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#7925 closed defect (fixed)

DICOM Browser: bundle forgot to override start_tool method

Reported by:	chimerax-bug-report@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:	1.5
Component:	DICOM	Version:
Keywords:		Cc:	Greg Couch
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.5rc202210140205 (2022-10-14 02:05:18 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5rc202210140205 (2022-10-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:\BUMPY\Molecular Docking and Dynamics\ChimeraX\5z62.pdb" format pdb

5z62.pdb title:  
Structure of human cytochrome C oxidase [more info...]  
  
Chain information for 5z62.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome C oxidase polypeptide I | COX1_HUMAN  
B | cytochrome C oxidase polypeptide II | COX2_HUMAN  
C | cytochrome C oxidase polypeptide III | COX3_HUMAN  
D | cytochrome C oxidase subunit 4 isoform 1, mitochondrial | COX41_HUMAN  
E | cytochrome C oxidase polypeptide VA | COX5A_HUMAN  
F | cytochrome C oxidase polypeptide VB | COX5B_HUMAN  
G | cytochrome C oxidase subunit 6A1, mitochondrial | CX6A1_HUMAN  
H | cytochrome C oxidase subunit 6B1 | CX6B1_HUMAN  
I | cytochrome C oxidase polypeptide VIC | COX6C_HUMAN  
J | cytochrome C oxidase subunit 7A2, mitochondrial | CX7A2_HUMAN  
K | cytochrome C oxidase polypeptide VIIB | COX7B_HUMAN  
L | cytochrome C oxidase polypeptide VIIC | COX7C_HUMAN  
M | cytochrome C oxidase subunit 8A, mitochondrial | COX8A_HUMAN  
N | cytochrome C oxidase subunit NDUFA4 | NDUA4_HUMAN  
  
Non-standard residues in 5z62.pdb #1  
---  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CU — copper (II) ion  
HEA — heme-A  
MG — magnesium ion  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
ZN — zinc ion  
  

> style stick

Changed 15037 atom styles  

> style ball

Changed 15037 atom styles  

> style sphere

Changed 15037 atom styles  

> hide atoms

> hide cartoons

> style sphere

Changed 15037 atom styles  

> show cartoons

> style sphere

Changed 15037 atom styles  

> show atoms

> hide atoms

> select /A:192

5 atoms, 4 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

[Repeated 2 time(s)]

> show sel atoms

> style sel stick

Changed 5 atom styles  

> style sel sphere

Changed 5 atom styles  

> hide sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> style sel sphere

Changed 5 atom styles  

> style sel sphere

Changed 5 atom styles  

> style sel stick

Changed 5 atom styles  

> view sel

[Repeated 1 time(s)]

> close session

> open "E:\BUMPY\Molecular Docking and Dynamics\ChimeraX\5z62.pdb" format pdb

5z62.pdb title:  
Structure of human cytochrome C oxidase [more info...]  
  
Chain information for 5z62.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome C oxidase polypeptide I | COX1_HUMAN  
B | cytochrome C oxidase polypeptide II | COX2_HUMAN  
C | cytochrome C oxidase polypeptide III | COX3_HUMAN  
D | cytochrome C oxidase subunit 4 isoform 1, mitochondrial | COX41_HUMAN  
E | cytochrome C oxidase polypeptide VA | COX5A_HUMAN  
F | cytochrome C oxidase polypeptide VB | COX5B_HUMAN  
G | cytochrome C oxidase subunit 6A1, mitochondrial | CX6A1_HUMAN  
H | cytochrome C oxidase subunit 6B1 | CX6B1_HUMAN  
I | cytochrome C oxidase polypeptide VIC | COX6C_HUMAN  
J | cytochrome C oxidase subunit 7A2, mitochondrial | CX7A2_HUMAN  
K | cytochrome C oxidase polypeptide VIIB | COX7B_HUMAN  
L | cytochrome C oxidase polypeptide VIIC | COX7C_HUMAN  
M | cytochrome C oxidase subunit 8A, mitochondrial | COX8A_HUMAN  
N | cytochrome C oxidase subunit NDUFA4 | NDUA4_HUMAN  
  
Non-standard residues in 5z62.pdb #1  
---  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CU — copper (II) ion  
HEA — heme-A  
MG — magnesium ion  
PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE)  
ZN — zinc ion  
  

