id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20750 numpy bool no longer accepted by QCheckBox.setChecked() Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26200-SP0 ChimeraX Version: 1.13.dev202607100053 (2026-07-10 00:53:17 UTC) Description Tried to launch the selection inspector with an atom selected. I'd just been messing with it in the altloc explorer, if that makes any difference. Log: UCSF ChimeraX version: 1.13.dev202607100053 (2026-07-10) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9rr6 structureFactors true Summary of feedback from opening 9rr6 fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_HL_A_iso, pdbx_HL_B_iso, pdbx_HL_C_iso, pdbx_HL_D_iso, phase_calc, fom Automatically choosing ""F_meas_au, F_meas_sigma_au"". notes | Fetching compressed 9rr6 structure factors from http://files.rcsb.org/download/9rr6-sf.cif Resolution: 0.9333392159018835 Launching live xmap mgr took 0.5529270172119141 seconds. Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 82,84,80, pixel 0.304,0.295,0.304, shown at level 1.58, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 82,84,80, pixel 0.304,0.295,0.304, shown at level -0.311,0.311, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_29 as #1.1.1.4, grid size 82,84,80, pixel 0.304,0.295,0.304, shown at level 0.273, step 1, values float32 Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 82,84,80, pixel 0.304,0.295,0.304, shown at level 1.55, step 1, values float32 Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 82,84,80, pixel 0.304,0.295,0.304, shown at level -0.691,0.691, step 1, values float32 Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 82,84,80, pixel 0.304,0.295,0.304, shown at level 1.53, step 1, values float32 9rr6 title: Galectin-3 with a bound inhibitor [more info...] 86 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 1363 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Chain information for 9rr6 #1.2 --- Chain | Description | UniProt A | Galectin-3 | LEG3_HUMAN 113-250 Non-standard residues in 9rr6 #1.2 --- A1JIR — (2~{S})-2-[4,4-bis(fluoranyl)-1-oxidanyl- cyclohexyl]-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3-methoxy-5-oxidanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-2-yl]sulfanyl-~{N}-methyl-~{N}-pyridin-2-yl- ethanamide DMS — dimethyl sulfoxide SCN — thiocyanate ion > ui tool show ""Selection Inspector"" > ui tool show ""Altloc Explorer"" > hbonds /A:127,129,140-141,168,194,205,208,220,241 & @@num_alt_locs>1 > interModel false reveal true name ""altloc H-bonds"" updateGroup true 29 hydrogen bonds found > ui tool show ""Altloc Explorer"" > hbonds /A:127,129,140-141,168,194,205,208,220,241 & @@num_alt_locs>1 > interModel false reveal true name ""altloc H-bonds"" updateGroup true 29 hydrogen bonds found > show /A:127 > view /A:127 > show /A:129 > view /A:129 > altlocs change A /A:129 Changed /A ARG 129 to alternate location A > hbonds /A:129 & @@num_alt_locs>1 interModel false reveal true name ""altloc > H-bonds"" updateGroup true 2 hydrogen bonds found > altlocs change B /A:129 Changed /A ARG 129 to alternate location B > hbonds /A:129 & @@num_alt_locs>1 interModel false reveal true name ""altloc > H-bonds"" updateGroup true 3 hydrogen bonds found > ui tool show Shell 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. > show /A:140 > view /A:140 > altlocs change B /A:140 Changed /A PRO 140 to alternate location B > hbonds /A:141 & @@num_alt_locs>1 interModel false reveal true name ""altloc > H-bonds"" updateGroup true 0 hydrogen bonds found > hbonds /A:140 & @@num_alt_locs>1 interModel false reveal true name ""altloc > H-bonds"" updateGroup true 1 hydrogen bonds found > altlocs change A /A:140 Changed /A PRO 140 to alternate location A > hbonds /A:141 & @@num_alt_locs>1 interModel false reveal true name ""altloc > H-bonds"" updateGroup true 0 hydrogen bonds found > hbonds /A:140 & @@num_alt_locs>1 interModel false reveal true name ""altloc > H-bonds"" updateGroup true 3 hydrogen bonds found > close #1.1.1.5-7 > select clear > select /A:140@CG 1 atom, 1 residue, 1 model selected > ui tool show ""Selection Inspector"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1400, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\sel_inspector\\__init__.py"", line 32, in start_tool return SelInspector(session, tool_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\sel_inspector\tool.py"", line 73, in __init__ self._new_items() File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\sel_inspector\tool.py"", line 141, in _new_items self._menu_cb() File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\sel_inspector\tool.py"", line 110, in _menu_cb self.refresh() File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\sel_inspector\tool.py"", line 190, in refresh option.display_for_items(items) File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\ui\options\options.py"", line 137, in display_for_items self.value = value ^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\ui\options\options.py"", line 323, in set_value