Render by attribute configure: 'MarkedHistogram' object has no attribute '_min_val'

[ever.odonnell@…]

The following bug report has been submitted:
Platform:        macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC)
Description
I get an error when i try to go back to previous colorings and the structure turns all white 

Log:
UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8hnh

8hnh title:  
Cryo-EM structure of human OATP1B1 in complex with simeprevir [more info...]  
  
Chain information for 8hnh #1  
---  
Chain | Description | UniProt  
A | Solute carrier organic anion transporter family member 1B1 | SO1B1_HUMAN 1-691  
  
Non-standard residues in 8hnh #1  
---  
30B —
(2R,3aR,10Z,11aS,12aR,14aR)-N-(cyclopropylsulfonyl)-2-({7-methoxy-8-methyl-2-[4-(1-methylethyl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)-5-methyl-4,14-dioxo-2,3,3a,4,5,6,7,8,9,11a,12,13,14,14a-tetradecahydrocyclopenta[c]cyclopropa[g][1,6]diazacyclotetradecine-12a(1H)-carboxamide  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> label delete

> select protein

4142 atoms, 4250 bonds, 3 pseudobonds, 563 residues, 2 models selected  

> hide sel atoms

> color (#!1 & sel) light gray

> graphics silhouettes true

> lighting soft

> select celar

Expected an objects specifier or a keyword  

> select clear

> open /Users/everodonnell/Documents/slco1b1DMS2024March.csv chains /A

Summary of feedback from opening
/Users/everodonnell/Documents/slco1b1DMS2024March.csv  
---  
notes | Ignored 2710 variants: 785 deletions p.(A112_L113del), p.(A13del), p.(A200_K201del) ..., 1925 insertions p.(A11_E12insG), p.(A11_E12insGS), p.(A11_E12insGSG) ...  
Associated 1 chain to mutation set slco1b1DMS2024March.  
Associated chain /A with 0 mismatches.  
  
Opened deep mutational scan data for 13465 mutations of 676 residues with
score names len, lfsr_ros, mean_ros, pos, score_GFP, score_MTX. Assigned
scores to 549 of 563 residues of chain #1/A. Found scores for 127 residues not
present in structures #1/A.  
Color the structure first, then you can adjust colors  

> mutationscores define mutation_score fromScoreName score_GFP combine mean

Defined score mutation_score having range -2.5 to 0.96 for 676 residues using
13450 mutations  
Set attribute mutation_score for 549 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white

4208 atoms, 565 residues, atom mutation_score range -2.5 to 0.96  

> ui tool show "Render/Select by Attribute"

Desktop color scheme is light  

> mutationscores scatterplot len lfsr_ros

Plotted 13435 mutations with len on x-axis and lfsr_ros on y-axis  

> mutationscores scatterplot len lfsr_ros

Plotted 13435 mutations with len on x-axis and lfsr_ros on y-axis  

> set bgColor white

Drag select of 16 atoms, 16 bonds  

> select clear

> select :NAG

42 atoms, 43 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select ::name="30B"

52 atoms, 58 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel forest green

> color sel hot pink

> color sel yellow

> color sel orange

> color sel byhetero

> select clear

> mutationscores define mutation_score fromScoreName score_GFP combine count

Defined score mutation_score having range 13 to 20 for 676 residues using
13450 mutations  
Re-registration of attr 'mutation_score' with Residue by Deep Mutational Scan
changes type information  
Set attribute mutation_score for 549 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> 19,blue:19.6,white:20.2,white:20.8,red noValueColor white

4208 atoms, 565 residues, atom mutation_score range 13 to 20  

> ui tool show "Render/Select by Attribute"

> help help:user/tools/mutationscores.html#coloring

> color byattribute r:raw_gfp #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white

All 'raw_gfp' values are None  

> color byattribute r:raw_gfp #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white

All 'raw_gfp' values are None  

> color byattribute r:raw_gfp #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white

All 'raw_gfp' values are None  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 964, in
_adjust_colors  
_show_render_by_attribute_panel(self.session, mset, options['attribute_name'],  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 338, in
_show_render_by_attribute_panel  
rba_gui.configure(models = models, target = 'residues', tab = 'render',
attr_name = attribute_name,  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 476, in configure  
marker = markers.append(arg)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 944, in append  
self.histogram._ensure_range(marker.xy)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range  
if x < self._min_val and (self._draw_min is None or x < self._draw_min):  
^^^^^^^^^^^^^  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range  
if x < self._min_val and (self._draw_min is None or x < self._draw_min):  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 964, in
_adjust_colors  
_show_render_by_attribute_panel(self.session, mset, options['attribute_name'],  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 338, in
_show_render_by_attribute_panel  
rba_gui.configure(models = models, target = 'residues', tab = 'render',
attr_name = attribute_name,  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 476, in configure  
marker = markers.append(arg)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 944, in append  
self.histogram._ensure_range(marker.xy)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range  
if x < self._min_val and (self._draw_min is None or x < self._draw_min):  
^^^^^^^^^^^^^  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range  
if x < self._min_val and (self._draw_min is None or x < self._draw_min):  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEH3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3 (23D56)
      Kernel Version: Darwin 23.3.0
      Time since boot: 1 hour, 30 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.2.0
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    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: 1.12rc202605142114
    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: 1.2.1
    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: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    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: 1.50.6
    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: 8.4.0
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
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    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: 3.15
    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
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    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
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    line_profiler: 5.0.0
    lxml: 6.0.2
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    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: 2.21.2
    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: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    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: 4.9.6
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    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: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.17.1
    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: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    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: 0.0.29
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 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: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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
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