id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16921	Crash in event loop	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x0000000200377840 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55)


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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/5nqq.pdb""

5nqq.pdb title:  
Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate
[more info...]  
  
Chain information for 5nqq.pdb #1  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  
Non-standard residues in 5nqq.pdb #1  
---  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
  
118 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #1 models

> hide target m

> show #1 models

> undo

> hide target m

> show target m

> color dark gray

> set bgColor white

> log metadata #1

Metadata for 5nqq.pdb #1  
---  
Title | Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate  
Citation | The self-inhibitory nature of metabolic networks and itsalleviation through compartmentalization. PMID: 28691704  
Non-standard residues | NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
Gene source | Oryctolagus cuniculus (rabbit)  
Experimental method | X-ray diffraction  
Resolution | 1.87Å  
  
> log chains #1

Chain information for 5nqq.pdb #1  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  

> select :OAA

22 atoms, 20 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 22 atom styles  

> color sel lime

> select :NAI

284 atoms, 300 bonds, 4 residues, 1 model selected  

> select :NAI

284 atoms, 300 bonds, 4 residues, 1 model selected  

> color sel red

> ui tool show ""Color Actions""

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/5nqq.pdb""

5nqq.pdb title:  
Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate
[more info...]  
  
Chain information for 5nqq.pdb #2  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  
Non-standard residues in 5nqq.pdb #2  
---  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
  
118 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select add #1

21668 atoms, 21110 bonds, 2085 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

21668 atoms, 21110 bonds, 2085 residues, 1 model selected  

> close

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/5nqq.pdb""

5nqq.pdb title:  
Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate
[more info...]  
  
Chain information for 5nqq.pdb #1  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  
Non-standard residues in 5nqq.pdb #1  
---  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
  
118 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide target m

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/5nqq.pdb""

5nqq.pdb title:  
Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate
[more info...]  
  
Chain information for 5nqq.pdb #2  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  
Non-standard residues in 5nqq.pdb #2  
---  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
  
118 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/5nqq.pdb""

5nqq.pdb title:  
Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate
[more info...]  
  
Chain information for 5nqq.pdb #1  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  
Non-standard residues in 5nqq.pdb #1  
---  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
  
118 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide target m

> show target m

> ui tool show ""Color Actions""

> color bychain

> log metadata #1

Metadata for 5nqq.pdb #1  
---  
Title | Rabbit muscle L-lactate dehydrogenase In complex with nadh and oxaloacetate  
Citation | The self-inhibitory nature of metabolic networks and itsalleviation through compartmentalization. PMID: 28691704  
Non-standard residues | NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
OAA — oxaloacetate ion  
SO4 — sulfate ion  
Gene source | Oryctolagus cuniculus (rabbit)  
Experimental method | X-ray diffraction  
Resolution | 1.87Å  
  
> log chains #1

Chain information for 5nqq.pdb #1  
---  
Chain | Description | UniProt  
A B C D | L-lactate dehydrogenase A chain | LDHA_RABIT 0-331  
  

> select :OAA

22 atoms, 20 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 22 atom styles  

> ui tool show ""Color Actions""

> color sel dark green

> color sel dark red

> select :NAI

284 atoms, 300 bonds, 4 residues, 1 model selected  

> style sel sphere

Changed 284 atom styles  

> color sel dark blue

> save /Users/danicalspencer/Desktop/image1.png supersample 3

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/1t2c.pdb""

1t2c.pdb title:  
Plasmodium falciparum lactate dehydrogenase complexed with nadh [more info...]  
  
Chain information for 1t2c.pdb #2  
---  
Chain | Description | UniProt  
A | LDH-P | LDH1_PLAFD 17-329  
  
Non-standard residues in 1t2c.pdb #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #1 models

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/1t2c.pdb""

1t2c.pdb title:  
Plasmodium falciparum lactate dehydrogenase complexed with nadh [more info...]  
  
Chain information for 1t2c.pdb #3  
---  
Chain | Description | UniProt  
A | LDH-P | LDH1_PLAFD 17-329  
  
Non-standard residues in 1t2c.pdb #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #2 models

> hide #3 models

> show #3 models

> close #3

> show #2 models

> select add #1

21668 atoms, 21110 bonds, 2085 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

21668 atoms, 21110 bonds, 2085 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #1 models

> ui tool show Matchmaker

> undo

> show #1 models

> ui tool show Matchmaker

> hide #1 models

> close #2

> show #1 models

> open ""/Users/danicalspencer/Desktop/GMU/SP 25/BioChem2/LAB/2.
> Bioinfo/1t2c.pdb""

1t2c.pdb title:  
Plasmodium falciparum lactate dehydrogenase complexed with nadh [more info...]  
  
Chain information for 1t2c.pdb #2  
---  
Chain | Description | UniProt  
A | LDH-P | LDH1_PLAFD 17-329  
  
Non-standard residues in 1t2c.pdb #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH)  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

> ui tool show Matchmaker

> matchmaker #2/A#2/A#2/A#2/A to #1/A#1/B#1/C#1/D pairing ss

Different number of reference/match chains (4 ref, 1 match)  

> select /B:1-331

5150 atoms, 5195 bonds, 331 residues, 1 model selected  

> select /C:1-331

5192 atoms, 5238 bonds, 331 residues, 1 model selected  

> select /D:1-331

5107 atoms, 5153 bonds, 331 residues, 1 model selected  

> select /A:1-331

7525 atoms, 7608 bonds, 646 residues, 2 models selected  

> sequence chain #1/A#1/B#1/C#1/D

Alignment identifier is 1  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Computing secondary structure  
Parameters  
---  
Chain pairing | ss  
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 5nqq.pdb, chain A (#1) with 1t2c.pdb, chain A (#2), sequence
alignment score = 656.5  
RMSD between 245 pruned atom pairs is 1.073 angstroms; (across all 308 pairs:
2.428)  
  

> ui windowfill toggle

> view sel

> save /Users/danicalspencer/Desktop/image2.png supersample 3


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: MLXX3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 50 days, 14 hours, 22 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Core		can't reproduce		Tom Goddard				all	ChimeraX