt.pdb #6  
---  
Chain | Description  
A B F G K L | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/7_Nup82complex_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/7_Nup82complex_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
46557 messages similar to the above omitted  
  
Chain information for 7_Nup82complex_rebuilt.pdb #7  
---  
Chain | Description  
A B I J Q R | No description available  
C D K L S T | No description available  
E F M N U V | No description available  
G H O P W X | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/8_Nup84complex_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/8_Nup84complex_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
201437 messages similar to the above omitted  
  
Chain information for 8_Nup84complex_rebuilt.pdb #8  
---  
Chain | Description  
A H O V c j | No description available  
B I P W d k | No description available  
C J Q X e l | No description available  
D K R Y f m | No description available  
E L S Z g n | No description available  
F M T a h o | No description available  
G N U b i p | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr  
---  
note | Assigned attribute 'testValues' to 9 molecules using match mode: 1-to-1  
  

> ui tool show "Render by Attribute"

> color byattribute m:testValues #4,6#!1-3,5,7-8 target abcs palette
> 2,#0fc7cf:5,white:8,#9e205e

699897 atoms, 86703 residues, atom testValues range 2 to 8  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr  
---  
note | Assigned attribute 'testValues' to 9 molecules using match mode: 1-to-1  
  

> ui tool show "Render by Attribute"

> color byattribute m:testValues #4,6#!1-3,5,7-8 target abcs palette
> 1,blue:29,white:57,red

699897 atoms, 86703 residues, atom testValues range 1 to 57  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr  
---  
note | Assigned attribute 'testValues' to 9 molecules using match mode: 1-to-1  
  

> ui tool show "Render by Attribute"

> color byattribute m:testValues #4,6#!1-3,5,7-8 target abcs palette
> 1,blue:29,white:57,red

699897 atoms, 86703 residues, atom testValues range 1 to 57  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Data line 16 in 2018NPC_Template.defattr not of the form: <tab> atomspec <tab>
value  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr  
---  
note | Assigned attribute 'testValues' to 9 molecules using match mode: 1-to-1  
  

> ui tool show "Render by Attribute"

> color byattribute m:testValues #4,6#!1-3,5,7-8 target abcs palette
> 1,blue:1.5,white:2,red

699897 atoms, 86703 residues, atom testValues range 1 to 2  

> color byattribute m:testValues #4,6#!1-3,5,7-8 target abcs palette
> 1,blue:1.5,white:2,red

699897 atoms, 86703 residues, atom testValues range 1 to 2  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr  
---  
note | Assigned attribute 'testValues' to 9 molecules using match mode: 1-to-1  
  

> ui tool show "Render by Attribute"

> color byattribute m:testValues #4,6#!1-3,5,7-8 target abcs palette
> 1,blue:1.5,white:2,red

699897 atoms, 86703 residues, atom testValues range 1 to 2  

> select #1/A

1165 atoms, 1193 bonds, 146 residues, 1 model selected  

> select #1/B

1165 atoms, 1193 bonds, 146 residues, 1 model selected  

> select #1/C

1165 atoms, 1193 bonds, 146 residues, 1 model selected  

> select #1/G

1152 atoms, 1178 bonds, 144 residues, 1 model selected  

> select add #1

24213 atoms, 24708 bonds, 3 pseudobonds, 2982 residues, 2 models selected  

> select subtract #1

Nothing selected  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/__init__.py", line 96, in open  
defattr(session, data, file_name=file_name, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/defattr.py", line 277, in defattr  
recip_class.register_attr(session, attr_name, "defattr command",
attr_type=attr_type,  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 89, in register_attr  
cls._attr_registration.register(session, attr_name, registerer, (attr_type,
can_return_none))  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
  
See log for complete Python traceback.  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/__init__.py", line 96, in open  
defattr(session, data, file_name=file_name, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/defattr.py", line 277, in defattr  
recip_class.register_attr(session, attr_name, "defattr command",
attr_type=attr_type,  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 89, in register_attr  
cls._attr_registration.register(session, attr_name, registerer, (attr_type,
can_return_none))  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
  
See log for complete Python traceback.  
  

