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Opened 4 hours ago
#20090 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL
> 250326/SCRIPTS/scImmTAC_reversed_script_chimerax_CLOUD.cxc"
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT DATA/scImmTAC.pdb"
Chain information for scImmTAC.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
> DATA/model_000650.pdb"
Chain information for model_000650.pdb #2
---
Chain | Description
D | No description available
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
> DATA/scImmTAC.ensemble_aln_rev.ca_cloud.pdb"
Summary of feedback from opening
/Users/elenabarba/Library/CloudStorage/OneDrive-
STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
DATA/scImmTAC.ensemble_aln_rev.ca_cloud.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK CA cloud from aligned models
Ignored bad PDB record found on line 2
REMARK B-factor encodes model number
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
> DATA/scImmTAC.ensemble_aln_rev.mrc"
Opened scImmTAC.ensemble_aln_rev.mrc as #4, grid size 136,97,94, pixel
1.67,1.67,1.67, shown at level 377, step 1, values float32
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
> DATA/cImmTAC_aln.pdb"
Chain information for cImmTAC_aln.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
> DATA/cImmTAC.ensemble_aln_rev.ca_cloud_aln.pdb"
Summary of feedback from opening
/Users/elenabarba/Library/CloudStorage/OneDrive-
STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
DATA/cImmTAC.ensemble_aln_rev.ca_cloud_aln.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK CA cloud from aligned models
Ignored bad PDB record found on line 2
REMARK B-factor encodes model number
> open "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/INPUT
> DATA/cImmTAC.ensemble_aln_rev_aln.mrc"
Opened cImmTAC.ensemble_aln_rev_aln.mrc as #7, grid size 136,97,94, pixel
1.67,1.67,1.67, shown at level 391, step 1, values float32
> measure sasa #5/E:22-274
Solvent accessible area for #5/E:22-274 (1888 atoms) = 12863
> measure sasa #1/D:516-765
Solvent accessible area for #1/D:516-765 (1866 atoms) = 12656
> molmap #3 8
Opened scImmTAC.ensemble_aln_rev.ca_cloud.pdb map 8 as #8, grid size 46,49,49,
pixel 2.67, shown at level 0.0116, step 1, values float32
> molmap #6 8
Opened cImmTAC.ensemble_aln_rev.ca_cloud_aln.pdb map 8 as #9, grid size
43,44,36, pixel 2.67, shown at level 0.0282, step 1, values float32
> volume #8 level 0.1
> volume #9 level 0.1
FYI: command is replacing existing command: "measure contactArea"
> measure area #8.1
Surface area for surface (#8.1) = 7578
FYI: command is replacing existing command: "measure contactArea"
> measure volume #8.1
Enclosed volume for surface (#8.1) = 1.56e+04
> measure area #9.1
Surface area for surface (#9.1) = 3314
> measure volume #9.1
Enclosed volume for surface (#9.1) = 8654
> hide #8 models
> hide #9 models
> lighting full
> graphics quality 4
> hide atoms
> show cartoons
> set bgColor white
> cartoon #1,2
> show #3 atoms
> style #3 sphere
Changed 1000 atom styles
> size atomRadius 1
Changed 36672 atom radii
> volume #4 level 5
> transparency #4 50 target s
> show #6 atoms
> style #6 sphere
Changed 968 atom styles
> size atomRadius 1
Changed 36672 atom radii
> volume #7 level 5
> transparency #7 50 target s
> cartoon style width 2.5 thickness 1
Computing secondary structure
[Repeated 1 time(s)]
> size stickRadius 0.3
Changed 35410 bond radii
> cartoon smooth 1.0
> set silhouettes true
> dssp #1,2,5 minHelixLen 2 minStrandLen 2
> graphics silhouettes true color black width 1 depthJump 0.1
> color #1,2 #949494
> color #1,2/D:20-138 #91cbf5
> color #1,2/D:139-221 #3fa9f5
> color #1,2/D:222-271 #fee028
> color #1,2/D:272-389 #1789D4
> color #1,2/D:390-515 #0062a3
> color #1,2/D:516-527 #f38382
> color #1,2/D:528-645 #009245
> color #1,2/D:660-767 #a2cc93
> color #1,2/A #a5a2a5
> color #1,2/B #a5a2a5
> color #1,2/C #33ff00
> color #3 #f38382
> color #4 #949490
> color #5 #949494
> color #5/D:20-138 #91cbf5
> color #5/D:139-221 #3fa9f5
> color #5/E:22-140 #009245
> color #5/E:156-260 #a2cc93
> color #5/E:261-274 #f38382
