Opened 22 months ago

Closed 22 months ago

#10370 closed defect (duplicate)

ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/aleja/Documents/Work/PhD/Projects/TAAR1/Partial-
> agonist/cryoEM-8jlp/8jlp.pdb

8jlp.pdb title:  
Ralmitaront(ro-6889450)-bound HTAAR1-GS protein complex [more info...]  
  
Chain information for 8jlp.pdb #1  
---  
Chain | Description  
A | GS  
B | transducin β chain 1  
R | soluble cytochrome B562,trace amine-associated receptor 1  
Y | G γ-I  
  
Non-standard residues in 8jlp.pdb #1  
---  
UJU —
5-ethyl-4-methyl-~{N}-[4-[(2~{S})-morpholin-2-yl]phenyl]-1~{H}-pyrazole-3-carboxamide
(ralmitaront)  
  

> open C:/Users/aleja/Documents/Work/PhD/Projects/TAAR1/Partial-
> agonist/cryoEM-8jlp/emd_36403.map

Opened emd_36403.map as #2, grid size 256,256,256, pixel 0.85, shown at level
0.111, step 1, values float32  

> volume #2 style mesh

> volume #2 color #0ab2a4

> volume #2 level 0.2493

> volume #2 level 0.3214

> ui tool show ISOLDE

> set selectionWidth 4

8jlp.pdb title:  
Ralmitaront(ro-6889450)-bound HTAAR1-GS protein complex [more info...]  
  
Chain information for 8jlp.pdb  
---  
Chain | Description  
1.2/A | GS  
1.2/B | transducin β chain 1  
1.2/R | soluble cytochrome B562,trace amine-associated receptor 1  
1.2/Y | G γ-I  
  
Non-standard residues in 8jlp.pdb #1.2  
---  
UJU —
5-ethyl-4-methyl-~{N}-[4-[(2~{S})-morpholin-2-yl]phenyl]-1~{H}-pyrazole-3-carboxamide
(ralmitaront)  
  
Done loading forcefield  
Opened emd_36403.map as #1.1.1.1, grid size 256,256,256, pixel 0.85, shown at
step 1, values float32  
Please select a single atom!  
Please select a single atom!  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open C:/Users/aleja/Documents/Work/PhD/Projects/TAAR1/Partial-
> agonist/cryoEM-8jlp/emd_36403.map

Opened emd_36403.map as #2, grid size 256,256,256, pixel 0.85, shown at level
0.111, step 1, values float32  
Opened emd_36403.map as #1.1.1.2, grid size 256,256,256, pixel 0.85, shown at
step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1152-1920-292 (frame:
1936x1191-1928-323) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY7". Resulting geometry: 1920x1057-1920-292 (frame:
1936x1096-1928-323) margins: 8, 31, 8, 8 minimum size: 394x1152 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=410,1191 maxtrack=0,0)  

Please select a single residue!  

> addh

Summary of feedback from adding hydrogens to 8jlp.pdb #1.2  
---  
warnings | Not adding hydrogens to /A ARG 258 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 259 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 260 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASN 261 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLN 262 CB because it is missing heavy-atom bond
partners  
2 messages similar to the above omitted  
notes | Termini for 8jlp.pdb (#1.2) chain A determined from SEQRES records  
Termini for 8jlp.pdb (#1.2) chain B determined from SEQRES records  
Termini for 8jlp.pdb (#1.2) chain R determined from SEQRES records  
Termini for 8jlp.pdb (#1.2) chain Y determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A ARG 13, /A SER 205,
/B GLU 3, /R SER 19, /R GLU 246, /Y THR 6  
Chain-final residues that are actual C termini: /A LEU 394, /B ASN 340  
Chain-final residues that are not actual C termini: /A ILE 62, /R GLN 229, /R
LEU 319, /Y GLU 63  
Missing OXT added to C-terminal residue /A LEU 394  
Missing OXT added to C-terminal residue /B ASN 340  
704 hydrogen bonds  
Adding 'H' to /A ARG 13  
Adding 'H' to /A SER 205  
Adding 'H' to /B GLU 3  
Adding 'H' to /R SER 19  
Adding 'H' to /R GLU 246  
1 messages similar to the above omitted  
/R LEU 319 is not terminus, removing H atom from 'C'  
/Y GLU 63 is not terminus, removing H atom from 'C'  
7276 hydrogens added  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "C:\Users\aleja\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\isolde\isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.98
OpenGL renderer: NVIDIA GeForce RTX 3080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Zephyrus Duo 15 SE GX551QS_GX551QS
OS: Microsoft Windows 11 Pro (Build 22000)
Memory: 33,722,601,472
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics        
OSLanguage: en-GB
Locale: ('es_CO', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-clipper: 0.16.0
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    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-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    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: 1.1.3
    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-ISOLDE: 1.2.2
    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: 1.2.1
    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: 1.0.1
    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: 1.7.6
    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: 5.0.9
    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: 2.0.1
    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: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    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 Eric Pettersen, 22 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted

comment:2 by Eric Pettersen, 22 months ago

Resolution: → duplicate
Status: assigned → closed

Old versions of ChimeraX and ISOLDE

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