id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16811	Crash hiding dock widget	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202410010214 (2024-10-01 02:14:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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Log:
UCSF ChimeraX version: 1.9.dev202410010214 (2024-10-01)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/melvinlopez/Library/Mobile Documents/com~apple~CloudDocs/School
> Stuff/Lab (Dr. Cordes)/3rlg_cholesterol_docking_02072025.cxs""

Log from Fri Feb 7 05:36:14 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9.dev202410010214 (2024-10-01)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Unable to load numpy_formathandler accelerator from OpenGL_accelerate  

> open /Users/melvinlopez/Desktop/Vina/3rlg_for_allo.pdbqt

Chain information for 3rlg_for_allo.pdb #1  
---  
Chain | Description  
A | No description available  
  
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  
Opened 3rlg_for_allo.pdbqt containing 1 structures (2683 atoms, 2732 bonds)  

> set bgColor white

> open /Users/melvinlopez/Desktop/Vina/cholesterol_out.pdbqt

Summary of feedback from opening
/Users/melvinlopez/Desktop/Vina/cholesterol_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -6.336 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.197  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -8.374  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -0.824  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -0.824  
  
275 messages similar to the above omitted  
  
Opened cholesterol_out.pdbqt containing 10 structures (290 atoms, 320 bonds)  

> viewdockx #2.1-10

> hide #2.2 models

> hide #2.3 models

> hide #2.4 models

> hide #2.5 models

> hide #2.6 models

> hide #2.7 models

> hide #2.8 models

> hide #2.9 models

> hide #2.10 models

> hide #2.1 models

> open /Users/melvinlopez/Downloads/stbh47n_dep_chaina_100124.pdb

Summary of feedback from opening
/Users/melvinlopez/Downloads/stbh47n_dep_chaina_100124.pdb  
---  
warnings | CONECT record for nonexistent atom: 3226  
Start residue of secondary structure not found: HELIX 10 10 ASP B 15 ASP B 25
1 11  
Start residue of secondary structure not found: HELIX 11 11 LYS B 62 THR B 74
1 13  
Start residue of secondary structure not found: HELIX 12 12 SER B 98 ASP B 122
1 25  
Start residue of secondary structure not found: HELIX 13 13 THR B 135 GLU B
152 1 18  
Start residue of secondary structure not found: HELIX 14 14 PHE B 154 TYR B
159 1 6  
14 messages similar to the above omitted  
  
Chain information for stbh47n_dep_chaina_100124.pdb #3  
---  
Chain | Description  
A | No description available  
  
129 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #!3 to #1

Computing secondary structure  
[Repeated 1 time(s)]  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 3rlg_for_allo.pdb, chain A (#1) with stbh47n_dep_chaina_100124.pdb,
chain A (#3), sequence alignment score = 858.3  
RMSD between 261 pruned atom pairs is 0.789 angstroms; (across all 276 pairs:
1.187)  
  

