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Opened 3 months ago
Closed 3 months ago
#18361 closed defect (fixed)
'ItemTable' object has no attribute 'AdjustToContents'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508010600 (2025-08-01 06:00:49 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11.dev202508010600 (2025-08-01)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zhangziyin/Desktop/SerSwt0Clip.cxs
Log from Tue Aug 5 12:08:29 2025UCSF ChimeraX version: 1.11.dev202508010600
(2025-08-01)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zhangziyin/Documents/博士工作记录/10. SerS paper/Manuscripts/3.
> 文章修改/Science advances返修/Revision figures/结构示意图/SerSwt.cxs" format session
Log from Mon Aug 4 17:53:51 2025UCSF ChimeraX version: 1.11.dev202508010600
(2025-08-01)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zhangziyin/Desktop/SerSwt.cxs
Log from Mon Aug 4 17:50:08 2025UCSF ChimeraX version: 1.11.dev202508010600
(2025-08-01)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zhangziyin/Downloads/fold_serswt (1)/fold_serswt_model_0.cif"
Chain information for fold_serswt_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/zhangziyin/Downloads/fold_serst (1)/fold_serst_model_0.cif"
Chain information for fold_serst_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> hide #1 models
> set bgColor white
[Repeated 1 time(s)]
> set bgColor black
> color #2 #7a81ffff
> show #1 models
> set bgColor white
[Repeated 1 time(s)]
> color #1 #ff2600ff
> color #1 #ff7e79ff
> set bgColor black
> view orient
> view
[Repeated 1 time(s)]
> select add #2
3401 atoms, 3459 bonds, 430 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #1 models
> log metadata #2
The model has no metadata
> log chains #2
Chain information for fold_serst_model_0.cif #2
---
Chain | Description
A | .
> volume region all imageMode "full region"
No volumes specified
> volume showOutlineBox true
No volumes specified
> view orient
> volume step 1
No volumes specified
> volume step 2
No volumes specified
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select /A:208/A:335/A:212
52 atoms, 48 bonds, 6 residues, 2 models selected
> color (#2 & sel) red
> color (#2 & sel) yellow
> label (#2 & sel) attribute name
> set bgColor white
> show sel & #!2 atoms
> coulombic sel & #!2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_serst_model_0.cif_A SES surface #2.2: minimum,
-21.25, mean -3.08, maximum 9.17
To also show corresponding color key, enter the above coulombic command and
add key true
> view orient
> show #1 models
> select add #1
3425 atoms, 3481 bonds, 433 residues, 3 models selected
> select add #2
6798 atoms, 6914 bonds, 860 residues, 4 models selected
> select subtract #2
3397 atoms, 3455 bonds, 430 residues, 2 models selected
> select add #2
6798 atoms, 6914 bonds, 860 residues, 3 models selected
> select subtract #1
3401 atoms, 3459 bonds, 430 residues, 3 models selected
> select add #1
6798 atoms, 6914 bonds, 860 residues, 4 models selected
> select subtract #1
3401 atoms, 3459 bonds, 430 residues, 3 models selected
> select add #1
6798 atoms, 6914 bonds, 860 residues, 4 models selected
> select clear
> select add #1
3397 atoms, 3455 bonds, 430 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right "move picked models"
> ui mousemode right zoom
> hide #1 models
> ui tool show Angles/Torsions
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/__init__.py", line 56, in start_tool
return get_tool(session, tool_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 18, in get_tool
_tool = StructMeasureTool(session)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 55, in __init__
self._add_tab(tab_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 86, in _add_tab
self._fill_axis_tab(tab_area)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 376, in _fill_axis_tab
self.apc_table = ItemTable(session=self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 323, in __init__
self.setSizeAdjustPolicy(self.AdjustToContents)
