SEQCROW: problem reading sqmout file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505160006 (2025-05-16 00:06:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x0000b2cc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
  File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

getting structure  

> select /a:1@H6

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> set bgColor white

> ui tool show "Build QM Input"

H, C have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

O, H, C have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

> select /a:1@H19

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

O, H, N, C have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

H, S, N, C have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

> select /a:1@H2

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

> undo

Undo failed, probably because structures have been modified.  
getting structure  

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> undo

Undo failed, probably because structures have been modified.  

> undo

Undo failed, probably because structures have been modified.  

> close

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

getting structure  

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> close

getting structure  

> select /a:1@H1

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

S, O, C, H, N have no basis  

method '' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
LIBXC(PWPB95)  
CPF/1  
MO-CCSD(T)  
QCISD  
QCISD(T)  

> undo

Undo failed, probably because structures have been modified.  
getting structure  

> close #1

> close

getting structure  
getting structure  
structure will appear when optimization completes  
job started: local sqm job "new"  

> close

getting structure  
structure will appear when optimization completes  
job finished: local sqm job "new"  

> open "C:\Users\iak10\SEQCROW_SCRATCH\new Sat Jun 21 10.21.16
> 2025\new.sqmout" format sqmout

Opened new.sqmout as an sqm output file  
job started: local sqm job "new"  
job finished: local sqm job "new"  

> open "C:\Users\iak10\SEQCROW_SCRATCH\new Sat Jun 21 10.42.43
> 2025\new.sqmout" format sqmout

Summary of feedback from opening C:\Users\iak10\SEQCROW_SCRATCH\new Sat Jun 21
10.42.43 2025\new.sqmout  
---  
errors | could not open new.sqmout  
sqm output file contains an error (UNKNOWN):  
  
  
ValueError('A 2-dimensional array must be passed.')  
warning | error or warning in new.sqmout:  
  
SEQCROW failed to open new.sqmout  

> close

getting structure  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 389.08
OpenGL renderer: Quadro K1100M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision M4800
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 34,260,357,120
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4910MQ CPU @ 2.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.3
    build: 1.2.2.post1
    certifi: 2025.4.26
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.6
    ChimeraX-AtomicLibrary: 14.1.18
    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-clix: 0.2.1
    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: 1.10rc202505160006
    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-DevelExtras: 0.4.2
    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: 2.2.1
    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: 1.1.2
    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: 1.2.0
    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: 1.45.1
    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
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    platformdirs: 4.2.2
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    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: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.4.0
    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: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.20
    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
    tomli: 2.0.1
    tornado: 6.5
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.13.2
    typing_extensions: 4.12.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1
    zipp: 3.19.2

[Tony Schaefer]

Something is probably wrong in the sqm input file. All the sqm errors I've
seen print what the issue is on the last line of the file, which
seqcrow should print to the log. It looks like the last line was blank in
this case, so I'm not sure where things went wrong.

On Mon, Jun 23, 2025 at 12:34 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>