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#17043 closed defect (can't reproduce)

Crash in atom-spec parsing with matchmaker, not a long atomspec.

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Core	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.8.0-48-generic-x86_64-with-glibc2.39
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

Thread 0x00007ead2f4006c0 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1297 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007eadfa146b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 150 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 150 in __iter__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 891 in atomspec_atoms
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 616 in _add_model_parts
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 465 in _check
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 479 in _check
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 459 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 601 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 444 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/args.py", line 25 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/args.py", line 60 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2488 in _parse_arg
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2629 in _process_positional_arguments
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2853 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 3457 in __call__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2918 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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  

> close

> cd /home/sebols/projects/rsv/

Current working directory is: /home/sebols/projects/rsv  

> open ./2025_epitopeAnalyzer/scrubbed/250226_LOR24_PreF_1Fab.pdb

Chain information for 250226_LOR24_PreF_1Fab.pdb #1  
---  
Chain | Description  
A B C | No description available  
H | No description available  
L | No description available  
  

> open ./2025_epitopeAnalyzer/scrubbed/250304_MPE8_PreF_1Fab.pdb

Chain information for 250304_MPE8_PreF_1Fab.pdb #2  
---  
Chain | Description  
A B C | No description available  
H | No description available  
L | No description available  
  

> open ./2025_epitopeAnalyzer/scrubbed/250304_LOR69_PreF_1Fab.pdb

Chain information for 250304_LOR69_PreF_1Fab.pdb #3  
---  
Chain | Description  
A B C | No description available  
H | No description available  
L | No description available  
  

> graphics bgColor white

> graphics silhouettes true width 2.5

> lighting gentle

> delete H

> color all byhetero

> view matrix camera
> -0.88749,0.029198,-0.45986,6.6496,-0.46047,-0.018822,0.88748,426.58,0.017253,0.99941,0.030162,156.84

> hide all atoms

> show all cartoons

> mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_MPE8_PreF_1Fab.pdb, chain A (#2), sequence alignment score = 47.9  
RMSD between 13 pruned atom pairs is 0.344 angstroms; (across all 13 pairs:
0.344)  
  
Matchmaker 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_LOR69_PreF_1Fab.pdb, chain A (#3), sequence alignment score = 68.7  
RMSD between 13 pruned atom pairs is 0.315 angstroms; (across all 13 pairs:
0.315)  
  

> delete /B,C

> color /A light gray

> color #1/H #6C96C4

> color #1/L #A5BCD6

> color #2/H #6EC25F

> color #2/L #A6D79D

> color #3/H #B25D56

> color #3/L #D69B96

> rename #1 LOR24-Fab

> rename #2 MPE8_5u68

> rename #3 LOR69-Fab

> hide #1.1 models

> hide #2.1 models

> hide #3.1 models

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #2/H

Alignment identifier is 2/H  

> sequence chain #2/L

Alignment identifier is 2/L  
Drag select of 421 residues  

> select clear

> hide #!1 models

> hide #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:509

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/A:474-509

293 atoms, 299 bonds, 36 residues, 1 model selected  

> select #2/A:61

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:61-75

112 atoms, 111 bonds, 15 residues, 1 model selected  

> select #2/A:50

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:50

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select
> #2/A:29-33,38-49,51-60,176-180,186-194,286-293,296-305,312-318,333-336,340-344,348-352,359-361,364-368,373-376,395-398,404-407,411-416,422-426,430-434,438-443,449-452,455-458,465-469

