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#18052 closed defect (can't reproduce)

'name' not in Surface session-restore data

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

Description

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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  

> open
> /Users/rag/Desktop/rec/20241225_ferritag_Aquilos_grid2_Position_2_3_rec.mrc

Opened 20241225_ferritag_Aquilos_grid2_Position_2_3_rec.mrc as #1, grid size
1024,1024,234, pixel 9.56,9.56,9.56, shown at level 52, step 4, values int8  

> volume #1 level 45.14

> open /Users/rag/Desktop/seg/2-3.obj
> /Users/rag/Desktop/seg/20241225_ferritag_Aquilos_grid2_Position_2_3_3.obj
> /Users/rag/Desktop/seg/20241225_ferritag_Aquilos_grid2_Position_2_3_rec.surf.obj

Opened OBJ file 2-3.obj containing 1 objects, 2975288 triangles  
Opened OBJ file 20241225_ferritag_Aquilos_grid2_Position_2_3_3.obj containing
1 objects, 752410 triangles  
Opened OBJ file 20241225_ferritag_Aquilos_grid2_Position_2_3_rec.surf.obj
containing 1 objects, 22420 triangles  

> volume #1 level 46.52

> hide #!1 models

> show #!1 models

> volume #1 level 31.87

> hide #!1 models

> show #!1 models

> hide #!1 models

> view orient

> color #2 #0433ffff

> hide #4 models

> show #4 models

> hide #4 models

> color #4 #ff2600ff

> show #4 models

> hide #4 models

> color #4 #942192ff

> color #3 #942192ff

> color #3 #00f900ff

> color #3 #ff9300ff

> show #4 models

> hide #4 models

> ui mousemode right "tape measure"

[Repeated 1 time(s)]

> set bgColor white

> set bgColor #ffffff00

> ui mousemode right "tape measure"

[Repeated 3 time(s)]

> view orient

[Repeated 1 time(s)]

> set bgColor black

> set bgColor transparent

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #5, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> show #4 models

> volume #5 level 0.007096

> ui mousemode right select

Drag select of 5 emd_30083_bin8.mrc  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,1808.1,0,1,0,2921.6,0,0,1,566.84

> view matrix models #5,1,0,0,1547.5,0,1,0,2780.6,0,0,1,-465.42

> view matrix models #5,1,0,0,1988.8,0,1,0,3079,0,0,1,-580.48

> view matrix models #5,1,0,0,1980.5,0,1,0,3080.1,0,0,1,-600.83

> view matrix models #5,1,0,0,1987.5,0,1,0,3089.2,0,0,1,-598.92

> view matrix models #5,1,0,0,1846.9,0,1,0,2993.5,0,0,1,-618.03

> volume #5 level 0.005821

> view matrix models #5,1,0,0,1984.1,0,1,0,3086.9,0,0,1,-599.39

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #6, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #7, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #8, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #9, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #10, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> ui mousemode right select

Drag select of 40 emd_30083_bin8.mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #6,1,0,0,-522.42,0,1,0,3465.1,0,0,1,26.508,#7,1,0,0,-522.42,0,1,0,3465.1,0,0,1,26.508,#8,1,0,0,-522.42,0,1,0,3465.1,0,0,1,26.508,#9,1,0,0,-522.42,0,1,0,3465.1,0,0,1,26.508,#10,1,0,0,-522.42,0,1,0,3465.1,0,0,1,26.508

> view matrix models
> #6,1,0,0,-523.2,0,1,0,3466.6,0,0,1,26.455,#7,1,0,0,-523.2,0,1,0,3466.6,0,0,1,26.455,#8,1,0,0,-523.2,0,1,0,3466.6,0,0,1,26.455,#9,1,0,0,-523.2,0,1,0,3466.6,0,0,1,26.455,#10,1,0,0,-523.2,0,1,0,3466.6,0,0,1,26.455

> ui mousemode right select

> select clear

[Repeated 1 time(s)]

> select #6

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,-397.49,0,1,0,3674.2,0,0,1,39.115

> view matrix models #6,1,0,0,-397.78,0,1,0,3673.1,0,0,1,39.024

> ui mousemode right select

> select #7

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,-312.19,0,1,0,3344.8,0,0,1,-14.301

> ui mousemode right select

> select clear

> ui mousemode right "translate selected models"

> ui mousemode right select

> select #7

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,-435.22,0,1,0,3338.3,0,0,1,0.0015096

> hide #!7 models

> show #!7 models

> select subtract #5

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,-326.7,0,1,0,3465.7,0,0,1,2.2527

