ISOLDE: close session: 'AtomicStructure' object has no attribute '_c_pointer_ref'

[maf95@…]

The following bug report has been submitted:
Platform:        macOS-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
I had to remove two site-directory packages in order to install iSOLDE as pointed out at https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-September/002690.html 

iSOLDE now runs, but now this error pops up.

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/markfrank/Desktop/iSOLDE/6wlb_emd21820.cxs format session

Opened emd_21820.map as #1.1.1.1, grid size 340,340,340, pixel 1.08, shown at
level 0.55, step 1, values float32  
Log from Wed Nov 30 07:35:16 2022 Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/markfrank/Downloads/6wlb.pdb

6wlb.pdb title:  
Structure of homotrimeric poplar cellulose synthase isoform 8 [more info...]  
  
Chain information for 6wlb.pdb #1  
---  
Chain | Description | UniProt  
A B C | cellulose synthase | Q6J8X0_POPPZ  
  
Non-standard residues in 6wlb.pdb #1  
---  
BGC — β-D-glucopyranose (β-D-glucose; D-glucose; glucose)  
  

> addh

Summary of feedback from adding hydrogens to 6wlb.pdb #1  
---  
notes | Termini for 6wlb.pdb (#1) chain A determined from SEQRES records  
Termini for 6wlb.pdb (#1) chain B determined from SEQRES records  
Termini for 6wlb.pdb (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLU 157, /A SER 610,
/A VAL 869, /B GLU 157, /B SER 610, /B VAL 869, /C GLU 157, /C SER 610, /C VAL
869  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PRO 549, /A GLY 846, /A
ASN 958, /B PRO 549, /B GLY 846, /B ASN 958, /C PRO 549, /C GLY 846, /C ASN
958  
1331 hydrogen bonds  
Adding 'H' to /A GLU 157  
Adding 'H' to /A SER 610  
Adding 'H' to /B GLU 157  
Adding 'H' to /B SER 610  
Adding 'H' to /C GLU 157  
1 messages similar to the above omitted  
/A ASN 958 is not terminus, removing H atom from 'C'  
/B ASN 958 is not terminus, removing H atom from 'C'  
/C ASN 958 is not terminus, removing H atom from 'C'  
555 hydrogens added  
  

> save /Users/markfrank/Desktop/DARC/pdbs/6wlb_H.pdb relModel #1

> open /Users/markfrank/Downloads/emd_21820.map

Opened emd_21820.map as #2, grid size 340,340,340, pixel 1.08, shown at level
0.137, step 2, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

Populating font family aliases took 138 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 187 residues in model #1 to IUPAC-IUB
standards.  
6wlb.pdb title:  
Structure of homotrimeric poplar cellulose synthase isoform 8 [more info...]  
  
Chain information for 6wlb.pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C | cellulose synthase | Q6J8X0_POPPZ  
  
Non-standard residues in 6wlb.pdb #1.2  
---  
BGC — β-D-glucopyranose (β-D-glucose; D-glucose; glucose)  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  

> clipper associate #2 toModel #1

Opened emd_21820.map as #1.1.1.1, grid size 340,340,340, pixel 1.08, shown at
step 1, values float32  

> isolde sim start sel

ISOLDE: stopped sim  

> select /A

11557 atoms, 11725 bonds, 2 pseudobonds, 720 residues, 2 models selected  

> select ::name="BGC"

324 atoms, 336 bonds, 15 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> close session

> open /Users/markfrank/Desktop/DARC/pdbs/6wlb_H.pdb format pdb

No such file/path: /Users/markfrank/Desktop/DARC/pdbs/6wlb_H.pdb  

> open /Users/markfrank/Desktop/DARC/pdbs/6wlb_H.pdb format pdb

No such file/path: /Users/markfrank/Desktop/DARC/pdbs/6wlb_H.pdb  

> open /Users/markfrank/Downloads/6wlb.pdb format pdb

6wlb.pdb title:  
Structure of homotrimeric poplar cellulose synthase isoform 8 [more info...]  
  
Chain information for 6wlb.pdb #1  
---  
Chain | Description | UniProt  
A B C | cellulose synthase | Q6J8X0_POPPZ  
  
Non-standard residues in 6wlb.pdb #1  
---  
BGC — β-D-glucopyranose (β-D-glucose; D-glucose; glucose)  
  

> close session

> open /Users/markfrank/Desktop/DARC/pdbs/6wlb_Hyadded.pdb

6wlb_Hyadded.pdb title:  
Structure of homotrimeric poplar cellulose synthase isoform 8 [more info...]  
  
Chain information for 6wlb_Hyadded.pdb #1  
---  
Chain | Description | UniProt  
A B C | cellulose synthase | Q6J8X0_POPPZ  
  
Non-standard residues in 6wlb_Hyadded.pdb #1  
---  
BGC — β-D-glucopyranose (β-D-glucose; D-glucose; glucose)  
  

> select ::name="BGC"

324 atoms, 336 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open /Users/markfrank/Downloads/emd_21820.map

Opened emd_21820.map as #2, grid size 340,340,340, pixel 1.08, shown at level
0.137, step 2, values float32  

> log metadata #1

Metadata for 6wlb_Hyadded.pdb #1  
---  
Title | Structure of homotrimeric poplar cellulose synthase isoform 8  
Citation | Architecture of A catalytically active homotrimeric plantcellulose
synthase complex. PMID: 32646917  
Gene source | Populus tremula X populus tremuloides (hybrid aspen)  
Experimental method | Electron microscopy  
Resolution | 3.50Å  
  
> ui tool show ISOLDE

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 187 residues in model #1 to IUPAC-IUB
standards.  
6wlb_Hyadded.pdb title:  
Structure of homotrimeric poplar cellulose synthase isoform 8 [more info...]  
  
Chain information for 6wlb_Hyadded.pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C | cellulose synthase | Q6J8X0_POPPZ  
  

> clipper associate #2 toModel #1

Opened emd_21820.map as #1.1.1.1, grid size 340,340,340, pixel 1.08, shown at
step 1, values float32  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> save "/Users/markfrank/Desktop/New Folder/iSOLDE_6wlb_map.cxs"

[Errno 20] Not a directory: '/Users/markfrank/Desktop/New Folder'  

> save /Users/markfrank/Desktop/iSOLDE/6wlb_emd21820.cxs

——— End of log from Wed Nov 30 07:35:16 2022 ———

opened ChimeraX session  

> ui tool show ISOLDE

> set selectionWidth 4

Populating font family aliases took 140 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> close session

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb  
sel = self.isolde.selected_atoms.unique_residues  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/Users/markfrank/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 2 days, 14 hours, 44 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        LU28R55:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-GenomeTools: 0.9
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ISOLDE: 1.5
    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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.7
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PhenixUI: 1.0.5
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RIBFIND: 0.2
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.3.1
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    SEQCROW: 1.5.9
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

Reported by Mark Frank.

User also had to manually deinstall UI bundle from the toolshed. Greg, please remove that bundle.

[Tristan Croll]

As of the next release, ISOLDE will now recover gracefully if the working model is closed while a simulation is active.