> save "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-GFP_Heat_Map/ChimeraX_Sessions/attr_test1.cxs"

——— End of log from Wed Apr 3 00:16:48 2024 ———

opened ChimeraX session  

> color bychain

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/__init__.py", line 96, in open  
defattr(session, data, file_name=file_name, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/defattr.py", line 277, in defattr  
recip_class.register_attr(session, attr_name, "defattr command",
attr_type=attr_type,  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 89, in register_attr  
cls._attr_registration.register(session, attr_name, registerer, (attr_type,
can_return_none))  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
  
See log for complete Python traceback.  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/__init__.py", line 96, in open  
defattr(session, data, file_name=file_name, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/defattr.py", line 277, in defattr  
recip_class.register_attr(session, attr_name, "defattr command",
attr_type=attr_type,  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 89, in register_attr  
cls._attr_registration.register(session, attr_name, registerer, (attr_type,
can_return_none))  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
  
See log for complete Python traceback.  
  

> close session

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/1_Cytoplasm_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/1_Cytoplasm_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
20771 messages similar to the above omitted  
  
Chain information for 1_Cytoplasm_rebuilt.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
G H K L O P | No description available  
J N R | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/2_Inner_ring_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/2_Inner_ring_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
233583 messages similar to the above omitted  
  
Chain information for 2_Inner_ring_rebuilt.pdb #2  
---  
Chain | Description  
A E I M Q U | No description available  
B F J N R V | No description available  
C G K O S W | No description available  
D H L P T X | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/3_Membrane_ring_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/3_Membrane_ring_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
42629 messages similar to the above omitted  
  
Chain information for 3_Membrane_ring_rebuilt.pdb #3  
---  
Chain | Description  
A F K P U Z | No description available  
B G L Q V a | No description available  
E J O T Y d | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/4_Mlps.pdb"

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/5_Nic96complex_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/5_Nic96complex_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
107139 messages similar to the above omitted  
  
Chain information for 5_Nic96complex_rebuilt.pdb #5  
---  
Chain | Description  
A E I M Q U Y c g k o s | No description available  
B F J N R V Z d h l p t | No description available  
C G K O S W a e i m q u | No description available  
D H L P T X b f j n r v | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/6_Nucleoplasm_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/6_Nucleoplasm_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
6029 messages similar to the above omitted  
  
Chain information for 6_Nucleoplasm_rebuilt.pdb #6  
---  
Chain | Description  
A B F G K L | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/7_Nup82complex_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/7_Nup82complex_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
46557 messages similar to the above omitted  
  
Chain information for 7_Nup82complex_rebuilt.pdb #7  
---  
Chain | Description  
A B I J Q R | No description available  
C D K L S T | No description available  
E F M N U V | No description available  
G H O P W X | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/8_Nup84complex_rebuilt.pdb"

Summary of feedback from opening /Users/chris/Library/CloudStorage/OneDrive-
rockefeller.edu/Brickner JH/2024_0318_Crm1-ppx-
GFP_Heat_Map/Data_Files/2018_Kim_et_al_Zenodo/npc2018-master/results/PDB_files/3spokes-C3/rebuilt_all/8_Nup84complex_rebuilt.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
201437 messages similar to the above omitted  
  
Chain information for 8_Nup84complex_rebuilt.pdb #8  
---  
Chain | Description  
A H O V c j | No description available  
B I P W d k | No description available  
C J Q X e l | No description available  
D K R Y f m | No description available  
E L S Z g n | No description available  
F M T a h o | No description available  
G N U b i p | No description available  
  

> open "/Users/chris/Library/CloudStorage/OneDrive-rockefeller.edu/Brickner
> JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/ChimeraX_Attribute_Files/2018NPC_Template.defattr"

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/__init__.py", line 96, in open  
defattr(session, data, file_name=file_name, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/defattr.py", line 277, in defattr  
recip_class.register_attr(session, attr_name, "defattr command",
attr_type=attr_type,  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 89, in register_attr  
cls._attr_registration.register(session, attr_name, registerer, (attr_type,
can_return_none))  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
chimerax.core.attributes.RegistrationConflict: Registration of attr
'testValues' with Structure by defattr command conflicts with previous
registration by defattr command  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 104, in register  
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6.3 (21G419)
      Kernel Version: Darwin 21.6.0
      Time since boot: 11:55

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Better handling of conflicting defattr registration

comment:2 by Eric Pettersen, 19 months ago

Resolution: → fixed
Status: accepted → closed

Re-registration by defattr now only warns instead of raising an error.

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