Crash in Residues.secondary_structure_ids

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001f0e25b40 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 197 in get_prop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 96 in _make_ribbon_graphics
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 589 in compute_ribbons
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 651 in _create_ribbon_graphics
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 347 in update_graphics_if_needed
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1809 in _update_graphics_if_needed
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138 in invoke
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 237 in _activate
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 206 in activate
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 283 in check_for_drawing_change
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
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  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,10",
  "coalitionID" : 5092,
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  "captureTime" : "2023-09-21 15:02:38.2125 -0700",
  "incident" : "5C9CB005-F208-4479-A059-4904159DD10A",
  "pid" : 41241,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-09-21 10:43:21.2148 -0700",
  "procStartAbsTime" : 622071472190,
  "procExitAbsTime" : 995437849648,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentProc" : "launchd",
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  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D897309D-33DF-108E-E503-53BC16DDF2D6",
  "throttleTimeout" : 2147483647,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
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  "wakeTime" : 21593,
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  "vmRegionInfo" : "0x208 is not in any region.  Bytes before following region: 105554055790072\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/tholenj/Library/CloudStorage/OneDrive-
> Personal/PhD/oligobuilding/604/604_Alike_4fit-coot-1.pdb

Summary of feedback from opening /Users/tholenj/Library/CloudStorage/OneDrive-
Personal/PhD/oligobuilding/604/604_Alike_4fit-coot-1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 9 9 SER A 400
ALA A 406 1 7  
Start residue of secondary structure not found: HELIX 91 91 THR F 31 LYS F 41
1 11  
Start residue of secondary structure not found: HELIX 92 92 ASP F 66 SER F 78
1 13  
Start residue of secondary structure not found: HELIX 93 93 ASN F 93 PHE F 98
1 6  
Start residue of secondary structure not found: SHEET 8 8 8 TYR A 412 VAL A
414 0  
6 messages similar to the above omitted  
  
Chain information for 604_Alike_4fit-coot-1.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
G | No description available  
h | No description available  
  

> open /Users/tholenj/Library/CloudStorage/OneDrive-
> Personal/PhD/oligobuilding/604/csJ235/cryosparc_P482_J246__localfilter_rescaled500px.mrc

Opened cryosparc_P482_J246__localfilter_rescaled500px.mrc as #2, grid size
498,498,498, pixel 0.325, shown at level 0.378, step 2, values float32  

> volume #2 step 1

> 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.  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
Done loading forcefield  
Removed all altlocs in #1 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 138 residues in model #1 to IUPAC-IUB
standards.  

Missing or corrupted symmetry information in the PDB file. This model will be
treated as a cryo-EM model until associated with an MTZ file containing
symmetry information.  

Chain information for 604_Alike_4fit-coot-1.pdb  
---  
Chain | Description  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/9 | No description available  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/E | No description available  
1.2/G | No description available  
1.2/h | No description available  
  
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 cryosparc_P482_J246__localfilter_rescaled500px.mrc as #1.1.1.1, grid
size 498,498,498, pixel 0.325, shown at step 1, values float32  

