Problem reading ORCA output file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.5-arm64-arm-64bit
ChimeraX Version: 1.5.dev202208130111 (2022-08-13 01:11:18 UTC)
Description
Tried to open an ORCA output file and it did not work.

Log:
UCSF ChimeraX version: 1.5.dev202208130111 (2022-08-13)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/monomers/c3po/casscf/frequency/c3po-
> opt-freq-casscf-tz.out

Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Applications/Chimera/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/__init__.py", line 429, in open  
return open_aarontools(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 27, in open_aarontools  
fr = FileReader(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1006, in __init__  
self.read_orca_out(f, get_all, just_geom)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1632, in read_orca_out  
self.atoms, n = get_atoms(f, n)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1587, in get_atoms  
rv += [Atom(element=element, coords=coords, name=str(i))]  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
ValueError: Unknown element detected: -  
  
ValueError: Unknown element detected: -  
  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 53 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.7
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.0
    ChimeraX-AddCharge: 1.2.4
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.5.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.40
    ChimeraX-AtomicLibrary: 7.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.1.1
    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ColorActions: 1.0.1
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202208130111
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
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    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.3
    ChimeraX-Help: 1.2.1
    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
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    ChimeraX-ListInfo: 1.1.1
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    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
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    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
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    ChimeraX-MDcrds: 2.6
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    ChimeraX-Meeting: 1.0.1
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    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
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    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-Segger: 1.0
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-ViewDockX: 1.1.3
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    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
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