Opened 3 months ago

Last modified 2 months ago

#18739 assigned defect

Open QChem output file: unsupported operand type(s) for +=: 'NoneType' and 'list'

Reported by: chimerax-bug-report@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
tired to open a qchem 6.2 output file but failed

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/jinqian_1/Desktop/Calculation Related
> files/Qchem/Grignard+Benzaldehyde/idea/idea_pdt_tddft.out"

Summary of feedback from opening /Users/jinqian_1/Desktop/Calculation Related
files/Qchem/Grignard+Benzaldehyde/idea/idea_pdt_tddft.out  
---  
error | unable to open idea_pdt_tddft.out as a Q-Chem output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_qchem_out   
error while parsing Q-Chem output  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
the following data has been read: charge, multiplicity, E(Nucleus-field),  
energy, E(SCF), E(Total), uv_vis, Mulliken Charges, finished  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 768, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2154, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.10.1.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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/__init__.py", line 639,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/io.py", line 46, in
open_aarontools  
raise e  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/io.py", line 33, in
open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
1652, in __init__  
self.read_qchem_out(f, get_all, just_geom, log=None)  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3518, in read_qchem_out  
raise e  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3286, in read_qchem_out  
return self.read_qchem_out(  
^^^^^^^^^^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3524, in read_qchem_out  
self.all_geom += [{  
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'list'  
  
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'list'  
  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3524, in read_qchem_out  
self.all_geom += [{  
  
See log for complete Python traceback.  
  

> open "/Users/jinqian_1/Desktop/Calculation Related
> files/Qchem/Grignard+Benzaldehyde/idea/idea_pdt_tddft.out"

Summary of feedback from opening /Users/jinqian_1/Desktop/Calculation Related
files/Qchem/Grignard+Benzaldehyde/idea/idea_pdt_tddft.out  
---  
error | unable to open idea_pdt_tddft.out as a Q-Chem output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_qchem_out   
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
the following data has been read: charge, multiplicity, E(Nucleus-field),  
energy, E(SCF), E(Total), uv_vis, Mulliken Charges, finished  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
the following data has been read: charge, multiplicity, E(Nucleus-field),  
energy, E(SCF), E(Total), uv_vis, Mulliken Charges, finished  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
the following data has been read: charge, multiplicity, E(Nucleus-field),  
energy, E(SCF), E(Total), uv_vis, Mulliken Charges, finished  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
error while parsing Q-Chem output  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
last line read: A Quantum Leap Into The Future Of Chemistry  
  
WARNING AaronTools.fileIO.FileReader.read_qchem_out  
the following data has been read: charge, multiplicity, E(Nucleus-field),  
energy, E(SCF), E(Total), uv_vis, Mulliken Charges, finished  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.10.1.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
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/__init__.py", line 639,
in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/io.py", line 46, in
open_aarontools  
raise e  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/SEQCROW/io.py", line 33, in
open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
1652, in __init__  
self.read_qchem_out(f, get_all, just_geom, log=None)  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3518, in read_qchem_out  
raise e  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3286, in read_qchem_out  
return self.read_qchem_out(  
^^^^^^^^^^^^^^^^^^^^  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3524, in read_qchem_out  
self.all_geom += [{  
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'list'  
  
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'list'  
  
File "/Users/jinqian_1/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/AaronTools/fileIO.py", line
3524, in read_qchem_out  
self.all_geom += [{  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,15
      Model Number: MQTM3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 94 days, 14 hours, 31 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    AaronTools: 1.1
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    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: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.0
    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
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    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: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    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
    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: 1.14.1
    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: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 1.5.1
    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: 2.17.1
    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: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    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: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    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: 2.3.2
    numpy: 1.26.4
    numpy: 2.2.2
    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: 25.0.1
    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
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    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: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.16.1
    scipy: 1.13.1
    scipy: 1.14.1
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.9.2
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
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    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
File attachment: idea_rct+THF_opt2.out

idea_rct+THF_opt2.out​

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Change History (3)

by chimerax-bug-report@…, 3 months ago

Attachment: idea_rct+THF_opt2.out​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Open QChem output file: unsupported operand type(s) for +=: 'NoneType' and 'list'

comment:2 by Tony Schaefer, 2 months ago 

I haven't been able to reproduce this. It looks like the user attached a
geometry optimization file, but the error occurred when opening a TD-DFT
file (at least based on the file name). We do have a q-chem license, so I
might try a couple TD-DFT jobs to see if I can get a similar error.

On Mon, Sep 8, 2025 at 2:19 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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