Opened 22 months ago

Closed 22 months ago

Last modified 22 months ago

#14481 closed defect (fixed)

SEQCROW: read_psi4_out: could not convert string to float

Reported by: rohan.cotton90@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Greg Couch, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Maybe, using "GeomeTRIC" optimizer in psi4 cause this error.

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7323 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/omega/Calc_new/r2scan3c/benzene_tcne_r2scan3c.out

Summary of feedback from opening
D:/omega/Calc_new/r2scan3c/benzene_tcne_r2scan3c.out  
---  
error | unable to open benzene_tcne_r2scan3c.out  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\\__init__.py", line 597, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\io.py", line 57, in open_aarontools  
raise e  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\io.py", line 34, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1550, in __init__  
self.read_psi4_out(f, get_all, just_geom)  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 2045, in read_psi4_out  
dE = float(dE_conv.split()[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string to float: '--------'  
  
ValueError: could not convert string to float: '--------'  
  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 2045, in read_psi4_out  
dE = float(dE_conv.split()[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open D:/omega/Calc_new/r2scan3c/benzene_tcne_r2scan3c.out

Summary of feedback from opening
D:/omega/Calc_new/r2scan3c/benzene_tcne_r2scan3c.out  
---  
error | unable to open benzene_tcne_r2scan3c.out  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\\__init__.py", line 597, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\io.py", line 57, in open_aarontools  
raise e  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\io.py", line 34, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1550, in __init__  
self.read_psi4_out(f, get_all, just_geom)  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 2045, in read_psi4_out  
dE = float(dE_conv.split()[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string to float: '--------'  
  
ValueError: could not convert string to float: '--------'  
  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 2045, in read_psi4_out  
dE = float(dE_conv.split()[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open D:/omega/Calc_new/r2scan3c/benzene_tcne_r2scan3c.out

Summary of feedback from opening
D:/omega/Calc_new/r2scan3c/benzene_tcne_r2scan3c.out  
---  
error | unable to open benzene_tcne_r2scan3c.out  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\\__init__.py", line 597, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\io.py", line 57, in open_aarontools  
raise e  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\io.py", line 34, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1550, in __init__  
self.read_psi4_out(f, get_all, just_geom)  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 2045, in read_psi4_out  
dE = float(dE_conv.split()[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not convert string to float: '--------'  
  
ValueError: could not convert string to float: '--------'  
  
File "C:\Users\user\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 2045, in read_psi4_out  
dE = float(dE_conv.split()[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7323
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 81F4
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 4,199,780,352
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-8130U CPU @ 2.20GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    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
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    Send2Trash: 1.8.2
    SEQCROW: 1.8.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1
File attachment: benzene_tcne_r2scan3c.out

benzene_tcne_r2scan3c.out​

Attachments (1)

benzene_tcne_r2scan3c.out​ (4.3 MB ) - added by rohan.cotton90@… 22 months ago.
Added by email2trac

Change History (18)

by rohan.cotton90@…, 22 months ago

Attachment: benzene_tcne_r2scan3c.out​ added

Added by email2trac

comment:1 by Eric Pettersen, 22 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW: read_psi4_out: could not convert string to float

Reported by Rohan Sharma

comment:2 by Tony Schaefer, 22 months ago 

Rohan,

Thanks for reporting this and including the output file. It looks like this
Psi4 version prints the optimization convergence a bit differently. On the
first step, it prints "-------" for criteria based on change from the
previous step (energy, displacement). The parser was expecting something it
could convert to a number. I'm not sure if that's a GeomeTRIC thing or a
Psi4 1.9 thing.

I've uploaded a patch to the tool shed that should fix the parser. To
update manually, go to Tools > More Tools... on the ChimeraX menu, find the
SEQCROW page and click the update button. It should prompt you to restart
ChimeraX.

Best,

Tony

On Thu, Jan 25, 2024 at 4:08 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:3 by rohan.cotton90@…, 22 months ago 

Thank you for your response.

I have followed the instructions you have provided. But, it is not working
in my case because the same error is occurred.

Regards,
Rohan



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comment:4 by Tony Schaefer, 22 months ago 

Rohan,

If you run the ChimeraX command `toolshed list installed` it will print the
version of each bundle you have. Does it say SEQCROW is 1.8.7?

Do any of the ChimeraX developers know if the pip bugs were fixed in 1.7,
or do you need to have 1.7.1 for that? I think some of those could prevent
bundles from updating correctly (e.g. #9471)

Tony

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comment:5 by rohan.cotton90@…, 22 months ago 

My version is

   - *SEQCROW <https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow>*
(1.8.3): *Structure
   Editing and Quantum Chemical Representation and Organization for Workflows*


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comment:6 by Eric Pettersen, 22 months ago

Cc: Greg Couch Eric Pettersen added

Rohan,

If you do Tools→Utilities→Updates, does the Updates tool say that a newer version of SEQCROW is available?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:7 by rohan.cotton90@…, 22 months ago 

Yes, It says the 1.8.7 version of SEQCROW is available.

On Sat, Jan 27, 2024 at 12:21 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:8 by Eric Pettersen, 22 months ago

If then use the Updates tool and install the 1.8.7 version, then quit and restart ChimeraX, what version of SEQCROW does toolshed list installed report?

--Eric

comment:9 by rohan.cotton90@…, 22 months ago 

1.8.3

On Tue, 30 Jan, 2024, 7:19 am ChimeraX, <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:10 by Eric Pettersen, 22 months ago

If you do "toolshed uninstall SEQCROW", what output do you get? If you then quit and restart ChimeraX, is SEQCROW still installed?

comment:11 by rohan.cotton90@…, 22 months ago 

Yes, it is!  The SEQCROW is still install after using  "toolshed uninstall
SEQCROW". The version is  *SEQCROW
<https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow>* (1.8.3).

-Rohan

On Thu, Feb 1, 2024 at 2:43 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:12 by Eric Pettersen, 22 months ago

...and what is the output from "toolshed uninstall SEQCROW"?

comment:13 by rohan.cotton90@…, 22 months ago 

It says " unloading module SEQCROW"

On Fri, Feb 2, 2024 at 12:16 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:14 by Eric Pettersen, 22 months ago

I think you are going to have to uninstall SEQCROW "by hand". In ChimeraX, find the folder where SEQROW is installed by using the command "info path user versioned data" and looking at the result in the Log. Go to that folder on your machine and remove the folder named SEQCROW, and the folder whose name begins with SEQCROW and ends with .dist-info . Then when you start ChimeraX, "toolshed list" should not list SEQCROW. Then I think you will be able to install the 1.8.7 version.

comment:15 by rohan.cotton90@…, 22 months ago 

I have uninstalled the SEQCROW by hand and then reinstalled the 1.8.7
version of SEQCROW.  Now, I can open the psi4 file with geometric. Thank
you so much for your help and give your time to look into this.

-Rohan

On Fri, Feb 2, 2024 at 4:11 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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comment:16 by Eric Pettersen, 22 months ago

Resolution: → fixed
Status: assigned → closed

Sorry it was such a hassle. Upgrading a bundle isn't usually this difficult!

--Eric

comment:17 by rohan.cotton90@…, 22 months ago 

Thanks for trying!

It will be a great help for me.

-Rohan


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