Opened 2 years ago
Closed 2 years ago
#10227 closed defect (duplicate)
'Tasks' object has no attribute 'remove'
Reported by: | Owned by: | Zach Pearson | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Task Manager/Web Services | 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: 1.4 (2022-06-03 23:39:42 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/itsadmin/Downloads/7l0q.pdb 7l0q.pdb title: Structure of NTS-NTSR1-gi complex In lipid nanodisc, canonical state, with ahd [more info...] Chain information for 7l0q.pdb #1 --- Chain | Description | UniProt A | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN B | transducin β chain 1 | GBB1_HUMAN C | neurotensin receptor type 1 | NTR1_RAT D | neurotensin | NEUT_RAT G | transducin γ chain | GBG1_HUMAN > select /D 58 atoms, 59 bonds, 6 residues, 1 model selected > ui tool show "Model Loops" > select ~sel 7798 atoms, 7950 bonds, 5 pseudobonds, 996 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > ui tool show "Show Sequence Viewer" > sequence chain /D Alignment identifier is 1/D > modeller refine 1/D:1:all-missing numModels 1 fast false adjacentFlexible 1 > protocol standard Webservices job id: SCTTOJXYXXK5J62M Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags<Qt::KeyboardModifier>(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with QFlags<Qt::KeyboardModifier>(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier) Destroying pre-existing alignment with identifier 1/D Alignment identifier is 1/D > ui tool show "Modeller Comparative" > modeller comparative 1/D:1 numModels 1 fast false multichain true > hetPreserve false hydrogens false waterPreserve false Webservices job id: BKWNQK1O41YVVTTN Modeller job ID BKWNQK1O41YVVTTN finished Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7l0q.pdb, chain D (#1) with chain_D, chain D (#), sequence alignment score = 29.6 RMSD between 6 pruned atom pairs is 0.942 angstroms; (across all 6 pairs: 0.942) Associated chain_D chain D to chain D with 0 mismatches and/or gaps Chain information for chain_D --- Chain | Description 2.1/D | No description available > ui tool show "Build Structure" > ui tool show Rotamers > toolshed show > ui tool show AlphaFold > alphafold match #1 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json Fetching compressed AlphaFold P20068 from https://alphafold.ebi.ac.uk/files/AF-P20068-F1-model_v2.cif 1 AlphaFold model found using UniProt identifier: P20068 (chain D) AlphaFold chains matching 7l0q.pdb --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id D | NEUT_RAT | P20068 | 2.50 | 6 | 6 | 100 Opened 1 AlphaFold model > alphafold search #1 Webservices job id: M9QM4A5C7CGTIAKZ BLAST search returned no results. > alphafold predict #1 Running AlphaFold prediction > show target ab > view #3.1 clip false > show #!2 target m > view #3 clip false [Repeated 1 time(s)] > hide #!2 target m > hide #!1 target m > show #!2 target m > show #2.1 target m [Repeated 1 time(s)] > show #!3 target m [Repeated 1 time(s)] > view #3 clip false [Repeated 2 time(s)] > show #!1 target m > hide #!2 target m > show #!2 target m > view #2 clip false [Repeated 1 time(s)] Populating font family aliases took 349 ms. Replace uses of missing font family ".AppleSystemUIFont" with one that exists to avoid this cost. > save /Users/itsadmin/Desktop/123456.pdb models #3 > save /Users/itsadmin/Desktop/1234567.pdb models #2 > close session Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1051, in <lambda> close_action.triggered.connect(lambda *, s=self, sess=session: s.file_close_cb(sess)) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 700, in file_close_cb run(session, 'close session') File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2897, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/close.py", line 60, in close_session session.reset() File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 541, in reset sm.reset_state(container, self) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tasks.py", line 547, in reset_state task.terminate() File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tasks.py", line 155, in terminate self.session.tasks.remove(self) AttributeError: 'Tasks' object has no attribute 'remove' AttributeError: 'Tasks' object has no attribute 'remove' File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tasks.py", line 155, in terminate self.session.tasks.remove(self) See log for complete Python traceback. > close session Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1051, in <lambda> close_action.triggered.connect(lambda *, s=self, sess=session: s.file_close_cb(sess)) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 700, in file_close_cb run(session, 'close session') File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2897, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/close.py", line 60, in close_session session.reset() File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 541, in reset sm.reset_state(container, self) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tasks.py", line 547, in reset_state task.terminate() File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tasks.py", line 155, in terminate self.session.tasks.remove(self) AttributeError: 'Tasks' object has no attribute 'remove' AttributeError: 'Tasks' object has no attribute 'remove' File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tasks.py", line 155, in terminate self.session.tasks.remove(self) See log for complete Python traceback. OpenGL version: 4.1 INTEL-20.6.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 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: 8 GB System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0) OS Loader Version: 577.140.2~15 Software: System Software Overview: System Version: macOS 13.6.1 (22G313) Kernel Version: Darwin 22.6.0 Time since boot: 4天9小时37分钟 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 2 years ago
Component: | Unassigned → Task Manager/Web Services |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → 'Tasks' object has no attribute 'remove' |
comment:2 by , 2 years ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
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