Testing bug reporting with updated prereqs

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202401162132 (2024-01-16 21:32:53 UTC)
Description
Testing bug reporting after updating many prerequisites.

Log:
UCSF ChimeraX version: 1.8.dev202401162132 (2024-01-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/chimerax/prereqs/pips/test.cxs format session

Log from Tue Jan 16 16:14:58 2024UCSF ChimeraX version: 1.8.dev202401162132
(2024-01-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Compositor returned null texture  

> open 8f76 format mmcif fromDatabase pdb

8f76 title:  
Human olfactory receptor OR51E2 bound to propionate in complex with miniGs399
[more info...]  
  
Chain information for 8f76 #1  
---  
Chain | Description | UniProt  
A | Olfactory receptor 51E2 | O51E2_HUMAN 2-320  
N | Nanobody 35 |  
X | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
GNAS2_HUMAN 5-195 204-394  
Y | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340  
Z | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71  
  
Non-standard residues in 8f76 #1  
---  
PPI — propanoic acid  
  

> open 1 fromDatabase pdbdev

Summary of feedback from opening 1 fetched from pdbdev  
---  
warning | No mmCIF models found.  
notes | aligned 3f3f A, 308 residues, rms 1.4  
aligned 2pm7 D, 288 residues, rms 1.345  
aligned ScNup84N_7-488_new2.pdb A, 440 residues, rms 1.315  
aligned ScNup84C_506-726_new2.pdb A, 209 residues, rms 1.359  
aligned ScNup85_44-744_new.pdb B, 604 residues, rms 22.16  
aligned ScNup120_1-1037_new.pdb C, 922 residues, rms 14.52  
aligned ScNup133N_56-480_new.pdb D, 373 residues, rms 1.303  
aligned ScNup133C_490_1157_new.pdb D, 658 residues, rms 1.335  
aligned ScNup145C_126-553_new2.pdb E, 416 residues, rms 1.346  
  
Entities and chains for PDBDEV_00000001.cif  
---  
Entity | Chains  
Nup120 | C  
Nup133 | D  
Nup145c | E  
Nup84 | A  
Nup85 | B  
Sec13 | G  
Seh1 | F  
  
3f3f A title:  
Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 [more
info...]  
  
2pm7 D title:  
Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat,
selenomethionine version [more info...]  
  
Opened nup84_kinked_from_class2.pgm 2D electron microscopy as #2.2.3, grid
size 120,120,1, pixel 5.91,5.91,1, shown at step 1, values uint8  
Opened nup84.mrc as #2.3.1.2.1, grid size 43,43,46, pixel 6.67,6.67,6.67,
shown at level 4.41, step 1, values float32  
Opened nup85.mrc as #2.3.1.2.2, grid size 45,45,48, pixel 6.67, shown at level
2.4, step 1, values float32  
Opened nup120.mrc as #2.3.1.2.3, grid size 48,44,44, pixel 6.67,6.67,6.67,
shown at level 4.63, step 1, values float32  
Opened nup133.mrc as #2.3.1.2.4, grid size 47,45,52, pixel 6.67,6.67,6.67,
shown at level 3.43, step 1, values float32  
Opened nup145c.mrc as #2.3.1.2.5, grid size 44,45,44, pixel 6.67,6.67,6.67,
shown at level 3.85, step 1, values float32  
Opened seh1.mrc as #2.3.1.2.6, grid size 40,38,41, pixel 6.67,6.67,6.67, shown
at level 3.09, step 1, values float32  
Opened sec13.mrc as #2.3.1.2.7, grid size 36,37,32, pixel 6.67,6.67,6.67,
shown at level 4.29, step 1, values float32  
Opened nup84.mrc as #2.3.2.2.1, grid size 44,44,44, pixel 6.67, shown at level
3.17, step 1, values float32  
Opened nup85.mrc as #2.3.2.2.2, grid size 45,48,41, pixel 6.67,6.67,6.67,
shown at level 2.18, step 1, values float32  
Opened nup120.mrc as #2.3.2.2.3, grid size 46,43,48, pixel 6.67,6.67,6.67,
shown at level 3.6, step 1, values float32  
Opened nup133.mrc as #2.3.2.2.4, grid size 46,45,52, pixel 6.67,6.67,6.67,
shown at level 2.63, step 1, values float32  
Opened nup145c.mrc as #2.3.2.2.5, grid size 41,43,43, pixel 6.67,6.67,6.67,
shown at level 3.95, step 1, values float32  
Opened seh1.mrc as #2.3.2.2.6, grid size 38,35,38, pixel 6.67,6.67,6.67, shown
at level 2.8, step 1, values float32  
Opened sec13.mrc as #2.3.2.2.7, grid size 37,34,32, pixel 6.67,6.67,6.67,
shown at level 4.49, step 1, values float32  
Opened IHM file /Users/goddard/Downloads/ChimeraX/PDBDev/PDBDEV_00000001.cif  
2 xray and nmr models  
7 comparative models  
7 sequence alignments  
20 templates  
164 DSS crosslinks, 127 EDC crosslinks  
1 electron microscopy images  
2 sphere models  
14 localization maps  

