ChimeraX bug report submission

[asadi1@…]

The following bug report has been submitted:
Platform:        macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.9.dev202405090425 (2024-05-09 04:25:54 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.9.dev202405090425 (2024-05-09)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mojganasadi/Downloads/4GA8.pdb

4GA8.pdb title:  
Human AKR1B10 mutant V301L complexed with nadp+ and sorbinil [more info...]  
  
Chain information for 4GA8.pdb #1  
---  
Chain | Description | UniProt  
A | ALDO-keto reductase family 1 member B10 | AK1BA_HUMAN 1-316  
  
Non-standard residues in 4GA8.pdb #1  
---  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
SBI — sorbinil  
  
170 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select ::name="SBI"

17 atoms, 19 bonds, 1 residue, 1 model selected  

> ui tool show "Model Loops"

Populating font family aliases took 53 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:220

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:220

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add /A:21

28 atoms, 30 bonds, 2 residues, 1 model selected  

> hide #* target a

> show sel target ab

> select clear

> select ::name="ARG"

110 atoms, 100 bonds, 10 residues, 1 model selected  

> select /A:218

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ARG"

110 atoms, 100 bonds, 10 residues, 1 model selected  

> select clear

> select add /A:297

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> select clear

> select /A:21@CH2

1 atom, 1 residue, 1 model selected  

> select add /A:220@CH2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance /A:21@CH2 /A:220@CH2

Distance between /A TRP 21 CH2 and TRP 220 CH2: 3.601Å  

> select /A:220@CZ3

1 atom, 1 residue, 1 model selected  

> ui tool show "Build Structure"

> build modify /A:220@CZ3 C 3 geometry tetrahedral resName UNK

> select clear

> select /A:220@HZ3

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /A:220@CZ3

1 atom, 1 residue, 1 model selected  

> select /A:220@NE1

1 atom, 1 residue, 1 model selected  

> select add /A:218@NE

2 atoms, 2 residues, 1 model selected  

> distance /A:220@NE1 /A:218@NE

Distance between /A UNK 220 NE1 and ARG 218 NE: 3.818Å  

> select clear

> select ::name="CYS"

24 atoms, 20 bonds, 4 residues, 1 model selected  

> hide #* target a

> show sel target ab

> hide sel target a

> select clear

> select add /A:210

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:211

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add /A:212

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select add /A:213

21 atoms, 19 bonds, 3 residues, 1 model selected  

> select add /A:214

25 atoms, 22 bonds, 4 residues, 1 model selected  

> select add /A:215

31 atoms, 27 bonds, 5 residues, 1 model selected  

> select add /A:216

38 atoms, 34 bonds, 6 residues, 1 model selected  

> select add /A:217

46 atoms, 41 bonds, 7 residues, 1 model selected  

> select add /A:219

53 atoms, 48 bonds, 8 residues, 1 model selected  

> select add /A:218

64 atoms, 58 bonds, 9 residues, 1 model selected  

> select add /A:220

78 atoms, 73 bonds, 10 residues, 1 model selected  

> select add /A:221

83 atoms, 77 bonds, 11 residues, 1 model selected  

> select add /A:222

92 atoms, 85 bonds, 12 residues, 1 model selected  

> select add /A:223

99 atoms, 92 bonds, 13 residues, 1 model selected  

> select add /A:224

108 atoms, 100 bonds, 14 residues, 1 model selected  

> select add /A:225

116 atoms, 107 bonds, 15 residues, 1 model selected  

> select add /A:226

123 atoms, 114 bonds, 16 residues, 1 model selected  

> color sel magenta

> select clear

> color byhetero

> ui tool show "Color Actions"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 64, in <lambda>  
button.released.connect(lambda *, clr=spaced_name: self._color(clr))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
TypeError: can only concatenate str (not "NoneType") to str  
  
TypeError: can only concatenate str (not "NoneType") to str  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
  
See log for complete Python traceback.  
  

> set bgColor white

> select ::name="TYR"

133 atoms, 133 bonds, 11 residues, 1 model selected  

> select /A:49

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="HIS"

90 atoms, 90 bonds, 9 residues, 1 model selected  

> select /A:111

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="CYS"

24 atoms, 20 bonds, 4 residues, 1 model selected  

> select /A:299

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> select /A:160

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:111

10 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 10 atom styles  

> style sel ball

Changed 10 atom styles  

> select clear

[Repeated 2 time(s)]

> select /A:49

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 12 atom styles  

> select clear

> select /A:299

6 atoms, 5 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 6 atom styles  

> select clear

> color blue

> show cartoons

> color purple

> ui tool show "Color Actions"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 188, in <lambda>  
button.released.connect(lambda *, clr=spaced_name: self._color(clr))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
TypeError: can only concatenate str (not "NoneType") to str  
  
TypeError: can only concatenate str (not "NoneType") to str  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Color Actions"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 188, in <lambda>  
button.released.connect(lambda *, clr=spaced_name: self._color(clr))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
TypeError: can only concatenate str (not "NoneType") to str  
  
TypeError: can only concatenate str (not "NoneType") to str  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Color Actions"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 188, in <lambda>  
button.released.connect(lambda *, clr=spaced_name: self._color(clr))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
TypeError: can only concatenate str (not "NoneType") to str  
  
TypeError: can only concatenate str (not "NoneType") to str  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z15Z0005ELL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 13822.61.10

Software:

    System Software Overview:

      System Version: macOS 26.2 (25C56)
      Kernel Version: Darwin 25.2.0
      Time since boot: 7 days, 11 hours, 21 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 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    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: 2023.11.17
    cftime: 1.6.3
    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: 2.12.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.3
    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: 1.2.3
    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: 1.0.4
    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.dev202405090425
    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
    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: 1.1.9
    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
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    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: 1.3.0
    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: 1.16.4
    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
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 1.2.1
    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: 4.51.0
    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: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    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: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.1
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    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
    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
    setuptools-scm: 8.0.4
    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
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10