> color #5/E:275-389 #1789D4
> color #5/E:390-515 #0062a3
> color #5/A #a5a2a5
> color #5/B #a5a2a5
> color #5/C #33ff00
> color #6 #f38382
> color #7 #949490
> view matrix camera
> 0.087507,0.97443,0.20701,128.65,-0.78322,-0.061112,0.61874,401.09,0.61556,-0.21627,0.75783,523.27
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0
> hide cartoons
> cartoon #1/D:20-515
> cartoon #2/D:516-765
> cartoon #5
> hide #!4 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> save "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/RESULTS
> FIGURES/scImmTACmodel.tif" width 4000 height 4000 transparentBackground true
> hide cartoons
> cartoon #1/A
> cartoon #1/B
> cartoon #1/C
> cartoon #1/D:20-515
> cartoon #2/D:516-765
> show #3 models
> cartoon #5
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> save "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/RESULTS
> FIGURES/scImmTACarea.tif" width 4000 height 4000 transparentBackground true
> hide cartoons
> cartoon #5/D:20-221
> cartoon #5/E:22-515
> cartoon #1
> cartoon #2
> show #5 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> save "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/RESULTS
> FIGURES/cImmTACmodel.tif" width 4000 height 4000 transparentBackground true
> hide cartoons
> cartoon #5/A
> cartoon #5/B
> cartoon #5/C
> cartoon #5/D:20-221
> cartoon #5/E:22-515
> cartoon #1
> cartoon #2
> show #5 models
> hide #6 models
> hide #7 models
> volume #7 level 0.8
> volume zone #7 nearAtoms #5/E:22-260 range 18
> show #7 models
> surface smooth #7 factor 0.4 iterations 12
> transparency #7 25 target s
> show #7 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> save "/Users/elenabarba/Library/CloudStorage/OneDrive-
> STAbTherapeutics/STAb/Experimentos/ImmTAC EBS/4. ImmTAC
> MODELIZATION/Git_analysis/ImmTAC_model/RFL 250326/RESULTS
> FIGURES/cImmTACarea.tif" width 4000 height 4000 transparentBackground true
> volume #7 level 0.8
> volume zone #7 nearAtoms #5/E:22-274 range 16
> show #7 models
> measure area #7.1
Surface area for surface (#7.1) = 6.083e+04
> measure volume #7.1
Enclosed volume for surface (#7.1) = 5.16e+05
> volume #4 level 0.8
> volume zone #4 nearAtoms #1/D:516-765 range 16
> show #4 models
> measure area #4.1
Surface area for surface (#4.1) = 7.879e+04
> measure volume #4.1
Enclosed volume for surface (#4.1) = 7.342e+05
executed scImmTAC_reversed_script_chimerax_CLOUD.cxc
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> hide #!8 models
> show #!9 models
> molmap #3 8
Opened scImmTAC.ensemble_aln_rev.ca_cloud.pdb map 8 as #8, grid size 46,49,49,
pixel 2.67, shown at level 0.0116, step 1, values float32
> molmap #6 8
Opened cImmTAC.ensemble_aln_rev.ca_cloud_aln.pdb map 8 as #9, grid size
43,44,36, pixel 2.67, shown at level 0.0282, step 1, values float32
> hide #!7 models
> hide #10 models
> hide #!9 models
> hide #!4 models
> hide #5 models
> show #5 models
> show #!2 models
> hide #5 models
> molmap #3 10
Opened scImmTAC.ensemble_aln_rev.ca_cloud.pdb map 10 as #8, grid size
41,43,43, pixel 3.33, shown at level 0.00909, step 1, values float32
> volume #8 level 0.15
> transparency #8 60 target s
> surface smooth #8.1 factor 0.5 iterations 10
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/sop.py", line 259, in surface_smooth
va, na, ta = surface.vertices.copy(), surface.normals.copy(),
surface.triangles.copy()
^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'copy'
AttributeError: 'NoneType' object has no attribute 'copy'
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/sop.py", line 259, in surface_smooth
va, na, ta = surface.vertices.copy(), surface.normals.copy(),
surface.triangles.copy()
^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac17,2
Model Number: Z1KH003R1Y/A
Chip: Apple M5
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 30 días, 20 horas y 38 minutos
Graphics/Displays:
Apple M5:
Chipset Model: Apple M5
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
HP P24v G5:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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