Scenes involving deleted atoms needs better error handling

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509250039 (2025-09-25 00:39:44 UTC)
Description
trying Scenes, not sure what generated the error, maybe clicking a thumbnail that was already selected?

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  

> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  
UCSF ChimeraX version: 1.11.dev202509250039 (2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Scenes

> open 4enl format mmcif fromDatabase pdb

4enl title:  
Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal-
bipyramidal geometry of the cation binding site [more info...]  
  
Chain information for 4enl #1  
---  
Chain | Description | UniProt  
A | ENOLASE | ENO1_YEAST 1-436  
  
Non-standard residues in 4enl #1  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open 1muc

1muc title:  
Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more
info...]  
  
Chain information for 1muc #2  
---  
Chain | Description | UniProt  
A B | MUCONATE LACTONIZING ENZYME | CATB_PSEPU 1-373  
  
Non-standard residues in 1muc #2  
---  
MN — manganese (II) ion  
  
1muc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close #2

> scenes save ""

> open 1muc

1muc title:  
Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more
info...]  
  
Chain information for 1muc #2  
---  
Chain | Description | UniProt  
A B | MUCONATE LACTONIZING ENZYME | CATB_PSEPU 1-373  
  
Non-standard residues in 1muc #2  
---  
MN — manganese (II) ion  
  
1muc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> set bgColor white

> scenes save ""

> graphics silhouettes true

> scenes restore 2

> scenes save 2

> graphics silhouettes true

> scenes save 2

> mmaker #2 to #1

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 4enl, chain A (#1) with 1muc, chain A (#2), sequence alignment
score = 233  
RMSD between 68 pruned atom pairs is 0.997 angstroms; (across all 308 pairs:
9.546)  
  

> delete /B

> view

> scenes restore 2

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/tool.py", line 130, in scene_selected_cb  
run(self.session, f'scene restore {StringArg.unparse(scene_name)}')  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.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
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/cmd.py", line 61, in restore_scene  
session.scenes.restore_scene(scene_name)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/manager.py", line 100, in restore_scene  
self.get_scene(scene_name).restore_scene()  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/scene.py", line 199, in restore_scene  
model.restore_scene(scene_data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1493, in restore_scene  
Structure.restore_scene(self, scene_data['structure state'])  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 272, in restore_scene  
setattr(collection, attr_name, values[attr_name])  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 5760 does not match objects array length 2886  
  
Error processing trigger "scene selected":  
ValueError: Values array length 5760 does not match objects array length 2886  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
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: iMac
      Model Identifier: Mac15,4
      Model Number: Z19700021LL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 35 days, 6 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
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    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
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    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.17
    ChimeraX-AtomicLibrary: 14.2
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BasicActions: 1.1.3
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    ChimeraX-BlastProtein: 3.0.0
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    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.dev202509250039
    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
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    ChimeraX-IUPAC: 1.0
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    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
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    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
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    ChimeraX-ModelSeries: 1.0.1
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    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-RotamerLibsDunbrack: 2.0
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.2
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-SpaceNavigator: 1.0
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    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
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    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.48.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.4.2
    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
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    colorama: 0.4.6
    comm: 0.2.3
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