> select add #3

2814 atoms, 2414 bonds, 17 pseudobonds, 727 residues, 2 models selected  

> hide (#!3 & sel) target a

> select #3/A:225

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

> show sel target ab

> color sel byhetero

> select #3/A:233

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

> show sel target ab

> color sel byhetero

> select add #3

2814 atoms, 2414 bonds, 17 pseudobonds, 727 residues, 2 models selected  

> select add #1

5497 atoms, 5146 bonds, 17 pseudobonds, 1005 residues, 3 models selected  

> select subtract #3

2683 atoms, 2732 bonds, 278 residues, 1 model selected  

> show sel target ab

> hide sel target a

> select #1/A:229

14 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel target ab

> select add #3

2828 atoms, 2428 bonds, 17 pseudobonds, 728 residues, 3 models selected  

> select add #1

5497 atoms, 5146 bonds, 17 pseudobonds, 1005 residues, 3 models selected  

> select subtract #3

2683 atoms, 2732 bonds, 278 residues, 1 model selected  

> hide #!3 models

> surface sel

> transparency (#!1 & sel) 70

> transparency (#!1 & sel) 90

> transparency (#!1 & sel) 50

> transparency (#!1 & sel) 20

> transparency (#!1 & sel) 40

> transparency (#!1 & sel) 30

> select #1/A:237

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

> show (#!1 & sel) target ab

> select add #1

2683 atoms, 2732 bonds, 278 residues, 2 models selected  

> hide #!1 models

> select add #3

5497 atoms, 5146 bonds, 17 pseudobonds, 1005 residues, 4 models selected  

> select subtract #1

2814 atoms, 2414 bonds, 17 pseudobonds, 727 residues, 3 models selected  

> show #!3 models

> select #3/A:228

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

> show sel target ab

> show #!1 models

> select add #1

2691 atoms, 2739 bonds, 279 residues, 2 models selected  

> select add #3

5497 atoms, 5146 bonds, 17 pseudobonds, 1005 residues, 4 models selected  

> select subtract #3

2683 atoms, 2732 bonds, 278 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> select #1/A:232

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

> show (#!1 & sel) target ab

> hide #!3 models

> select add #1

2683 atoms, 2732 bonds, 278 residues, 2 models selected  

> surface (#!1 & sel)

> show #2.1 models

> select ::name=""HOH""

441 atoms, 441 residues, 1 model selected  

> show #1#2.1#!2 target ab

> hide #1#2.1#!2 target a

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> select add #2

731 atoms, 320 bonds, 451 residues, 12 models selected  

> show (#2.1 & sel) target ab

> select add #1

3414 atoms, 3052 bonds, 729 residues, 13 models selected  

> select subtract #2

3124 atoms, 2732 bonds, 719 residues, 3 models selected  

> select add #3

5497 atoms, 5146 bonds, 17 pseudobonds, 1005 residues, 4 models selected  

> select subtract #3

2683 atoms, 2732 bonds, 278 residues, 2 models selected  

> select ::name=""HOH""

441 atoms, 441 residues, 1 model selected  

> show #1#2.1#!2 target ab

> hide #1#2.1#!2 target a

> select add #2

731 atoms, 320 bonds, 451 residues, 12 models selected  

> show (#2.1 & sel) target ab

> select add #1

3414 atoms, 3052 bonds, 729 residues, 13 models selected  

Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.  

> show #2.2 models

> hide #2.2 models

> select subtract #2

3124 atoms, 2732 bonds, 719 residues, 3 models selected  

> open /Users/melvinlopez/Desktop/Vina/cholesterol_1_out.pdbqt

Summary of feedback from opening
/Users/melvinlopez/Desktop/Vina/cholesterol_1_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -6.281 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.425  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -8.300  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -1.125  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -1.125  
  
275 messages similar to the above omitted  
  
Opened cholesterol_1_out.pdbqt containing 10 structures (290 atoms, 320 bonds)  

> viewdockx #4.1-10

> hide #4.10 models

> hide #4.9 models

> hide #4.8 models

> hide #4.7 models

> hide #4.6 models

> hide #4.5 models

> hide #4.4 models

> hide #4.3 models

> hide #4.2 models

> hide #4.1 models

> show #4.1 models

> hide #!2 models

> show #4.2 models

> hide #4.1 models

> show #4.1 models

> show #4.3 models

> show #4.4 models

> show #4.5 models

> hide #4.2 models

> hide #4.1 models

> hide #4.3 models

> hide #4.4 models

> show #4.1 models

> hide #4.5 models

> hide #!4 models

> hide #4.1 models

Cell requested for row 3 is out of bounds for table with 14 rows! Resizing
table model.  

