id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3831 Start Build Structure: name 'Atoms' is not defined Tony Schaefer Eric Pettersen "{{{ 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 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 }}} " defect closed normal Core fixed all ChimeraX