'MarkedHistogram' object has no attribute '_min_val'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8av5 fromDatabase pdb format mmcif

8av5 title:  
Glycosylated PaDa-I mutant of Unspecific Peroxygenase from Agrocybe aegerita
[more info...]  
  
Chain information for 8av5 #1  
---  
Chain | Description | UniProt  
A | Aromatic peroxygenase | APO1_AGRAE 4-327  
  
Non-standard residues in 8av5 #1  
---  
ACT — acetate ion  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CL — chloride ion  
HEM — protoporphyrin IX containing Fe (HEME)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
MG — magnesium ion  
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)  
  
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> surface

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> volume style image

No volumes specified  

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> mlp

Map values for surface "8av5_A SES surface": minimum -30.57, mean -4.768,
maximum 22.89  
To also show corresponding color key, enter the above mlp command and add key
true  

> rainbow

> color bypolymer

> color bychain

> color byhetero

> mlp

Map values for surface "8av5_A SES surface": minimum -30.57, mean -4.768,
maximum 22.89  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/A LYS 261 CE  
/A LYS 261 NZ  
/A GLU 20 OE1  
/A GLU 20 CD  
/A GLU 20 CG  
/A GLU 20 OE2  
/A ARG 327 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 8av5_A SES surface #1.2: minimum, -13.52, mean -2.31,
maximum 12.37  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "8av5_A SES surface": minimum -30.57, mean -4.768,
maximum 22.89  
To also show corresponding color key, enter the above mlp command and add key
true  
Alignment identifier is 1/A  

> LPPG

Unknown command: LPPG  

> label #1 attribute label_one_letter_code

> ~label #1 residues

> label height 1

Label command requires an atom specifier to create labels.  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> show target ab

> surface

> color byhetero

> color bychain

> color bypolymer

> coulombic

Coulombic values for 8av5_A SES surface #1.2: minimum, -13.52, mean -2.31,
maximum 12.37  
To also show corresponding color key, enter the above coulombic command and
add key true  

> style stick

Changed 3075 atom styles  

> cartoon

> surface hidePatches

> surface

> set bgColor white

> lighting simple

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting simple

> set bgColor black

> set bgColor white

> style sphere

Changed 3075 atom styles  

> style sphere

Changed 3075 atom styles  

> style stick

Changed 3075 atom styles  

> style ball

Changed 3075 atom styles  

> style ball

Changed 3075 atom styles  

> style stick

Changed 3075 atom styles  

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> save C:\Users\sob/Desktop\image1.png supersample 3

> volume style surface

No volumes specified  

> ui tool show "Render/Select by Attribute"

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> undo

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> surface hidePatches

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> hide target a

> undo

> hide target a

> surface

> mlp

Map values for surface "8av5_A SES surface": minimum -30.57, mean -4.768,
maximum 22.89  
To also show corresponding color key, enter the above mlp command and add key
true  

> measure sasa

Solvent accessible area for all atoms (3075 atoms) = 15377  

> measure sasa

Solvent accessible area for all atoms (3075 atoms) = 15377  

> sasa protein

Unknown command: sasa protein  

> measure sasa protein

Solvent accessible area for protein (2504 atoms) = 13696  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 332, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 466, in _dispatch  
self.select(apply=apply)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 417, in select  
markers.coord_type = "absolute"  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 953, in coord_type  
self._convert_coords()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 1112, in _convert_coords  
m.xy = conv_func(m.xy)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2111
OpenGL renderer: Intel(R) HD Graphics 630
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 5050
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,031,229,440
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7500 CPU @ 3.40GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

[Eric Pettersen]

Duplicate of #15759