The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.9.dev202406152048 (2024-06-15 20:48:09 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9.dev202406152048 (2024-06-15)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:\Users\Dell\Desktop\6KpHol_2a527\6KpHol_2a527_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> format pdb
Chain information for
6KpHol_2a527_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1
---
Chain | Description
A | No description available
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> ~worm
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> nucleotides tube/slab shape box
[Repeated 3 time(s)]
> show surfaces
[Repeated 1 time(s)]
> undo
[Repeated 2 time(s)]
> show cartoons
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> style stick
Changed 644 atom styles
> open C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527.done.txt
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_coverage.png
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_pae.png
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_plddt.png
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_predicted_aligned_error_v1.json
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_scores_rank_002_alphafold2_ptm_model_4_seed_000.json
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_scores_rank_003_alphafold2_ptm_model_5_seed_000.json
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_scores_rank_004_alphafold2_ptm_model_1_seed_000.json
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_scores_rank_005_alphafold2_ptm_model_3_seed_000.json
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/cite.bibtex
Unrecognized file suffix '.txt'
> open
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
> C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol_2a527_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
6KpHol_2a527_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #2
---
Chain | Description
A | No description available
Chain information for
6KpHol_2a527_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #3
---
Chain | Description
A | No description available
Chain information for
6KpHol_2a527_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb #4
---
Chain | Description
A | No description available
Chain information for
6KpHol_2a527_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #5
---
Chain | Description
A | No description available
Chain information for
6KpHol_2a527_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb #6
---
Chain | Description
A | No description available
> hide #!1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #6 models
> view clip false
> show #5 cartoons
> rainbow #5
> select helix
3060 atoms, 3107 bonds, 407 residues, 6 models selected
> cartoon style (#5 & sel) xsection rectangle modeHelix default
> select coil
804 atoms, 809 bonds, 91 residues, 6 models selected
> select strand
Nothing selected
> lighting soft
> lighting full
> lighting simple
> save "C:/Users/Dell/Desktop/6KpHol_2a527/6KpHol 3D struture prediction.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 263, in discovery
uid = _UniqueName.from_obj(self.session, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 143, in from_obj
raise RuntimeError('No bundle information for %s.%s' % (
RuntimeError: No bundle information for chimerax.core.tasks.Tasks
RuntimeError: No bundle information for chimerax.core.tasks.Tasks
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 143, in from_obj
raise RuntimeError('No bundle information for %s.%s' % (
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\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 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 263, in discovery
uid = _UniqueName.from_obj(self.session, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 143, in from_obj
raise RuntimeError('No bundle information for %s.%s' % (
RuntimeError: No bundle information for chimerax.core.tasks.Tasks
RuntimeError: No bundle information for chimerax.core.tasks.Tasks
File "C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\session.py", line 143, in from_obj
raise RuntimeError('No bundle information for %s.%s' % (
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.4575
OpenGL renderer: Intel(R) Iris(R) Xe 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: Dell Inc.
Model: Inspiron 3501
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 4,004,290,560
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
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: 2.13
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.2
ChimeraX-AtomicLibrary: 14.1.1
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: 2.13
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: 1.9.dev202406152048
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-DeepMutationalScan: 1.0
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: 2.1.4
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: 2.7.6
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: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.12.1
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: 1.16.6
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: 1.39.2
ChimeraX-uniprot: 2.3.1
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
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
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
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
RandomWords: 0.4.0
requests: 2.32.0
scipy: 1.13.0
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Caused by the same pkg_utils bug as #15472