Opened 3 years ago
Closed 3 years ago
#8310 closed defect (duplicate)
MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "C:/Users/levi0/OneDrive - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005 - 副本 - 副本 (2).pdb" > "C:/Users/levi0/OneDrive - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005 - 副本 - 副本.pdb" > "C:/Users/levi0/OneDrive - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005 - 副本.pdb" "C:/Users/levi0/OneDrive > - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005.pdb" Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005 - 副本 - 副本 (2).pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005 - 副本 - 副本.pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005 - 副本.pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005.pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Chain information for six_layer4_real_space_refined_005 - 副本 - 副本 (2).pdb #1 --- Chain | Description A C E G I K | No description available B D F H J L | No description available Chain information for six_layer4_real_space_refined_005 - 副本 - 副本.pdb #2 --- Chain | Description A C E G I K | No description available B D F H J L | No description available Chain information for six_layer4_real_space_refined_005 - 副本.pdb #3 --- Chain | Description A C E G I K | No description available B D F H J L | No description available Chain information for six_layer4_real_space_refined_005.pdb #4 --- Chain | Description A C E G I K | No description available B D F H J L | No description available > set bgColor gray > ui tool show Matchmaker > matchmaker #3/A to #4/K pairing ss 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 six_layer4_real_space_refined_005.pdb, chain K (#4) with six_layer4_real_space_refined_005 - 副本.pdb, chain A (#3), sequence alignment score = 209 RMSD between 39 pruned atom pairs is 0.001 angstroms; (across all 39 pairs: 0.001) > matchmaker #2/A to #3/K pairing ss 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 six_layer4_real_space_refined_005 - 副本.pdb, chain K (#3) with six_layer4_real_space_refined_005 - 副本 - 副本.pdb, chain A (#2), sequence alignment score = 209 RMSD between 39 pruned atom pairs is 0.001 angstroms; (across all 39 pairs: 0.001) Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "changes": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > matchmaker #1/A to #2/K pairing ss 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 six_layer4_real_space_refined_005 - 副本 - 副本.pdb, chain K (#2) with six_layer4_real_space_refined_005 - 副本 - 副本 (2).pdb, chain A (#1), sequence alignment score = 209 RMSD between 39 pruned atom pairs is 0.001 angstroms; (across all 39 pairs: 0.001) Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "changes": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "changes": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > open "C:/Users/levi0/OneDrive - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005 - 副本 - 副本 (3).pdb" > "C:/Users/levi0/OneDrive - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005 - 副本 - 副本 (4).pdb" > "C:/Users/levi0/OneDrive - University of Texas Southwestern/INS > project/six_layer4_real_space_refined_005 - 副本 - 副本 (5).pdb" Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005 - 副本 - 副本 (3).pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005 - 副本 - 副本 (4).pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Summary of feedback from opening C:/Users/levi0/OneDrive - University of Texas Southwestern/INS project/six_layer4_real_space_refined_005 - 副本 - 副本 (5).pdb --- warnings | Ignored bad PDB record found on line 718 TER Ignored bad PDB record found on line 1184 TER Ignored bad PDB record found on line 1779 TER Ignored bad PDB record found on line 2245 TER Ignored bad PDB record found on line 2840 TER 7 messages similar to the above omitted Chain information for six_layer4_real_space_refined_005 - 副本 - 副本 (3).pdb #5 --- Chain | Description A C E G I K | No description available B D F H J L | No description available Chain information for six_layer4_real_space_refined_005 - 副本 - 副本 (4).pdb #6 --- Chain | Description A C E G I K | No description available B D F H J L | No description available Chain information for six_layer4_real_space_refined_005 - 副本 - 副本 (5).pdb #7 --- Chain | Description A C E G I K | No description available B D F H J L | No description available Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "add models": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "add models": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "changes": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger "changes": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File "D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 526.98 OpenGL renderer: NVIDIA GeForce GTX 1660/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 Pro (Build 19044) Memory: 34,286,243,840 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9400F CPU @ 2.90GHz" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 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 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 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: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 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: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 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: 2.0 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: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 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 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 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 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: 1.2.3 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: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 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: 2020.6.3 tinyarray: 1.2.2 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 , 3 years ago
Component: | Unassigned → Structure Analysis |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 3 years ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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