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Opened 13 months ago
Last modified 13 months ago
#16072 assigned defect
SEQCROW: np is None
| Reported by: | 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: Windows-10-10.0.26120
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
It was not possible to plot the IR of some log. file.
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\Gaussian Rhodes 22\Oct 2022\Sobola 2024\L6a_sob.log" format log
Summary of feedback from opening D:\Gaussian Rhodes 22\Oct 2022\Sobola
2024\L6a_sob.log
---
notes | opt=readfc
None
None
L6a_sob.log has 0 imaginary harmonic vibrational modes
Opened L6a_sob.log as a Gaussian output file
> open "D:\Gaussian Rhodes 22\Oct 2022\Sobola 2024\L6a_sob.log" format log
Summary of feedback from opening D:\Gaussian Rhodes 22\Oct 2022\Sobola
2024\L6a_sob.log
---
notes | opt=readfc
None
None
L6a_sob.log has 0 imaginary harmonic vibrational modes
Opened L6a_sob.log as a Gaussian output file
> ui tool show "IR Spectrum"
AttributeError: 'NoneType' object has no attribute 'log'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 448, in <lambda>
tabs.currentChanged.connect(lambda ndx: self.refresh_plot() if ndx == 1 else
None)
^^^^^^^^^^^^^^^^^^^
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1123, in refresh_plot
mixed_spectra = self.get_mixed_spectrum()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\tools\ir_plot.py", line 1016, in get_mixed_spectrum
freqs[-1].append(CompOutput(fr))
^^^^^^^^^^^^^^
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\comp_output.py", line 151, in __init__
self.grimme_g = self.calc_Grimme_G()
^^^^^^^^^^^^^^^^^^^^
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\comp_output.py", line 446, in calc_Grimme_G
Gcorr_qRRHO = self.calc_G_corr(
^^^^^^^^^^^^^^^^^
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\comp_output.py", line 432, in calc_G_corr
Ecorr, Hcorr, Stot = self.therm_corr(temperature, v0, method, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\comp_output.py", line 337, in therm_corr
Se = PHYSICAL.GAS_CONSTANT * (np.log(mult))
^^^^^^^^^^^^
TypeError: loop of ufunc does not support argument 0 of type NoneType which
has no callable log method
TypeError: loop of ufunc does not support argument 0 of type NoneType which
has no callable log method
File "C:\Users\rafsh\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\comp_output.py", line 337, in therm_corr
Se = PHYSICAL.GAS_CONSTANT * (np.log(mult))
^^^^^^^^^^^^
See log for complete Python traceback.
Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable
OpenGL version: 3.3.0 - Build 31.0.101.2125
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Microsoft Corporation
Model: Surface Pro 7
OS: Microsoft Windows 11 Home (Build 26120)
Memory: 8,155,979,776
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G4 CPU @ 1.10GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.4
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openpyxl: 3.1.5
openvr: 1.26.701
packaging: 24.1
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
seaborn: 0.13.2
Send2Trash: 1.8.3
SEQCROW: 1.8.12
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
File attachment: L6a_sob.log
Attachments (1)
Change History (4)
by , 13 months ago
| Attachment: | L6a_sob.log added |
|---|
comment:1 by , 13 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW: np is None |
Reported by Larry
comment:2 by , 13 months ago
Larry, It looks like this is an issue with the parser not handling geom=allcheck. I'll see what I can do about that. Best, Tony On Mon, Oct 7, 2024 at 12:36 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > >
comment:3 by , 13 months ago
I've just uploaded a version that should fix this. To update, you can go to Tools > More Tools... on the ChimeraX menu to pull up the toolshed. Then find the SEQCROW page and click the update button. On Mon, Oct 7, 2024 at 12:45 PM Tony Schaefer <tony.schaefer.chem@gmail.com> wrote: > > > > > >> #16072: SEQCROW: np is None >> ----------------------------------+--------------------------- >> Reporter: rshaibu@… | Owner: Tony Schaefer >> Type: defect | Status: assigned >> Priority: normal | Milestone: >> Component: Third Party | Version: >> Resolution: | Keywords: >> Blocked By: | Blocking: >> Notify when closed: | Platform: all >> Project: ChimeraX | >> ----------------------------------+--------------------------- >> Changes (by pett): >> >> * component: Unassigned => Third Party >> * owner: (none) => Tony Schaefer >> * platform: => all >> * project: => ChimeraX >> * status: new => assigned >> * summary: ChimeraX bug report submission => SEQCROW: np is None >> >> Comment: >> >> Reported by Larry >> -- >> Ticket URL: < >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16072#comment:1> >> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> >> ChimeraX Issue Tracker >> >
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