SEQCROW: reading ORCA output: index 0 is out of bounds for axis 0 with size 0

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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/nkd/Desktop/SDSU_Computational_Chem/Nilay_qchem_research/nkd_cyclopropanation_oniom_project/JACS_revision/NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R/NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R.out

Summary of feedback from opening
/Users/nkd/Desktop/SDSU_Computational_Chem/Nilay_qchem_research/nkd_cyclopropanation_oniom_project/JACS_revision/NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R/NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R.out  
---  
error | unable to open NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
  
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
last line read: 1 C : -0.001086767 -0.001060958 -0.000758689  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
last line read: 1 C : -0.001086767 -0.001060958 -0.000758689  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, charge, multiplicity,  
n_basis, scf_energy, n_alpha, n_beta, dispersion correction energy, energy,  
energy_context  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
last line read: 1 C : -0.001086767 -0.001060958 -0.000758689  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, charge, multiplicity,  
n_basis, scf_energy, n_alpha, n_beta, dispersion correction energy, energy,  
energy_context  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R.inp  
| 1> !PBEh-3c NEB-TS FREQ PAL16 SMD(dichloromethane)  
| 2> %NEB NEB_END_XYZFILE  
"nkd_product_quinoline_substratescope_r_CF3CF3_OCH3_R_opt.xyz" END  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
last line read: 1 C : -0.001086767 -0.001060958 -0.000758689  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, charge, multiplicity,  
n_basis, scf_energy, n_alpha, n_beta, dispersion correction energy, energy,  
energy_context  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
INPUT FILE  
================================================================================  
NAME = NEBTS_react_cyclopropCF3CF3_OCH3_R_product_quinolineCF3CF3_OCH3_R.inp  
| 1> !PBEh-3c NEB-TS FREQ PAL16 SMD(dichloromethane)  
| 2> %NEB NEB_END_XYZFILE  
"nkd_product_quinoline_substratescope_r_CF3CF3_OCH3_R_opt.xyz" END  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
  
the following data has been read: error, opt_steps, charge, multiplicity,  
n_basis, scf_energy, n_alpha, n_beta, dispersion correction energy, energy,  
energy_context  
  
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/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/SEQCROW/__init__.py", line 605, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "/Users/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/SEQCROW/io.py", line 46, in open_aarontools  
raise e  
File "/Users/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/SEQCROW/io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "/Users/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/AaronTools/fileIO.py", line 1632, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "/Users/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/AaronTools/fileIO.py", line 3280, in read_orca_out  
raise e  
File "/Users/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/AaronTools/fileIO.py", line 2711, in read_orca_out  
gradient[i] = np.array([float(x) for x in info[3:]])  
~~~~~~~~^^^  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  
File "/Users/nkd/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/AaronTools/fileIO.py", line 2711, in read_orca_out  
gradient[i] = np.array([float(x) for x in info[3:]])  
~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
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: Mac16,13
      Model Number: MC6K4LL/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 24 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 13822.1.2

Software:

    System Software Overview:

      System Version: macOS 26.0.1 (25A362)
      Kernel Version: Darwin 25.0.0
      Time since boot: 6 days, 2 hours, 20 minutes

Graphics/Displays:

    Apple M4:

      Chipset Model: Apple M4
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      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
        ARZOPA:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
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    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
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    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
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    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
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    ChimeraX-MapFit: 2.0
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    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
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    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
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    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
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    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
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    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
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    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-SDF: 2.0.3
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    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
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    ChimeraX-Shell: 1.0.1
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    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-Test: 1.0
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    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
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    ChimeraX-WavefrontOBJ: 1.0
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    ChimeraX-WebServices: 1.1.5
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    nest-asyncio: 1.6.0
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    PyQt6_sip: 13.10.0
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    RandomWords: 0.4.0
    requests: 2.32.3
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    SEQCROW: 1.9.4
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    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
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    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
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    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
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14