ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "I:\Group Data\Group Lamers\Loeff\Pilar Bobadilla
> Ugarte\AlphaFold\fold_2026_08_06_10_34_druh\fold_2026_08_06_10_34_druh_model_1.cif"
> format mmcif

Chain information for fold_2026_08_06_10_34_druh_model_1.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> set bgColor white

> show atoms

[Repeated 1 time(s)]

> hide atoms

> show cartoons

> hide cartoons

> show cartoons

> show atoms

> hide cartoons

> style stick

Changed 8817 atom styles  

> show cartoons

> style sphere

Changed 8817 atom styles  

> style sphere

Changed 8817 atom styles  

> style ball

Changed 8817 atom styles  

> style stick

Changed 8817 atom styles  

> hide atoms

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right zone

[Repeated 1 time(s)]

> show cartoons

> show surfaces

> hide surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_2026_08_06_10_34_druh_model_1.cif_A SES surface
#1.1: minimum, -17.98, mean -2.15, maximum 13.53  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "fold_2026_08_06_10_34_druh_model_1.cif_A SES surface":
minimum -28.49, mean -5.489, maximum 23.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for fold_2026_08_06_10_34_druh_model_1.cif_A SES surface
#1.1: minimum, -17.98, mean -2.15, maximum 13.53  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "fold_2026_08_06_10_34_druh_model_1.cif_A SES surface":
minimum -28.49, mean -5.489, maximum 23.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor

8817 atoms, 1115 residues, 1 surfaces, atom bfactor range 31.1 to 97.7  

> color bypolymer

> color byhetero

> color bychain

> color bypolymer

> rainbow

> zone /A:574

> zone /A:574 residueDistance 6.51 labelDistance 5.21 surfaceDistance 10.4

> zone /A:565

> zone /A:565 residueDistance 8.66 labelDistance 6.93 surfaceDistance 13.9

> zone /A:565 residueDistance 12.2 labelDistance 9.75 surfaceDistance 19.5

> zone /A:82

> ui mousemode right rotate

> ui mousemode right label

> label #1/A:93

> label #1/A:35

[Repeated 1 time(s)]

> mlp

Map values for surface "fold_2026_08_06_10_34_druh_model_1.cif_A SES surface":
minimum -28.49, mean -5.489, maximum 23.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> style stick

Changed 8817 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> hide surfaces

> label #1/A:66

> label #1/A:14

> label #1/A:75

> label #1/A:433

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> sequence chain #1/A

Alignment identifier is 1/A  

> view /A:28

No displayed objects specified.  

> view /A:28

No displayed objects specified.  

> view /A:28

No displayed objects specified.  

> ui mousemode right zone

> zone label false

> zone clear

> zone /A:947

> zone label false

> zone clear

> view /A:28

No displayed objects specified.  

> view /A:30

No displayed objects specified.  

> show atoms

> view /A:28

> zone /A:28

> zone label false

> zone clear

> zone /A:232

> zone label false

> zone clear

> zone /A:126

> zone label false

> zone clear

> close

> open "I:\Group Data\Group Lamers\Loeff\Pilar Bobadilla
> Ugarte\AlphaFold\fold_2026_08_06_10_34_druh\fold_2026_08_06_10_34_druh_model_1.cif"
> format mmcif

Chain information for fold_2026_08_06_10_34_druh_model_1.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> color #1 #aaaaffff

> zone /A:60

> zone label false

> zone clear

> ui mousemode right rotate

> ui mousemode right "translate selected models"

> color bychain

> color bypolymer

> rainbow

> sequence chain #1/A

Alignment identifier is 1/A  

> view /A:28

No displayed objects specified.  