^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ItemTable' object has no attribute 'AdjustToContents'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3230, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool
Angles/Torsions in bundle ChimeraX-StructMeasure:
'ItemTable' object has no attribute 'AdjustToContents'
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool
Angles/Torsions in bundle ChimeraX-StructMeasure:
'ItemTable' object has no attribute 'AdjustToContents'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed show
> show #1 models
> hide #!2 models
> select /A:208/A:335/A:212
52 atoms, 48 bonds, 6 residues, 2 models selected
> color (#1 & sel) yellow
> show sel & #1 cartoons
> show sel & #1 atoms
> coulombic sel & #1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select /A:208/A:335/A:212
52 atoms, 48 bonds, 6 residues, 2 models selected
> label (#!1 & sel) attribute name
> select clear
> ui mousemode right select
> select #1/A:206
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:207
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
> select #1/A:207
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:208/A:335/A:212/A:207
66 atoms, 62 bonds, 8 residues, 2 models selected
> coulombic sel & #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1/A:206
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:208/A:335/A:212/A:207/206
66 atoms, 62 bonds, 8 residues, 2 models selected
> select /A:208/A:335/A:212/A:207/A:206
74 atoms, 70 bonds, 10 residues, 2 models selected
> color (#!1 & sel) yellow
> undo
> select /A:208/A:335/A:212/A:207/A:206
74 atoms, 70 bonds, 10 residues, 2 models selected
> coulombic sel & #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> select /A:208/A:335/A:212/A:207
66 atoms, 62 bonds, 8 residues, 2 models selected
> coulombic sel & #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select /A:208/A:335/A:212/A:207
66 atoms, 62 bonds, 8 residues, 2 models selected
> label (#!1 & sel) attribute name
> select clear
> save /Users/zhangziyin/Desktop/SerSwt-ZOOM.cxs
> save /Users/zhangziyin/Desktop/SerSwt.cxs
——— End of log from Mon Aug 4 17:50:08 2025 ———
> view name session-start
opened ChimeraX session
> color #1 #7a81ffff
> show #!2 models
> color #2 #ff7e79ff
> hide #!2 models
> select /A:208/A:335/A:212/A:207
66 atoms, 62 bonds, 8 residues, 2 models selected
> hide sel & #!1 surfaces
> color (#!1 & sel) yellow
> coulombic sel & #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> save /Users/zhangziyin/Desktop/SerSwt.cxs
> select clear
> save /Users/zhangziyin/Desktop/SerSwt-ZOOM.cxs
> save /Users/zhangziyin/Desktop/SerSwt.cxs
——— End of log from Mon Aug 4 17:53:51 2025 ———
> view name session-start
opened ChimeraX session
> hide #!1 atoms
> hide #!1 surfaces
> coulombic #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 surfaces
> show #!1 surfaces
[Repeated 1 time(s)]
> hide #!1 surfaces
> clip
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1662, in color_by_editor
cd.setOption(cd.NoButtons, True)
^^^^^^^^^^^^
AttributeError: 'PySide6.QtWidgets.QColorDialog' object has no attribute
'NoButtons'
AttributeError: 'PySide6.QtWidgets.QColorDialog' object has no attribute
'NoButtons'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1662, in color_by_editor
cd.setOption(cd.NoButtons, True)
^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Color Actions"
> coulombic #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> color bynucleotide target s
> color bychain target s
> color bypolymer target s
> undo
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color bychain target s
> undo
> hide #!1.1 models
> show #1.1 models
> hide #!1.1 models
> show #1.1 models
> ui tool show "Color Actions"
> color byhetero target s
[Repeated 1 time(s)]
> color byelement target s
[Repeated 1 time(s)]
> color bynucleotide target s
> color bypolymer target s
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py:1674: RuntimeWarning: Failed to disconnect (None)
from signal "currentColorChanged(QColor)".