> volume #1.1.1.1 level 0.3782

> Sel 443-772

Unknown command: Sel 443-772  

> select 443-772

Expected an objects specifier or a keyword  

> select #1.2/443-772

Nothing selected  

> select #1.2/C.443-772

Expected an objects specifier or a keyword  

> select #1.2/C:443-772

2364 atoms, 2402 bonds, 4 pseudobonds, 306 residues, 2 models selected  

> select #1.2/A:1-1060

4511 atoms, 4588 bonds, 570 residues, 1 model selected  

> select

20232 atoms, 20435 bonds, 27 pseudobonds, 2747 residues, 18 models selected  

> addh

Summary of feedback from adding hydrogens to 604_Alike_4fit-coot-1.pdb #1.2  
---  
warnings | Not adding hydrogens to /1 LYS 76 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /1 LYS 77 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /2 G 33 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /9 HIS 433 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /9 ARG 436 CB because it is missing heavy-atom bond
partners  
20 messages similar to the above omitted  
notes | Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain 1 determined from
SEQRES records  
Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain 2 determined from SEQRES
records  
Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain 9 determined from SEQRES
records  
No usable SEQRES records for 604_Alike_4fit-coot-1.pdb (#1.2) chain A;
guessing termini instead  
Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain B determined from SEQRES
records  
Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain C determined from SEQRES
records  
Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain E determined from SEQRES
records  
Termini for 604_Alike_4fit-coot-1.pdb (#1.2) chain G determined from SEQRES
records  
No usable SEQRES records for 604_Alike_4fit-coot-1.pdb (#1.2) chain h;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 491, /C MET 1, /A GLU
491  
Chain-initial residues that are not actual N termini: /1 ASP 43, /9 TRP 395,
/B ASN 458, /B ILE 566, /B ASP 704, /C GLU 369, /C GLU 492, /C PHE 662, /C GLY
695, /C ARG 718, /C LEU 1076, /E SER 16, /G ALA 2  
Chain-final residues that are actual C termini: /A LEU 1304, /C PHE 1217, /A
LEU 1304  
Chain-final residues that are not actual C termini: /1 ALA 83, /9 TYR 492, /B
ARG 537, /B GLU 598, /B SER 714, /C GLY 365, /C GLY 488, /C MET 645, /C THR
691, /C MET 715, /C VAL 1066, /E ALA 80, /G VAL 89  
Chain-initial residues that are not actual 5' termini: /2 G 33  
3313 hydrogen bonds  
Adding 'H' to /1 ASP 43  
Adding 'H' to /9 TRP 395  
Adding 'H' to /B ASN 458  
Adding 'H' to /B ILE 566  
Adding 'H' to /B ASP 704  
8 messages similar to the above omitted  
/1 ALA 83 is not terminus, removing H atom from 'C'  
/9 TYR 492 is not terminus, removing H atom from 'C'  
/B SER 714 is not terminus, removing H atom from 'C'  
/E ALA 80 is not terminus, removing H atom from 'C'  
/G VAL 89 is not terminus, removing H atom from 'C'  
/2 G 63 is not terminus, removing H atom from O3'  
20045 hydrogens added  
  

> select #1.2/C:443-772

4740 atoms, 4778 bonds, 4 pseudobonds, 306 residues, 2 models selected  

> sel

Unknown command: isolde restrain sel  

> selisolde restrain distances sel

Unknown command: isolde restrain selisolde restrain distances sel  

> isolde restrain distances sel

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select #1.2/A:1-1060

9217 atoms, 9294 bonds, 570 residues, 1 model selected  

> isolde restrain distances sel

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select #1.2/B

2133 atoms, 2147 bonds, 2 pseudobonds, 139 residues, 2 models selected  

> isolde restrain distances sel

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain ligands #1

> isolde restrain distances #1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain basepairs sel

Deleted the following atoms from residue G 242: OP1, HO3'  

MD template MODRNA_PSU for residue PSU 243 contains extra atoms that are not
in a coordinate template, and are not directly connected to existing atoms.
Since MD templates do not explicitly provide geometry,these atoms will not be
built.  

The atom C3' in MD template MODRNA_PSU bonds to more than one existing atom in
residue PSU. Since MD templates do not explicitly specify geometry, this type
of atom addition is not currently supported. The resulting residue will
contain only those atoms which the MD and coordinate templates have in common  
Failed to add atoms ["H1'"] to atom C1' because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MODRNA_PSU). If this template is
built into ISOLDE, please report this using Help/Report a bug  

MD template MODRNA_PSU for residue PSU 243 contains extra atoms that are not
in a coordinate template, and are not directly connected to existing atoms.
Since MD templates do not explicitly provide geometry,these atoms will not be
built.  

The atom C3' in MD template MODRNA_PSU bonds to more than one existing atom in
residue PSU. Since MD templates do not explicitly specify geometry, this type
of atom addition is not currently supported. The resulting residue will
contain only those atoms which the MD and coordinate templates have in common  
Traceback (most recent call last):  
File "/Users/tholenj/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/Users/tholenj/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ["H3'"] to atom C3' because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MODRNA_PSU). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> delete sel


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,10
      Model Number: Z1740017JLL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (a) (22E772610a)
      Kernel Version: Darwin 22.4.0
      Time since boot: 1 day, 39 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U3421WE:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    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: 2021.10.8
    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-Clipper: 0.21.0
    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-ISOLDE: 1.6.0
    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
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    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
    ChimeraX-OpenCommand: 1.10.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    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
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    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: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[pett]

Would need a reproducible test case

[Tom Goddard]

ISOLDE was running. Looks like maybe a deleted residue was accessed. ISOLDE creates symmetry copies of crystallographic asymmetric units as needed so may be frequently deleting residues, and maybe that is involved in this crash.