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Opened 11 days ago
Closed 10 days ago
#20090 closed defect (fixed)
surface smooth: 'NoneType' object has no attribute 'copy'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
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
Change History (4)
comment:1 by , 11 days ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → surface smooth: 'NoneType' object has no attribute 'copy' |
comment:3 by , 10 days ago
comment:4 by , 10 days ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Ignore surfaces that have vertices, triangles or normals equal to None.
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I am puzzled how this could happen. molmap was run to produce a volume and somehow the surface had vertices, normals or triangles set to None. It is easy to fix the error in the surface smoothing. But how did the surface end up having None geometry? My best guess is the surface had not been computed. Why not?