self.widget.setChecked(value) TypeError: setChecked(self, a0: bool): argument 1 has unexpected type 'numpy.bool' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1956, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\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-Daily\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 246, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Selection Inspector in bundle ChimeraX-SelInspector: setChecked(self, a0: bool): argument 1 has unexpected type 'numpy.bool' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Selection Inspector in bundle ChimeraX-SelInspector: setChecked(self, a0: bool): argument 1 has unexpected type 'numpy.bool' File ""C:\Program Files\ChimeraX-Daily\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 610.62 OpenGL renderer: NVIDIA GeForce RTX 5070 Ti Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.15 Locale: en_GB.cp1252 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: windows Manufacturer: LENOVO Model: 83LU OS: Microsoft Windows 11 Pro (Build 26200.8655) Memory: 33,752,997,888 MaxProcessMemory: 137,438,953,344 CPU: 24 Intel(R) Core(TM) Ultra 9 275HX OSLanguage: en-US Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.7.1 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.14.1 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 autocommand: 2.2.2 babel: 2.18.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.8.0 build: 1.5.0 certifi: 2026.6.17 cftime: 1.6.5 charset-normalizer: 3.4.9 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.3.1 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.70.1 ChimeraX-AtomicLibrary: 14.4.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Clipper: 0.28.dev0 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.13.dev202607100053 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.6 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.2 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: 1.4.1 ChimeraX-Hbonds: 2.5.4 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.4 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 ChimeraX-Map: 1.3 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-MatchAlign: 1.2.1 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19.2 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.4.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.17 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.24 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.16.2 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.10.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.19.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.20 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.53.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.5 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.4.2 colorama: 0.4.6 comm: 0.2.3 comtypes: 1.4.11 contourpy: 1.3.3 coverage: 7.15.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.21 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 1.0.1 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h2: 4.3.0 h5py: 3.16.0 hpack: 4.2.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 hyperframe: 6.1.0 idna: 3.18 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 importlib_metadata: 8.7.1 iniconfig: 2.3.0 ipykernel: 7.3.0 ipython: 9.14.1 ipython_pygments_lexers: 1.1.1 jaraco.context: 6.1.0 jaraco.functools: 4.4.0 jaraco.text: 4.0.0 jedi: 0.20.0 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.9.1 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 markdown-it-py: 4.2.0 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.18.0 mdurl: 0.1.2 more-itertools: 10.8.0 msgpack: 1.1.1 multidict: 6.7.1 ndindex: 1.10.1 nest-asyncio2: 1.7.2 netCDF4: 1.7.4 networkx: 3.3 numexpr: 2.14.1 numpy: 2.4.6 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.4.0 OpenMM-CUDA-12: 8.4.0 openvr: 1.26.701 packaging: 25.0 packaging: 26.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 11.3.0 pip: 26.1.2 pkginfo: 1.12.1.2 platformdirs: 4.10.0 platformdirs: 4.4.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.2 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.20.0 Pygments: 2.18.0 pynmrstar: 3.5.1 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.1.1 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.32 pywin32: 311 pyzmq: 27.1.0 qtconsole: 5.7.2 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 rich: 15.0.0 roman-numerals: 4.1.0 rpds-py: 2026.6.3 scipy: 1.17.1 setuptools: 82.0.1 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.8.4 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.5 stack-data: 0.6.3 starlette: 1.3.1 superqt: 0.7.6 tables: 3.11.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tomli: 2.4.0 tornado: 6.5.7 traitlets: 5.15.1 typing-inspection: 0.4.2 typing_extensions: 4.16.0 urllib3: 2.7.0 uv: 0.11.26 uvicorn: 0.51.0 wcwidth: 0.8.2 webcolors: 24.11.1 wheel: 0.47.0 wheel: 0.46.3 wheel-filename: 1.4.2 WMI: 1.5.1 yarl: 1.24.2 zipp: 3.23.0 }}} " defect closed normal Window Toolkit fixed chimera-programmers all ChimeraX