> select subtract #7

Nothing selected  

> select add #8

2 models selected  

> select add #10

4 models selected  

> select add #9

6 models selected  

> select subtract #9

4 models selected  

> select subtract #10

2 models selected  

> view matrix models #8,1,0,0,-641.51,0,1,0,3676.1,0,0,1,66.555

> select subtract #8

Nothing selected  

> hide #!6 models

> show #!6 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> select add #9

2 models selected  

> view matrix models #9,1,0,0,-655.47,0,1,0,3438,0,0,1,39.18

> show #!9 models

> select subtract #9

Nothing selected  

> select add #6

2 models selected  

> view matrix models #6,1,0,0,1671.8,0,1,0,3272.7,0,0,1,-263.68

> view matrix models #6,1,0,0,1655.3,0,1,0,3254.3,0,0,1,-332.25

> view matrix models #6,1,0,0,1684.5,0,1,0,3290.3,0,0,1,-333.19

> select subtract #6

Nothing selected  

> select add #7

2 models selected  

> view matrix models #7,1,0,0,1610.9,0,1,0,3624.9,0,0,1,616.94

> view matrix models #7,1,0,0,1747.2,0,1,0,3426.2,0,0,1,273.52

> view matrix models #7,1,0,0,1732.4,0,1,0,3401.4,0,0,1,279.41

> select add #8

4 models selected  

> select subtract #7

2 models selected  

> view matrix models #8,1,0,0,5051.3,0,1,0,2399.3,0,0,1,-471

> view matrix models #8,1,0,0,5115.3,0,1,0,2789.1,0,0,1,115.77

> view matrix models #8,1,0,0,5120.1,0,1,0,2800.4,0,0,1,160.25

> view matrix models #8,1,0,0,5127.5,0,1,0,2789.1,0,0,1,142.58

> view matrix models #8,1,0,0,5136.8,0,1,0,2763.6,0,0,1,148.97

> view matrix models #8,1,0,0,5137.3,0,1,0,2766.6,0,0,1,159.83

> view matrix models #8,1,0,0,5131.9,0,1,0,2778.2,0,0,1,159.92

> select subtract #8

Nothing selected  

> select add #9

2 models selected  

> view matrix models #9,1,0,0,6079.3,0,1,0,3446.4,0,0,1,-119.03

> view matrix models #9,1,0,0,6087.7,0,1,0,3410.7,0,0,1,114.62

> view matrix models #9,1,0,0,6100.1,0,1,0,3431.6,0,0,1,108.91

> view matrix models #9,1,0,0,6088.9,0,1,0,3419.5,0,0,1,108.59

> select subtract #9

Nothing selected  

> select add #10

2 models selected  

> view matrix models #10,1,0,0,6173.7,0,1,0,4750.3,0,0,1,-2812.5

> view matrix models #10,1,0,0,5799.5,0,1,0,4680.5,0,0,1,406.2

> view matrix models #10,1,0,0,6724.5,0,1,0,4707,0,0,1,593.23

> view matrix models #10,1,0,0,6836.4,0,1,0,4666.2,0,0,1,286.11

> view matrix models #10,1,0,0,6846.3,0,1,0,4783.5,0,0,1,278.41

> view matrix models #10,1,0,0,6826.7,0,1,0,4765.2,0,0,1,274.92

> select subtract #10

Nothing selected  

> open /Users/rag/Desktop/seg/emd_30083_bin8.mrc

Opened emd_30083_bin8.mrc as #11, grid size 36,36,36, pixel 6.96, shown at
level 0.0116, step 1, values float32  

> select add #11

2 models selected  

> view matrix models #11,1,0,0,7527.1,0,1,0,4792.4,0,0,1,-1741.1

> color #11 #ff40ffff models

> color #11 #878787ff models

> view matrix models #11,1,0,0,6828.8,0,1,0,4895.7,0,0,1,170.15

> view matrix models #11,1,0,0,6923.1,0,1,0,4918.8,0,0,1,177.52

> view matrix models #11,1,0,0,6918.1,0,1,0,4934.3,0,0,1,187.95

> color #11 #ff40ffff models

> color #10 #ff40ffff models

> color #9 #ff40ffff models

> color #8 #ff40ffff models

> color #7 #ff40ffff models

> color #6 #ff40ffff models

> color #5 #ff40ffff models

> hide #4 models

> show #4 models

> color #4 #fffb00ff

> open /Users/rag/Desktop/seg/2-2.cxs

Error opening map "/Users/rag/Desktop/seg/2-2.cxs": File 2-2.cxs, format mrc  
MRC header value nsymbt (875113504) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 575, in restore_snapshot  
m = Surface(data['name'], session)  
~~~~^^^^^^^^  
KeyError: 'name'  
  
opened ChimeraX session  

> open /Users/rag/Desktop/seg/2-2.cxs format session

Error opening map "/Users/rag/Desktop/seg/2-2.cxs": File 2-2.cxs, format mrc  
MRC header value nsymbt (875113504) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 575, in restore_snapshot  
m = Surface(data['name'], session)  
~~~~^^^^^^^^  
KeyError: 'name'  
  
opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.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 Pro
      Model Identifier: Mac16,7
      Model Number: MX2U3CH/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 1天6小时19分钟

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        LG HDR 4K:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          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

Change History (2)

comment:1 by pett, 4 months ago

Component:	Unassigned → Sessions
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → 'name' not in Surface session-restore data

comment:2 by Tom Goddard, 4 months ago

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

User has a session 2-2.cxs that refers to an MRC file that has bad metadata and fails to open.

File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 575, in restore_snapshot
m = Surface(dataname, session)

KeyError: 'name'

But that should not cause the session restore to fail, and in my test with a bad MRC file linked from a session the session still restores without the volume. So this session file has some other problem.

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