Opened 3 years ago
Closed 3 years ago
#6861 closed defect (can't reproduce)
Color Key: wrapped C/C++ object of type QDockWidget has been deleted
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | UI | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/amar/Desktop/JetABC_Head_structures/Maps/JetC_DNA_Isolde_saved.pdb Summary of feedback from opening /Users/amar/Desktop/JetABC_Head_structures/Maps/JetC_DNA_Isolde_saved.pdb --- warnings | CONECT record for nonexistent atom: 7029 Cannot find LINK/SSBOND residue AGS (1101 ) Chain information for JetC_DNA_Isolde_saved.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available P | No description available Q | No description available > hide cartoons > open > /Users/amar/Desktop/JetABC_Head_structures/Maps/P22J312_JetC_head_final_sharp.mrc Opened P22J312_JetC_head_final_sharp.mrc as #2, grid size 300,300,300, pixel 1.1, shown at level 0.00228, step 2, values float32 > volume #2 step 1 > volume #2 level 0.07197 > ui tool show ISOLDE > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for JetC_DNA_Isolde_saved.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/P | No description available 1.2/Q | No description available Done loading forcefield Opened P22J312_JetC_head_final_sharp.mrc as #1.1.1.1, grid size 300,300,300, pixel 1.1, shown at step 1, values float32 > set bgColor white > select all 17280 atoms, 17560 bonds, 4 pseudobonds, 1057 residues, 13 models selected Populating font family aliases took 749 ms. Replace uses of missing font family "Carlito" with one that exists to avoid this cost. ISOLDE: started sim ISOLDE: resumed sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select up 86 atoms, 87 bonds, 6 residues, 1 model selected > select up 7027 atoms, 7090 bonds, 455 residues, 1 model selected > select down 86 atoms, 87 bonds, 6 residues, 1 model selected > select /A:886 20 atoms, 20 bonds, 1 residue, 1 model selected > select /A:887 17 atoms, 16 bonds, 1 residue, 1 model selected ISOLDE: started sim > select /A:887 17 atoms, 16 bonds, 1 residue, 1 model selected ISOLDE: paused sim ISOLDE: resumed sim > select /A:886 20 atoms, 20 bonds, 1 residue, 1 model selected ISOLDE: paused sim ISOLDE: resumed sim > select /A:888 14 atoms, 14 bonds, 1 residue, 1 model selected ISOLDE: paused sim ISOLDE: resumed sim ISOLDE: paused sim ISOLDE: resumed sim > select all 17280 atoms, 17560 bonds, 4 pseudobonds, 1057 residues, 19 models selected ISOLDE: paused sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim > volume sel style surface > transparency sel 50 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/amar/Desktop/JetC_DNA.pdb > select clear > select up 426 atoms, 427 bonds, 26 residues, 1 model selected ISOLDE: started sim > select 17280 atoms, 17560 bonds, 4 pseudobonds, 1057 residues, 19 models selected > select /B:857-883 440 atoms, 441 bonds, 27 residues, 1 model selected ISOLDE: paused sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /B:857-883 440 atoms, 441 bonds, 27 residues, 1 model selected ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /B:857 14 atoms, 13 bonds, 1 residue, 1 model selected > cview /B:857 [Repeated 1 time(s)] > select /B:857 14 atoms, 13 bonds, 1 residue, 1 model selected ISOLDE: started sim > ui mousemode right "color key" > ui mousemode right ISOLDE_mouse_tug > mousemode rightMode ISOLDE_mouse_tug Invalid "rightMode" argument: Should be one of 'bond rotation', 'clip', 'clip rotate', 'color key', 'contour level', 'crop volume', 'delete markers', 'distance', 'identify object', 'label', 'link markers', 'map eraser', 'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface', 'minimize', 'move label', 'move markers', 'move picked models', 'move planes', 'next docked', 'none', 'pick blobs', 'pivot', 'play coordinates', 'play map series', 'resize markers', 'rotate', 'rotate and select', 'rotate selected atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models', 'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe as scroll', 'tape measure', 'translate', 'translate selected atoms', 'translate selected models', 'translate xy selected models', 'tug', 'windowing', 'zone', or 'zoom' > ui mousemode right swapaa > swapaa mousemode /B:858 GLN ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim Traceback (most recent call last): File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 381, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/color_key/__init__.py", line 41, in run_provider run(session,"ui tool show 'Color Key'", log=False) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2856, in run result = ci.function(session, **kw_args) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py", line 210, in ui_tool_show ti.display(_show) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tools.py", line 174, in display self.session.ui.thread_safe( File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 382, in thread_safe func(*args, **kw) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tools.py", line 175, in <lambda> lambda s=self, show=b: s.session.ui.set_tool_shown(s, show)) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 364, in set_tool_shown self.main_window.set_tool_shown(tool_instance, shown) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 805, in set_tool_shown tool_windows[0].shown = shown File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 2095, in shown ui.main_window._tool_window_request_shown(self, shown) File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1885, in _tool_window_request_shown if shown and not tool_window.floating: File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1994, in _get_floating return self.__toolkit.dock_widget.isFloating() RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted File "/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1994, in _get_floating return self.__toolkit.dock_widget.isFloating() See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.15 OpenGL renderer: AMD Radeon Pro 450 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro13,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 447.80.3.0.0 OS Loader Version: 540.100.7~23 SMC Version (system): 2.38f12 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 8 days 14:31 Graphics/Displays: Intel HD Graphics 530: Chipset Model: Intel HD Graphics 530 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x191b Revision ID: 0x0006 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal Family: Supported, Metal GPUFamily macOS 2 Radeon Pro 450: Chipset Model: AMD Radeon Pro 450 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00ef ROM Revision: 113-C980AF-908 VBIOS Version: 113-C9801AL-028 EFI Driver Version: 01.A0.908 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → UI |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Color Key: wrapped C/C++ object of type QDockWidget has been deleted |
comment:2 by , 3 years ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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