ISOLDE holding ref to deleted structure

[leofrancalima@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-47-generic-x86_64-with-glibc2.35
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 chain-A.pdb

Chain information for chain-A.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /srv/home/leonardo/Documents/From_Ewe_To_Leo/No-
> modification/onlyeIF2alpha.mrc

Opened onlyeIF2alpha.mrc as #2, grid size 81,91,84, pixel 1.1,1.1,1.1, shown
at level 0.0113, step 1, values float32  

> clipper associate #2 toModel #1

Opened onlyeIF2alpha.mrc as #1.1.1.1, grid size 81,91,84, pixel 1.1,1.1,1.1,
shown at level 0.012, step 1, values float32  
Chain information for chain-A.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 14 residues in model #1.2 to IUPAC-IUB
standards.  

> set bgColor white

> ui tool show "Ramachandran Plot"

> addh

Summary of feedback from adding hydrogens to chain-A.pdb #1.2  
---  
notes | No usable SEQRES records for chain-A.pdb (#1.2) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A CYS 6  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 271  
139 hydrogen bonds  
/A VAL 271 is not terminus, removing H atom from 'C'  
2194 hydrogens added  
  

> isolde restrain ligands

Missing or invalid "models" argument: empty atom specifier  

> isolde restrain ligands #1

> select #1

4340 atoms, 4371 bonds, 266 residues, 15 models selected  

> isolde sim start sel

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> isolde sim pause

> ui tool show "Ramachandran Plot"

> close

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb  
sel = self.isolde.selected_atoms.unique_residues  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       3.3Gi        19Gi       140Mi       8.1Gi        27Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)	
	Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    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-Clipper: 0.18.0
    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-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    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
    distro: 1.6.0
    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: 21.3
    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
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    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
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    setuptools: 59.8.0
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    tifffile: 2021.11.2
    tinyarray: 1.2.4
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    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
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    wheel: 0.37.1
    wheel-filename: 1.3.0