Opened 5 years ago

Closed 5 years ago

#3831 closed defect (fixed)

Start Build Structure: name 'Atoms' is not defined

Reported by: Tony Schaefer Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.2.dev202010150613 (2020-10-15 06:13:25 UTC)
Description
tried to open the "Build Structure" tool

Log:
> cd "C:\Users\Tony Schaefer/Desktop"

Current working directory is: C:\Users\Tony Schaefer\Desktop  

> graphics silhouettes true

UCSF ChimeraX version: 1.2.dev202010150613 (2020-10-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Build Structure"

Traceback (most recent call last):  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 524, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1251, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\build_structure\\__init__.py", line 35, in start_tool  
return BuildStructureTool(session, tool_name)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 54, in __init__  
getattr(self, "_layout_" + category.lower().replace(' ', '_'))(widget)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 217, in
_layout_modify_structure  
self._ms_sel_changed()  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\build_structure\tool.py", line 368, in _ms_sel_changed  
sel_atoms = selected_atoms(self.session)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2166, in selected_atoms  
return changes.selected_atoms(session)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\atomic\changes.py", line 171, in selected_atoms  
return _ordered_sel if _ordered_sel is not None else (_full_sel if _full_sel
is not None else Atoms())  
NameError: name 'Atoms' is not defined  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\gui.py", line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 529, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Build
Structure in bundle ChimeraX-BuildStructure:  
name 'Atoms' is not defined  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Build
Structure in bundle ChimeraX-BuildStructure:  
name 'Atoms' is not defined  
  
File "D:\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 529, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.38
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Education (Build 17763)
Memory: 17,107,533,824
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor         
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202010150613
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    Send2Trash: 1.5.0
    SEQCROW: 0.15
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Start Build Structure: name 'Atoms' is not defined

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Hi Tony,

Thanks for reporting this problem. Fixed now and the fix will be tomorrow's build. The (awkward) workaround until then is to open any structure, select something on it, close it, then you will be able to start Build Structure.

--Eric

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