id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15570	Context menu: self.bundle_info is None	wh-kelvin.chung@…	Eric Pettersen	"{{{
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
right click the panel listing all the PDB file. 
some file were generated directly from alphafold server

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/admin/Documents/PolyU Project/glycosaminoglycan/Structrure/Sa
> Hyal Q59801.pdb""

Sa Hyal Q59801.pdb title:  
Alphafold monomer V2.0 prediction for hyaluronate lyase (Q59801) [more
info...]  
  
Chain information for Sa Hyal Q59801.pdb #1  
---  
Chain | Description | UniProt  
A | hyaluronate lyase | HYSA_STAA8 1-807  
  

> open ""C:/Users/admin/Documents/PolyU
> Project/glycosaminoglycan/Structrure/Vibrio Fischeri Hyal Q5DYT2.pdb""

Vibrio Fischeri Hyal Q5DYT2.pdb title:  
Alphafold monomer V2.0 prediction for hyaluronate lyase (Q5DYT2) [more
info...]  
  
Chain information for Vibrio Fischeri Hyal Q5DYT2.pdb #2  
---  
Chain | Description | UniProt  
A | hyaluronate lyase | Q5DYT2_ALIF1 1-802  
  

> open ""C:/Users/admin/Documents/PolyU
> Project/glycosaminoglycan/Structrure/HCLase Vibrio
> AIL54323_b2561_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb""

Chain information for HCLase Vibrio
AIL54323_b2561_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open ""C:/Users/admin/Documents/PolyU
> Project/glycosaminoglycan/Structrure/ChABC II.pdb""

ChABC II.pdb title:  
Alphafold monomer V2.0 prediction for chondroitin sulfate abc exolyase
(C7S340) [more info...]  
  
Chain information for ChABC II.pdb #4  
---  
Chain | Description | UniProt  
A | chondroitin sulfate abc exolyase | CABC2_PROVU 1-990  
  

> mmaker #3 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChABC II.pdb, chain A (#4) with HCLase Vibrio
AIL54323_b2561_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#3), sequence alignment score = 721.8  
RMSD between 254 pruned atom pairs is 1.061 angstroms; (across all 737 pairs:
14.924)  
  

> mmaker #2 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChABC II.pdb, chain A (#4) with Vibrio Fischeri Hyal Q5DYT2.pdb,
chain A (#2), sequence alignment score = 714.4  
RMSD between 233 pruned atom pairs is 1.081 angstroms; (across all 710 pairs:
11.854)  
  

> mmaker #1 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChABC II.pdb, chain A (#4) with Sa Hyal Q59801.pdb, chain A (#1),
sequence alignment score = 624.2  
RMSD between 197 pruned atom pairs is 1.093 angstroms; (across all 734 pairs:
20.395)  
  

> hide #4 models

> show #1-3 atoms

> hide #1 models

> open 1hmw

1hmw title:  
Active site of chondroitinase Ac lyase revealed by the structure of enzyme-
oligosaccharide complexes and mutagenesis [more info...]  
  
Chain information for 1hmw #5  
---  
Chain | Description | UniProt  
A | CHONDROITINASE AC | CHAC_PEDHE 1-700  
  
Non-standard residues in 1hmw #5  
---  
ASG — 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose  
BDP — beta-D-glucopyranuronic acid (D-glucuronic acid)  
CA — calcium ion  
GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid  
GCU — alpha-D-glucopyranuronic acid  
MAN — alpha-D-mannopyranose  
MXY — 2-O-methyl-beta-L-fucopyranose  
NG6 — 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose  
RAM — alpha-L-rhamnopyranose  
XYP — beta-D-xylopyranose  
  

> mmaker #5 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChABC II.pdb, chain A (#4) with 1hmw, chain A (#5), sequence
alignment score = 610.4  
RMSD between 205 pruned atom pairs is 1.107 angstroms; (across all 622 pairs:
10.392)  
  

> hide #2-3#!5 atoms

> hide #2 models

> show #1 models

> hide #1,3#!5 atoms

> hide #3 models

> show #4 models

> hide #!5 models

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\ui\gui.py"", line 2470, in <lambda>  
self.ui_area.contextMenuEvent = lambda e, *, self=self:
self.show_context_menu(e)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\ui\gui.py"", line 2646, in show_context_menu  
self.tool_window.tool_instance.tool_info in self.main_window._tools_cache,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\tools.py"", line 158, in tool_info  
for ti in self.bundle_info.tools:  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'tools'  
  
AttributeError: 'NoneType' object has no attribute 'tools'  
  
File ""C:\Program Files\ChimeraX 1.9.dev202406152048\bin\Lib\site-
packages\chimerax\core\tools.py"", line 158, in tool_info  
for ti in self.bundle_info.tools:  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.1999
OpenGL renderer: Intel(R) HD Graphics Gen11
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: Default string
Model: Default string
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 16,914,849,792
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Celeron(R) N5105 @ 2.00GHz
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
}}}
"	defect	closed	normal		UI		fixed		Greg Couch				all	ChimeraX