wrapped C/C++ object of type DICOMTable has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> select clear

> select ::name="MOL"::name="NA"::name="SOL"

111267 atoms, 74201 bonds, 37071 residues, 1 model selected  

> select ::name="SOL"

111171 atoms, 74114 bonds, 37057 residues, 1 model selected  

> select down

111171 atoms, 74114 bonds, 37057 residues, 1 model selected  

> select ::name="SOL"

111171 atoms, 74114 bonds, 37057 residues, 1 model selected  

> ui tool show "Selection Inspector"

> delete atoms sel

> delete bonds sel

> select ::name="NA"

13 atoms, 13 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select :mol

83 atoms, 87 bonds, 1 residue, 1 model selected  

> ui tool show "DICOM Browser"

Pick at least one series to show metadata  

> toolshed show

> view sel

> hide ~sel

> ui tool show H-Bonds

> hbonds reveal true

614 hydrogen bonds found  

> undo

[Repeated 3 time(s)]Undo failed, probably because structures have been
modified.  

> open D:\Users\GMX\200.pdb format pdb

Summary of feedback from opening D:\Users\GMX\200.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
200.pdb title:  
Protein in water t= 199980.00000 step= 99990000 [more info...]  
  
Chain information for 200.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 200.pdb #2  
---  
MOL — (MOL)  
NA — (NA)  
SOL — (SOL)  
  

> close session

> surface cap mesh false

> open D:/Users/GMX/200.pdb

Summary of feedback from opening D:/Users/GMX/200.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
200.pdb title:  
Protein in water t= 199980.00000 step= 99990000 [more info...]  
  
Chain information for 200.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 200.pdb #1  
---  
MOL — (MOL)  
NA — (NA)  
SOL — (SOL)  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_browser.py", line 137, in <lambda>  
ADD_MODELS, lambda *args: self._add_patient(*args)  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_browser.py", line 176, in _add_patient  
self._resync_tables()  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_browser.py", line 179, in
_resync_tables  
self.patient_table.data = []  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 477, in data  
emit_signal = self.selected  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 571, in selected  
for i in self.selectionModel().selectedRows()]  
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted  
  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 571, in selected  
for i in self.selectionModel().selectedRows()]  
  
See log for complete Python traceback.  
  
Drag select of 119 atoms, 76 bonds  
Drag select of 129 atoms, 8 residues, 82 bonds  
Drag select of 133 atoms, 88 bonds  
Drag select of 101 atoms, 64 bonds  

> delete atoms sel

> delete bonds sel

Drag select of 70 atoms, 46 bonds  
Drag select of 106 atoms, 68 bonds  

> delete atoms sel

> delete bonds sel

> select ::name="SOL"

110973 atoms, 73982 bonds, 36991 residues, 1 model selected  

> open D:/Users/GMX/200.pdb

Summary of feedback from opening D:/Users/GMX/200.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
200.pdb title:  
Protein in water t= 199980.00000 step= 99990000 [more info...]  
  
Chain information for 200.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 200.pdb #2  
---  
MOL — (MOL)  
NA — (NA)  
SOL — (SOL)  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_browser.py", line 137, in <lambda>  
ADD_MODELS, lambda *args: self._add_patient(*args)  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_browser.py", line 176, in _add_patient  
self._resync_tables()  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_browser.py", line 179, in
_resync_tables  
self.patient_table.data = []  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 477, in data  
emit_signal = self.selected  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 571, in selected  
for i in self.selectionModel().selectedRows()]  
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted  
  
File "D:\Program Files (x86)\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\item_table.py", line 571, in selected  
for i in self.selectionModel().selectedRows()]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 532.10
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82WK
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,907,100,160
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
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    ChimeraX-MMTF: 2.2
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    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
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    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
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    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
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    comm: 0.1.3
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    h5py: 3.8.0
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    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
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    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
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    line-profiler: 4.0.2
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    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Zach Pearson]

Should have been fixed by ​this commit. User was on 1.6.1, issue should not affect 1.7 or later.