Opened 10 months ago

Closed 10 months ago

#16488 closed defect (fixed)

Sample code link broken

Reported by: deng.luo@… Owned by: pett
Priority: normal Milestone:
Component: Documentation Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202411070255 (2024-11-07 02:55:45 UTC)
Description
Clicking the "sample code" link on the building and distributing bundles web page

    https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html

returns the message "Bundle sample code not available."


Log:
UCSF ChimeraX version: 1.9.dev202411070255 (2024-11-07)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.179846  
ChimeraX bin clustering: 0:00:13.356153  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.150872  
ChimeraX bin clustering, 5124 clusters: 0:00:13.403455  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/scripting.py", line 94, in open_python_script  
code = compile(data, stream.name, 'exec')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "fit_res_clustering_benchmark_mod3.py", line 54  
return tf.rotation_angle() < angle:  
^  
SyntaxError: invalid syntax  
  
Error opening python file fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.163246  
Traceback (most recent call last):  
File "fit_res_clustering_benchmark_mod3.py", line 68, in <module>  
close = any_close_transform(b, ptf)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "fit_res_clustering_benchmark_mod3.py", line 42, in any_close_transform  
if bc in b.bins.bins:  
^^^^^^^^^^^^^^^^^  
TypeError: unhashable type: 'list'  
  
Error opening python file fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.236596  
Traceback (most recent call last):  
File "fit_res_clustering_benchmark_mod3.py", line 68, in <module>  
close = any_close_transform(b, ptf)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "fit_res_clustering_benchmark_mod3.py", line 45, in any_close_transform  
for btf in tflist:  
TypeError: 'Place' object is not iterable  
  
Error opening python file fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.192578  
ChimeraX bin clustering, 5124 clusters: 0:00:07.530036  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.269716  
ChimeraX bin clustering, 5114 clusters: 0:00:06.699166  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.242794  
ChimeraX bin clustering, 5118 clusters: 0:00:06.691703  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.242251  
ChimeraX bin clustering, 5109 clusters: 0:00:08.460144  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.244295  
ChimeraX bin clustering, 5124 clusters: 0:00:09.167058  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.201608  
ChimeraX bin clustering, 5124 clusters: 0:00:07.471888  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.278825  
ChimeraX bin clustering, 5124 clusters: 0:00:07.531410  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.211783  
ChimeraX bin clustering, 5114 clusters: 0:00:06.671910  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.281134  
ChimeraX bin clustering, 5114 clusters: 0:00:06.681882  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.207248  
ChimeraX bin clustering, 5124 clusters: 0:00:12.686955  
executed fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.243002  
Traceback (most recent call last):  
File "fit_res_clustering_benchmark_mod3.py", line 60, in <module>  
b = bins.Binned_Transforms(angle_tolerance * pi / 180, shift_tolerance,
mol_center, bfactor)  
^^^^^^^  
NameError: name 'bfactor' is not defined  
  
Error opening python file fit_res_clustering_benchmark_mod3.py  

> open fit_res_clustering_benchmark_mod3.py

Clustering 250000 fits  
Convert to matrix time: 0:00:01.230716  
ChimeraX bin clustering, 5124 clusters: 0:00:32.311184  
executed fit_res_clustering_benchmark_mod3.py  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
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: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 105 days, 16 hours, 13 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: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.84
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    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: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.10
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-Clipper: 0.23.0
    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: 1.9.dev202411070255
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NIHPresets: 1.2.6
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.2.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 2.5.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.42
    ChimeraX-Umap: 1.0
    ChimeraX-Ummbas-Anaglyph: 0.1
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    DiffFit: 0.4.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    fsspec: 2024.9.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    joblib: 1.4.2
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    llvmlite: 0.43.0
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    mpmath: 1.3.0
    mrcfile: 1.5.3
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.60.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scikit-learn: 1.5.1
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    sympy: 1.13.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    threadpoolctl: 3.5.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 2.4.1
    tornado: 6.4.1
    tqdm: 4.66.4
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    umap-learn: 0.5.6
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (3)

comment:1 by Tom Goddard, 10 months ago

Cc: Tom Goddard added
Component: Unassigned → Documentation
Owner: set to pett
Platform: → all
Project: → ChimeraX
Reporter: changed from goddard@… to deng.luo@…
Status: new → assigned
Summary: ChimeraX bug report submission → Sample code link broken

comment:2 by Roden Deng Luo, 10 months ago 

Hi, Thanks for putting it up. Please also consider including the C++ source
code in the sample code or removing the "Because the sample code includes
C++ source code that need to be compiled" and C++-related from
https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html.

Best,
Roden


On Tue, Dec 17, 2024 at 10:30 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

comment:3 by pett, 10 months ago

Resolution: → fixed
Status: assigned → closed

Fixed. The git code checkout had changed file systems, so git config had to be notified that the new checkout directory was "safe".

The sample bundle does include the C++ source code (under its "src" directory).

Note: See TracTickets for help on using tickets.