Error saving session

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
When I tried to save the Chimera Session, an error was thrown and the file was not saved. I was using Loop Maker to add missing structure to a .pdb and I measured some distances.

save C:/tempCh/testest.cxs
Traceback (most recent call last):   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 322, in process     data = sm.take_snapshot(obj, session, self.state_flags)            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\atomic\molobject.py", line 1461, in take_snapshot     'ses_id': self.structure.session_chain_to_id(self._c_pointer),               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'session_chain_to_id' The above exception was the direct cause of the following exception: Traceback (most recent call last):   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 297, in discovery     self.processed[key] = self.process(obj, parents)                           ^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 329, in process     raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [<chimerax.help_viewer.tool.HelpUI object at 0x0000025C35187ED0>, <chimerax.cmd_line.tool.CommandLine object at 0x0000025C7FE839D0>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x0000025C330DBB10>, <chimerax.toolbar.tool.ToolbarTool object at 0x0000025C2D844550>, <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190>, <chimerax.modeller.tool.ModellerResultsViewer object at 0x0000025C2AE70750>, <chimerax.model_panel.tool.ModelPanel object at 0x0000025C55639590>, <chimerax.log.tool.Log object at 0x0000025C2C101BD0>] -> <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190> -> <chimerax.atomic.molobject.Chain object at 0x0000025C330B4550> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last):   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 1048, in save     session.save(output, version=version, include_maps=include_maps)   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 731, in save     mgr.discovery(self._state_containers)   File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 301, in discovery     raise ValueError( ValueError: error processing: 'tools' -> [<chimerax.help_viewer.tool.HelpUI object at 0x0000025C35187ED0>, <chimerax.cmd_line.tool.CommandLine object at 0x0000025C7FE839D0>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x0000025C330DBB10>, <chimerax.toolbar.tool.ToolbarTool object at 0x0000025C2D844550>, <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190>, <chimerax.modeller.tool.ModellerResultsViewer object at 0x0000025C2AE70750>, <chimerax.model_panel.tool.ModelPanel object at 0x0000025C55639590>, <chimerax.log.tool.Log object at 0x0000025C2C101BD0>] -> <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190> -> <chimerax.atomic.molobject.Chain object at 0x0000025C330B4550> 'chain A': Error while saving session data for 'tools' -> [<chimerax.help_viewer.tool.HelpUI object at 0x0000025C35187ED0>, <chimerax.cmd_line.tool.CommandLine object at 0x0000025C7FE839D0>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x0000025C330DBB10>, <chimerax.toolbar.tool.ToolbarTool object at 0x0000025C2D844550>, <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190>, <chimerax.modeller.tool.ModellerResultsViewer object at 0x0000025C2AE70750>, <chimerax.model_panel.tool.ModelPanel object at 0x0000025C55639590>, <chimerax.log.tool.Log object at 0x0000025C2C101BD0>] -> <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190> -> <chimerax.atomic.molobject.Chain object at 0x0000025C330B4550> 'chain A' ValueError: error processing: 'tools' -> [, , , , , , , ] -> -> 'chain A': Error while saving session data for 'tools' -> [, , , , , , , ] -> -> 'chain A'

File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(

See log for complete Python traceback.

Traceback (most recent call last):
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 322, in process
    data = sm.take_snapshot(obj, session, self.state_flags)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\atomic\molobject.py", line 1461, in take_snapshot
    'ses_id': self.structure.session_chain_to_id(self._c_pointer),
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session_chain_to_id'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 297, in discovery
    self.processed[key] = self.process(obj, parents)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 329, in process
    raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' -> [<chimerax.help_viewer.tool.HelpUI object at 0x0000025C35187ED0>, <chimerax.cmd_line.tool.CommandLine object at 0x0000025C7FE839D0>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x0000025C330DBB10>, <chimerax.toolbar.tool.ToolbarTool object at 0x0000025C2D844550>, <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190>, <chimerax.modeller.tool.ModellerResultsViewer object at 0x0000025C2AE70750>, <chimerax.model_panel.tool.ModelPanel object at 0x0000025C55639590>, <chimerax.log.tool.Log object at 0x0000025C2C101BD0>] -> <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190> -> <chimerax.atomic.molobject.Chain object at 0x0000025C330B4550> 'chain A'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\save_command\dialog.py", line 133, in <lambda>
    lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file",
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
    _dlg.display(session, **kw)
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\save_command\dialog.py", line 68, in display
    run(session, cmd)
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\save_command\cmd.py", line 86, in cmd_save
    Command(session, registry=registry).run(provider_cmd_text, log=log)
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\save_command\cmd.py", line 101, in provider_save
    saver_info.save(session, path, **provider_kw)
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core_formats\__init__.py", line 95, in save
    return cxs_save(session, path, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 1048, in save
    session.save(output, version=version, include_maps=include_maps)
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 731, in save
    mgr.discovery(self._state_containers)
  File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 301, in discovery
    raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.help_viewer.tool.HelpUI object at 0x0000025C35187ED0>, <chimerax.cmd_line.tool.CommandLine object at 0x0000025C7FE839D0>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x0000025C330DBB10>, <chimerax.toolbar.tool.ToolbarTool object at 0x0000025C2D844550>, <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190>, <chimerax.modeller.tool.ModellerResultsViewer object at 0x0000025C2AE70750>, <chimerax.model_panel.tool.ModelPanel object at 0x0000025C55639590>, <chimerax.log.tool.Log object at 0x0000025C2C101BD0>] -> <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190> -> <chimerax.atomic.molobject.Chain object at 0x0000025C330B4550> 'chain A': Error while saving session data for 'tools' -> [<chimerax.help_viewer.tool.HelpUI object at 0x0000025C35187ED0>, <chimerax.cmd_line.tool.CommandLine object at 0x0000025C7FE839D0>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x0000025C330DBB10>, <chimerax.toolbar.tool.ToolbarTool object at 0x0000025C2D844550>, <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190>, <chimerax.modeller.tool.ModellerResultsViewer object at 0x0000025C2AE70750>, <chimerax.model_panel.tool.ModelPanel object at 0x0000025C55639590>, <chimerax.log.tool.Log object at 0x0000025C2C101BD0>] -> <chimerax.seq_view.tool.SequenceViewer object at 0x0000025C2BF2B190> -> <chimerax.atomic.molobject.Chain object at 0x0000025C330B4550> 'chain A'

ValueError: error processing: 'tools' -> [, , , , , , , ] -> -> 'chain A': Error while saving session data for 'tools' -> [, , , , , , , ] -> -> 'chain A'

File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(

See log for complete Python traceback.

OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.22.14 27.20.11022.14001
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.9
Locale: sl_SI.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HUAWEI
Model: KLVL-WXX9
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 16,505,966,592
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics         
OSLanguage: en-GB

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
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    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
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    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BasicActions: 1.1.3
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    ChimeraX-BugReporter: 1.0.2
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    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
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    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
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    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0

[Eric Pettersen]

Maybe Greg can decrypt the stack trace and determine what actually failed.