> close #1

> view

> close

> open /Users/goddard/ucsf/data/allen_cell/AICS-10/AICS-10_1.ome.tif

Opened multi-channel map AICS-10_1.ome.tif as #1, 8 channels, grid size
1024,1024,64, pixel 0.065,0.065,0.29, shown at step 2, values uint16  

> volume #1.1 level 514.1,0 level 3334,0.8 level 1.617e+04,1

> volume #1.1 level 514.1,0 level 2920,0.8588 level 1.617e+04,1

> close

> open 8f76 format mmcif fromDatabase pdb

8f76 title:  
Human olfactory receptor OR51E2 bound to propionate in complex with miniGs399
[more info...]  
  
Chain information for 8f76 #1  
---  
Chain | Description | UniProt  
A | Olfactory receptor 51E2 | O51E2_HUMAN 2-320  
N | Nanobody 35 |  
X | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
GNAS2_HUMAN 5-195 204-394  
Y | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340  
Z | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71  
  
Non-standard residues in 8f76 #1  
---  
PPI — propanoic acid  
  

> save test.cxs

——— End of log from Tue Jan 16 16:14:58 2024 ———

opened ChimeraX session  

> interfaces ~solvent

5 buried areas: Y Z 2196, Y X 1476, A X 1220, X N 843, Y N 602  

> close

> open 28896 format ccp4 fromDatabase emdb

Opened emdb 28896 as #1, grid size 288,288,288, pixel 0.81, shown at level
0.54, step 2, values float32, fit PDB 8f76  

> volume #1 level 1.089

> volume #1 step 1

> lighting soft

> volume gaussian #1 sDev 2

Opened emdb 28896 gaussian as #2, grid size 288,288,288, pixel 0.81, shown at
step 1, values float32  

> volume #2 level 0.4005

> close #2

> open 8f76 format mmcif fromDatabase pdb

8f76 title:  
Human olfactory receptor OR51E2 bound to propionate in complex with miniGs399
[more info...]  
  
Chain information for 8f76 #2  
---  
Chain | Description | UniProt  
A | Olfactory receptor 51E2 | O51E2_HUMAN 2-320  
N | Nanobody 35 |  
X | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
GNAS2_HUMAN 5-195 204-394  
Y | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340  
Z | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71  
  
Non-standard residues in 8f76 #2  
---  
PPI — propanoic acid  
  

> hide atoms

> show cartoons

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 8165 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 11 days, 15 hours, 6 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    alphashape: 1.3.1
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.15
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.52
    ChimeraX-AtomicLibrary: 12.1.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.11
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202401162132
    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-DistMonitor: 1.4
    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: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    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: 1.0.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.2.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.15
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.5
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    click: 8.1.7
    click-log: 0.4.0
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.3
    MarkupSafe: 2.1.3
    matplotlib: 3.8.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.7
    nest-asyncio: 1.5.9
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.26.3
    openvr: 1.26.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.7
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynmrstar: 3.3.2
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3301
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.1
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.1
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    Rtree: 1.1.0
    scipy: 1.11.4
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    shapely: 2.0.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.12.9
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    trimesh: 4.0.8
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Tom Goddard]

All working.