cd.currentColorChanged.disconnect()
> undo
[Repeated 6 time(s)]
> show #1.1 models
> color #1 byelement
> undo
> ui tool show "Color Actions"
> color byhetero target s
[Repeated 1 time(s)]
> color byelement target s
[Repeated 1 time(s)]
> color bynucleotide target s
> color bychain target s
[Repeated 1 time(s)]
> color bypolymer target s
[Repeated 1 time(s)]
> color bychain target s
> color bypolymer target s
> coulombic #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 surfaces
[Repeated 1 time(s)]
> show #!1 surfaces
> hide #!1 surfaces
> coulombic #!1
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.2 models
> show #1.2 models
> hide #!1 surfaces
[Repeated 1 time(s)]
> show #!1 surfaces
> hide #1.2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #1.1
3397 atoms, 430 residues, 2 models selected
> select subtract #1.1
1 model selected
> select add #1.1
3397 atoms, 430 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bynucleotide target s
> color sel byelement target s
> color sel bynucleotide target s
> coulombic sel
Coulombic values for fold_serswt_model_0.cif_A SES surface #1.1: minimum,
-18.30, mean -2.88, maximum 10.35
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #1.1
1 model selected
> show #1.2 models
> hide #!1 surfaces
[Repeated 1 time(s)]
> show #!1 surfaces
> hide #1.2 models
> save /Users/zhangziyin/Desktop/SerSwt0Clip.cxs
——— End of log from Tue Aug 5 12:08:29 2025 ———
> view name session-start
opened ChimeraX session
> ui mousemode right clip
> hide #!1 surfaces
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> select #1/A:208-209
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:208-209
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:208
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:208
4 atoms, 3 bonds, 1 residue, 1 model selected
> show (#!1 & sel) target ab
[Repeated 1 time(s)]Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1068, in show_select_zone_dialog
self._select_zone_dialog = SelZoneDialog(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 3048, in __init__
self._update_button_states()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 3070, in _update_button_states
self.bbox.button(self.bbox.Ok).setEnabled(
^^^^^^^^^^^^
AttributeError: 'PySide6.QtWidgets.QDialogButtonBox' object has no attribute
'Ok'
AttributeError: 'PySide6.QtWidgets.QDialogButtonBox' object has no attribute
'Ok'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 3070, in _update_button_states
self.bbox.button(self.bbox.Ok).setEnabled(
^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Rotamers
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/__init__.py", line 54, in start_tool
return prep_rotamers_dialog(session, tool_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 22, in prep_rotamers_dialog
_prd = PrepRotamersDialog(session, rotamers_tool_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 73, in __init__
= self._make_citation_widget()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 147, in _make_citation_widget
return Citation(self.session, self.rot_lib.citation, prefix="Publications
using %s rotamers should"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/citation.py", line 34, in __init__
self.setFrameStyle(self.Panel | self.Raised)
^^^^^^^^^^
AttributeError: 'Citation' object has no attribute 'Panel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3230, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Rotamers in
bundle ChimeraX-SwapRes:
'Citation' object has no attribute 'Panel'
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Rotamers in
bundle ChimeraX-SwapRes:
'Citation' object has no attribute 'Panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show Rotamers
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 100, in <lambda>
self._menu_choose_cb(action, button, cb))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 156, in _menu_choose_cb
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 213, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'showing'
KeyError: 'showing'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Rotamers
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 100, in <lambda>
self._menu_choose_cb(action, button, cb))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 156, in _menu_choose_cb
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 213, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'showing'
KeyError: 'showing'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 100, in <lambda>
self._menu_choose_cb(action, button, cb))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 156, in _menu_choose_cb
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 213, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'showing'
KeyError: 'showing'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> drag
Unknown command: drag
> drag
Unknown command: drag
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 100, in <lambda>
self._menu_choose_cb(action, button, cb))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 156, in _menu_choose_cb
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 213, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'showing'
KeyError: 'showing'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 100, in <lambda>
self._menu_choose_cb(action, button, cb))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 156, in _menu_choose_cb
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 213, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'showing'
KeyError: 'showing'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 100, in <lambda>
self._menu_choose_cb(action, button, cb))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rotamers/manager.py", line 156, in _menu_choose_cb
callback()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 213, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'showing'
KeyError: 'showing'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/swap_res/tool.py", line 128, in _lib_change_cb
prev_cite = self.citation_widgets['showing']
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PySide6 6.9.1, Qt 6.9.1
Qt runtime version: 6.9.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z12Z00035CH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 4天21小时23分钟
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.4
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.10
ChimeraX-AtomicLibrary: 14.1.21
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508010600
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.15
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.4
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.47
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.10.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.2
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 5.0.0
lxml: 5.3.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.2
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PySide6: 6.9.1
PySide6_Addons: 6.9.1
PySide6_Essentials: 6.9.1
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shiboken6: 6.9.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.5
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → UI |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'ItemTable' object has no attribute 'AdjustToContents' |
comment:2 by , 3 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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These errors appear to be fixed by the same promote_enums fix from #18360