> show atoms

> view /A:28

> hide cartoons

> show cartoons

> hide cartoons

> ui mousemode right zone

> ui mousemode right label

> label #1/A:28

[Repeated 1 time(s)]

> label #1/A:220

> label #1/A:26

> label delete residues

> label #1/A:14

> label delete residues

> label #1/A:28

> label #1/A:220

> label #1/A:30

> label #1/A:27

> label #1/A:23

> label #1/A:22

> ui mousemode right "clip rotate"

> ui mousemode right zone

> zone /A:28

> zone label false

> zone clear

> zone /A:27

> zone label false

> zone clear

> zone /A:217

[Repeated 1 time(s)]

> zone /A:25

> zone label false

> ui mousemode right label

> label #1/A:28

> label #1/A:22

> label #1/A:220

> label #1/A:227

> label #1/A:26

> label #1/A:33

> label delete residues

> label #1/A:30

> label #1/A:227

> label #1/A:28

> label #1/A:27

> label #1/A:20

> label #1/A:22

> label #1/A:217

> label #1/A:220

> label #1/A:67

> label #1/A:68

> close

> open "I:\Group Data\Group Lamers\Loeff\Pilar Bobadilla
> Ugarte\AlphaFold\fold_2026_08_06_10_34_druh\fold_2026_08_06_10_34_druh_model_1.cif"
> format mmcif

Chain information for fold_2026_08_06_10_34_druh_model_1.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> color /E:764 magenta

> color /E:764,762, 92 red

> style /E:764,762, 92

> color /A:764,762, 92 red

> show atoms

> hide atoms

> show atoms

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> close

> open "I:\Group Data\Group Lamers\Loeff\Pilar Bobadilla
> Ugarte\AlphaFold\fold_2026_08_06_10_34_druh\fold_2026_08_06_10_34_druh_model_1.cif"
> format mmcif

Chain information for fold_2026_08_06_10_34_druh_model_1.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> color /A:764,762, 790, 91, 92, 827 red

> style /A:764,762, 790, 91, 92, 827 stick

Changed 56 atom styles  

> label #1/A:863

> label delete residues

> show atoms

> color bychain

> hide cartoons

> show cartoons

> hide atoms

> hide surfaces

> color bynucleotide

> color /A:764,762, 790, 91, 92, 827 red

> label #1/A:827

> label #1/A:91

> label #1/A:762

> label #1/A:764

> label #1/A:790

> ui mousemode right zone

> zone /A:762

> zone label false

> zone clear

> zone /A:762

> ui mousemode right label

> label #1/A:764

> label delete residues

> label #1/A:790

> label delete residues

> label #1/A:762

> label #1/A:790

> label #1/A:827

> label #1/A:764

> label #1/A:92

> label #1/A:91

> show atoms

> hide atoms

> show atoms

> hide cartoons

> show cartoons

> hide atoms

> ui mousemode right label

> label #1/A:91

> label #1/A:764

> ui mousemode right zone

> zone /A:764

> zone label false

> zone /A:92

> zone label false

> zone clear

> zone /A:92

> zone label false

> zone /A:863

> zone label false

> zone /A:1105

> zone label false

> zone /A:759

> zone label false

> zone clear

> zone /A:876

> zone /A:868

> close

> open "I:\Group Data\Group Lamers\Loeff\Pilar Bobadilla
> Ugarte\AlphaFold\fold_2026_08_06_10_34_druh\fold_2026_08_06_10_34_druh_model_1.cif"
> format mmcif

Chain information for fold_2026_08_06_10_34_druh_model_1.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> zone label false

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 683, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 594, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 237, in mouse_drag  
self._scale_range(scale)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 223, in _scale_range  
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\zone\zone.py", line 64, in _show_zone  
ratoms = residue.atoms  
^^^^^^^^^^^^^  
File "atomic_cpp/cymol.pyx", line 1046, in
chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 1046, in
chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.6881
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows

Manufacturer: HP
Model: HP Elite SFF 600 G9 Desktop PC
OS: Microsoft Windows 11 Enterprise (Build 22631.7376)
Memory: 16,833,437,696
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-12500
OSLanguage: en-US

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.5.20
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    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: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    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: 1.2.2
    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: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    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: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    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
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    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: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
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    referencing: 0.37.0
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