> hide cartoons

> hide atoms

> hide surfaces

> style stick

Changed 15037 atom styles  

> hide surfaces

[Repeated 1 time(s)]

> show surfaces

[Repeated 1 time(s)]

> hide surfaces

> show cartoons

> hide cartoons

> show atoms

> hide cartoons

> hide surfaces

> hide cartoons

> hide atoms

> hide cartoons

> hide surfaces

> show atoms

> style stick

Changed 15037 atom styles  

> style sphere

Changed 15037 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 15037 atom styles  

> style stick

Changed 15037 atom styles  

> nucleotides tube/slab shape box

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> select /A

4201 atoms, 4345 bonds, 15 pseudobonds, 518 residues, 2 models selected  

> select C

9913 atoms, 8082 bonds, 1861 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> close session

> open "E:\BUMPY\Molecular Docking and Dynamics\ChimeraX\1uz9.pdb" format pdb

1uz9.pdb title:  
Crystallographic and solution studies of N-lithocholyl insulin: A new
generation of prolonged-acting insulins. [more info...]  
  
Chain information for 1uz9.pdb #1  
---  
Chain | Description | UniProt  
A | insulin | INS_HUMAN  
B | insulin | INS_HUMAN  
  
Non-standard residues in 1uz9.pdb #1  
---  
CL — chloride ion  
CRS — M-cresol  
UZ9 —
(2S)-2-amino-6-({(4R)-4-[(10R,13S)-10,13-dimethyl-3-oxohexadecahydro-1H-cyclopenta[A]phenanthren-17-yl]pentanoyl}amino)hexanoicacid  
ZN — zinc ion  
  

> show atoms

> show cartoons

> show surfaces

[Repeated 1 time(s)]

> hide surfaces

> mlp

Map values for surface "1uz9.pdb_A SES surface": minimum -24.48, mean -4.085,
maximum 19.86  
Map values for surface "1uz9.pdb_B SES surface": minimum -23.88, mean -0.855,
maximum 21.86  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "1uz9.pdb_A SES surface": minimum -24.48, mean -4.085,
maximum 19.86  
Map values for surface "1uz9.pdb_B SES surface": minimum -23.88, mean -0.855,
maximum 21.86  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

[Repeated 2 time(s)]

> hide surfaces

> style sphere

Changed 484 atom styles  

> style sphere

Changed 484 atom styles  

> style stick

Changed 484 atom styles  

> hbonds reveal true

154 hydrogen bonds found  

> ~hbonds

Alignment identifier is 1/A  
Alignment identifier is 1/B  

> interfaces ~solvent

1 buried areas: B A 632  

> close session

> open "E:/BUMPY/Molecular Docking and Dynamics/ChimeraX/7df4.pdb"

7df4.pdb title:  
Sars-cov-2 S-ACE2 complex [more info...]  
  
Chain information for 7df4.pdb #1  
---  
Chain | Description | UniProt  
A | angiotensin-converting enzyme 2 | ACE2_HUMAN  
B C D | spike glycoprotein | SPIKE_SARS2  
  
Non-standard residues in 7df4.pdb #1  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> style sphere

Changed 30920 atom styles  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show "DICOM Browser"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 560, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1269, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1318, in _get_func  
raise ToolshedError("bundle forgot to override %s method" % func_name)  
chimerax.core.toolshed.ToolshedError: bundle forgot to override start_tool
method  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1660, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DICOM
Browser in bundle ChimeraX-Dicom:  
bundle forgot to override start_tool method  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DICOM
Browser in bundle ChimeraX-Dicom:  
bundle forgot to override start_tool method  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.78
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_IN.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Dash F15 FX516PC_FX516PCZ
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 8,266,268,672
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-11300H @ 3.10GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210140205
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.4
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.9.0

Change History (4)

comment:1 by pett, 3 years ago

Cc:	Greg Couch added
Component:	Unassigned → DICOM
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → DICOM Browser: bundle forgot to override start_tool method

comment:2 by Zach Pearson, 3 years ago

Milestone:	→ 1.5

comment:3 by Zach Pearson, 3 years ago

start_tool has been implemented, so this ticket is superseded by #8015.

comment:4 by Zach Pearson, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

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