1052 atoms, 1054 bonds, 135 residues, 1 model selected  

> select #2/A:51

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/A:51-148

475 atoms, 479 bonds, 1 pseudobond, 61 residues, 2 models selected  

> select #2/A:51

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/A:51-217

990 atoms, 998 bonds, 1 pseudobond, 130 residues, 2 models selected  

> select #2/A:51

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/A:51-253

1279 atoms, 1291 bonds, 1 pseudobond, 166 residues, 2 models selected  

> select #2/A:277

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:277-283

59 atoms, 58 bonds, 7 residues, 1 model selected  

> select #2/A:278

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:278-279

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:278

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:278-339

492 atoms, 500 bonds, 62 residues, 1 model selected  

> select #2/A:278

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:278-293

131 atoms, 131 bonds, 16 residues, 1 model selected  

> select #2/A:278

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:278-306

239 atoms, 242 bonds, 29 residues, 1 model selected  

> select #2/A:278

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:278-299

181 atoms, 182 bonds, 22 residues, 1 model selected  

> select #2/A:302

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:302

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:304

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:304

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:315-316

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #2/A:315-321

55 atoms, 56 bonds, 7 residues, 1 model selected  

> select #2/A:333

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/A:333-341

76 atoms, 77 bonds, 9 residues, 1 model selected  

> select #2/A:323

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:323-327

38 atoms, 37 bonds, 5 residues, 1 model selected  

> select #2/A:319

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/A:319-321

21 atoms, 21 bonds, 3 residues, 1 model selected  

> select #2/A:322

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/A:322-344

181 atoms, 183 bonds, 23 residues, 1 model selected  

> select #2/A:335

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:335-337

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #2/A:353

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:353-358

43 atoms, 43 bonds, 6 residues, 1 model selected  

> select #2/A:353

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:353-382

228 atoms, 230 bonds, 30 residues, 1 model selected  

> select #2/A:392

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:392

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:392-407

116 atoms, 115 bonds, 16 residues, 1 model selected  

> select #2/A:392

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:392-437

335 atoms, 336 bonds, 46 residues, 1 model selected  

> select #2/A:465

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:465-469

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select #2/A:462

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:462

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:461

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:461-462

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #2/A:461-462

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #2/A:461-462

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #2/A:461

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:461

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:462-463

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #2/A:462-463

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:51-253,278-304,322-339,353-376,392-463,474-530

7939 atoms, 8010 bonds, 3 pseudobonds, 1049 residues, 6 models selected  

> select #2/A:190

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/A:176

9 atoms, 8 bonds, 1 residue, 1 model selected  

> close

> cd /home/sebols/projects/rsv/

Current working directory is: /home/sebols/projects/rsv  

> open ./2025_epitopeAnalyzer/scrubbed/250226_LOR24_PreF_1Fab.pdb

Chain information for 250226_LOR24_PreF_1Fab.pdb #1  
---  
Chain | Description  
A B C | No description available  
H | No description available  
L | No description available  
  

> open ./2025_epitopeAnalyzer/scrubbed/250304_MPE8_PreF_1Fab.pdb

Chain information for 250304_MPE8_PreF_1Fab.pdb #2  
---  
Chain | Description  
A B C | No description available  
H | No description available  
L | No description available  
  

> open ./2025_epitopeAnalyzer/scrubbed/250304_LOR69_PreF_1Fab.pdb

Chain information for 250304_LOR69_PreF_1Fab.pdb #3  
---  
Chain | Description  
A B C | No description available  
H | No description available  
L | No description available  
  

> graphics bgColor white

> graphics silhouettes true width 2.5

> lighting gentle

> delete H

> color all byhetero

> view matrix camera
> -0.88749,0.029198,-0.45986,6.6496,-0.46047,-0.018822,0.88748,426.58,0.017253,0.99941,0.030162,156.84

> hide all atoms

> show all cartoons

> mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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: 4.6 (Core Profile) Mesa 24.0.9-0ubuntu0.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 770 (ADL-S GT1)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
WAYLAND_DISPLAY=wayland-0
Manufacturer: Shuttle Inc.
Model: DH670
OS: Ubuntu 24.04 Noble Numbat
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi        12Gi       4.4Gi       2.6Gi        16Gi        18Gi
	Swap:             0B          0B          0B

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation AlderLake-S GT1 [8086:4680] (rev 0c)	
	DeviceName: Onboard - Video	
	Subsystem: Holco Enterprise Co, Ltd/Shuttle Computer AlderLake-S GT1 [1297:4132]

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-LinuxSupport: 1.0.1
    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
    distro: 1.7.0
    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: 2022.9.26
    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: 23.1
    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
    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

Change History (2)

comment:1 by Tom Goddard, 8 months ago

Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash in atom-spec parsing with matchmaker, not a long atomspec.

comment:2 by Tom Goddard, 8 months ago

Resolution:	→ can't reproduce
Status:	assigned → closed

In old ChimeraX 1.6.

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