> open /Users/melvinlopez/Desktop/Vina/cholesterol_2_out.pdbqt

Summary of feedback from opening
/Users/melvinlopez/Desktop/Vina/cholesterol_2_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -6.128 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.269  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -8.099  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -1.170  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -1.170  
  
275 messages similar to the above omitted  
  
Opened cholesterol_2_out.pdbqt containing 10 structures (290 atoms, 320 bonds)  

> viewdockx #5.1-10

> hide #5.2 models

> hide #5.3 models

> hide #5.4 models

> hide #5.5 models

> hide #5.6 models

> hide #5.7 models

> hide #5.8 models

> hide #5.9 models

> hide #5.10 models

> show #5.2 models

> hide #5.1 models

> hide #5.2 models

> show #5.1 models

> select add #3

5497 atoms, 5146 bonds, 17 pseudobonds, 1005 residues, 4 models selected  

> select subtract #3

2683 atoms, 2732 bonds, 278 residues, 2 models selected  

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!2 models

> show #4.1 models

> hide #!2 models

> hide #!4 models

> hide #!5 models

> open /Users/melvinlopez/Desktop/Vina/cholesterol_3_out.pdbqt

Summary of feedback from opening
/Users/melvinlopez/Desktop/Vina/cholesterol_3_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.894 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -9.051  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -7.789  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -1.262  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -1.262  
  
275 messages similar to the above omitted  
  
Opened cholesterol_3_out.pdbqt containing 10 structures (290 atoms, 320 bonds)  

> viewdockx #6.1-10

> hide #6.2 models

> hide #6.3 models

> hide #6.4 models

> hide #6.5 models

> hide #6.6 models

> hide #6.7 models

> hide #6.8 models

> hide #6.9 models

> hide #6.10 models

> surface hidePatches (#!1 & sel)

> select #1/A:229

14 atoms, 14 bonds, 1 residue, 1 model selected  

> show (#!1 & sel) target ab

> select #1/A:237

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

> show (#!1 & sel) target ab

> select #1/A:232

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

> show (#!1 & sel) target ab

> hide #!6 models

Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.  

> show #!2 models

> hide #!2 models

> open /Users/melvinlopez/Desktop/Vina/cholesterol_4_out.pdbqt

Summary of feedback from opening
/Users/melvinlopez/Desktop/Vina/cholesterol_4_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -5.616 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK INTER + INTRA: -8.993  
  
Ignored bad PDB record found on line 4  
REMARK INTER: -7.422  
  
Ignored bad PDB record found on line 5  
REMARK INTRA: -1.571  
  
Ignored bad PDB record found on line 6  
REMARK UNBOUND: -1.571  
  
275 messages similar to the above omitted  
  
Opened cholesterol_4_out.pdbqt containing 10 structures (290 atoms, 320 bonds)  

> viewdockx #7.1-10

> hide #7.2 models

> hide #7.3 models

> hide #7.4 models

> hide #7.5 models

> hide #7.6 models

> hide #7.7 models

> hide #7.8 models

> hide #7.9 models

> hide #7.10 models

> show #7.2 models

> show #7.3 models

> hide #7.1 models

> hide #7.2 models

> hide #7.3 models

> show #7.2 models

> show #7.3 models

> hide #7.2 models

> hide #7.3 models

> show #7.1 models

> hide #!7 models

> save /Users/melvinlopez/Downloads/3rlg_cholesterol_docking_02072025.cxs

——— End of log from Fri Feb 7 05:36:14 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
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: MacBookAir10,1
      Model Number: MGN63LL/A
      Chip: Apple M1
      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: 6 days, 22 hours, 38 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.14
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.7
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.3.4
    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.dev202410010214
    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-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DiffPlot: 1.0
    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-Label: 1.1.11
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-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
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    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: 3.2.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.13
    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-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: 1.3.0
    coverage: 7.6.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.6
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    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: 2.1.5
    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: 2.10.1
    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
    pluggy: 1.5.0
    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
    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: 3.1.4
    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
    pytest: 8.3.3
    pytest-cov: 5.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    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
    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: 6.4.1
    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		Window Toolkit		can't reproduce						all	ChimeraX