Opened 4 years ago
Closed 4 years ago
#5014 closed defect (duplicate)
MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Comparison | 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: 1.2 (2021-04-27 05:33:30 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2 (2021-04-27) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\\\Users\\\sjone\\\Downloads\\\1ydy.pdb 1ydy.pdb title: Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from escherichia coli [more info...] Chain information for 1ydy.pdb #1 --- Chain | Description A B | glycerophosphodiester phosphodiesterase Non-standard residues in 1ydy.pdb #1 --- CA — calcium ion GOL — glycerol (glycerin; propane-1,2,3-triol) > open "C:/Users/sjone/Downloads/PDBe _ PISA _ EMBL-EBI.html" Opened PDBe _ PISA _ EMBL-EBI.html > open "C:/Users/sjone/Desktop/PD PISA output.txt" Unrecognized file suffix '.txt' > open "C:/Users/sjone/Desktop/PD PISA output.pdb" Summary of feedback from opening C:/Users/sjone/Desktop/PD PISA output.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 5496 messages similar to the above omitted Chain information for PD PISA output.pdb #2 --- Chain | Description A D | No description available > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb 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 1ydy.pdb, chain A (#1) with PD PISA output.pdb, chain A (#2), sequence alignment score = 1329.8 RMSD between 313 pruned atom pairs is 0.741 angstroms; (across all 328 pairs: 1.007) > matchmaker #2 to #1 Parameters --- Chain pairing | bb 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 1ydy.pdb, chain A (#1) with PD PISA output.pdb, chain A (#2), sequence alignment score = 1329.8 RMSD between 313 pruned atom pairs is 0.741 angstroms; (across all 328 pairs: 1.007) > select #2/D:51@CB 1 atom, 1 residue, 1 model selected > select #2/D:157 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/D:195 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/B:208 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Matchmaker > hide #!1 models > open C:/Users/sjone/Downloads/4r7o.pdb 4r7o.pdb title: Crystal structure of putative glycerophosphoryl diester phosphodiesterasefrom bacillus anthraci [more info...] Chain information for 4r7o.pdb #3 --- Chain | Description A B C D E F G | putative glycerophosphoryl diester phosphodiesterase Non-standard residues in 4r7o.pdb #3 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion PEG — di(hydroxyethyl)ether SO4 — sulfate ion Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "C:\Program Files\ChimeraX 1.2\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 "C:\Program Files\ChimeraX 1.2\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. > hide #!3 models OpenGL version: 3.3.0 NVIDIA 465.89 OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Razer Model: Blade 15 Base Model (Early 2021) - RZ09-0369 OS: Microsoft Windows 10 Home (Build 19042) Memory: 17,036,509,184 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.3 ChimeraX-AtomicLibrary: 3.1.2 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: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 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-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.1 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: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 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: 1.2 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 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: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.3 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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: 5.0.7 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 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: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 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: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 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: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
Component: | Unassigned → Structure Comparison |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 4 years ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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