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Opened 14 months ago
Last modified 14 months ago
#15791 assigned defect
SEQCROW: `y` must contain only finite values
| 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: Linux-6.5.0-44-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> close #
Expected a models specifier or a keyword
> open /home/usuario/Descargas/ch.log
Unrecognized file suffix '.log'
> toolshed show
Downloading bundle SEQCROW-1.8.12-py3-none-any.whl
Installed SEQCROW (1.8.12)
> open /home/usuario/Descargas/ch.log
Summary of feedback from opening /home/usuario/Descargas/ch.log
---
note | ch.log has 0 imaginary harmonic vibrational modes
Opened ch.log as a Gaussian output file
> view clip false
[Repeated 2 time(s)]
> hide #1 models
> show #1 models
> ui tool show "Selection Inspector"
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right select
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right label
> ui mousemode right "color key"
> key labelColor default
> ui mousemode right label
> color bypolymer
> ui mousemode right "color key"
> key delete
> ui mousemode right label
> ui mousemode right distance
> set bgColor white
[Repeated 1 time(s)]
> set bgColor black
> volume style surface
No volumes specified
> style stick
Changed 2 atom styles
> style sphere
Changed 2 atom styles
> style sphere
Changed 2 atom styles
> style ball
Changed 2 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 2 atom styles
> set bgColor gray
> style ball
Changed 2 atom styles
> graphics silhouettes true
> set bgColor black
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
> lighting simple
> ui tool show "Side View"
> view
> view orient
> view
> transparency 50
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow sticks
Using preset: SEQCROW / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow vdw
Using preset: SEQCROW / VDW
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset seqcrow "index labels"
Using preset: SEQCROW / Index Labels
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style ball
Changed 2 atom styles
> lighting soft
> lighting simple
> lighting full
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color #1 #dc8addff
> select add #1
2 atoms, 1 bond, 1 residue, 2 models selected
> select subtract #1
1 model selected
> hide #!1 models
> show #!1 models
> ui tool show "IR Spectrum"
> ui tool show "Visualize Normal Modes"
Traceback (most recent call last):
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/normal_modes.py", line 716, in show_anim
S = Pathway(np.array([Xf, X, Xr, X, Xf]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 33, in __init__
self._build_interpolation(**interpolator_kwargs)
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 74, in _build_interpolation
self._interpolation = [
^
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 75, in <listcomp>
interp_func(self.x_vals, coord, **interpolator_kwargs) for coord in coords.T
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 60, in <lambda>
interp_func = lambda *args: scipy.interpolate.CubicSpline(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_cubic.py", line 742, in __init__
x, dx, y, axis, _ = prepare_input(x, y, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_cubic.py", line 63, in prepare_input
raise ValueError("`y` must contain only finite values.")
ValueError: `y` must contain only finite values.
ValueError: `y` must contain only finite values.
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_cubic.py", line 63, in prepare_input
raise ValueError("`y` must contain only finite values.")
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/normal_modes.py", line 716, in show_anim
S = Pathway(np.array([Xf, X, Xr, X, Xf]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 33, in __init__
self._build_interpolation(**interpolator_kwargs)
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 74, in _build_interpolation
self._interpolation = [
^
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 75, in <listcomp>
interp_func(self.x_vals, coord, **interpolator_kwargs) for coord in coords.T
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/usuario/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/pathway.py", line 60, in <lambda>
interp_func = lambda *args: scipy.interpolate.CubicSpline(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_cubic.py", line 742, in __init__
x, dx, y, axis, _ = prepare_input(x, y, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_cubic.py", line 63, in prepare_input
raise ValueError("`y` must contain only finite values.")
ValueError: `y` must contain only finite values.
ValueError: `y` must contain only finite values.
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_cubic.py", line 63, in prepare_input
raise ValueError("`y` must contain only finite values.")
See log for complete Python traceback.
OpenGL version: 4.3 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: NVD9
OpenGL vendor: Mesa
Python: 3.11.4
Locale: es_CL.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer:
Model:
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 7.7Gi 2.9Gi 154Mi 90Mi 4.7Gi 4.5Gi
Swap: 2.0Gi 0.0Ki 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF119 [GeForce GT 610] [10de:104a] (rev a1)
Subsystem: ZOTAC International (MCO) Ltd. GF119 [GeForce GT 610] [19da:6222]
Kernel driver in use: nouveau
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-LinuxSupport: 1.0.1
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-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
distro: 1.9.0
docutils: 0.20.1
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
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
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
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
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
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
Change History (1)
comment:1 by , 14 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW: `y` must contain only finite values |
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