Opened 4 months ago

Closed 4 months ago

#17979 closed defect (nonchimerax)

alphafold contacts: Permission denied

Reported by: barnabas.williams@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
When using "alphafold contacts /B to /C outputFile contact.txt" i receive the following error. Unsure if it is my PC not having permission or something

"PermissionError: [Errno 13] Permission denied: 'contact.txt'

File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts
with open(output_file, 'w') as f:
^^^^^^^^^^^^^^^^^^^^^^

See log for complete Python traceback."

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "F:\\\Draper Group Share\\\PERSONAL FOLDERS\\\Barney\\\Projects\\\BGW10
> - MRC RIPR\\\02 Sequences\\\AF predictions
> Pv\\\fold_pvpcr_tail_trunc_full_data_0.json"

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open F:\\\Draper Group Share\\\PERSONAL FOLDERS\\\Barney\\\Projects\\\BGW10 -
MRC RIPR\\\02 Sequences\\\AF predictions
Pv\\\fold_pvpcr_tail_trunc_full_data_0.json structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open "F:\Draper Group Share\PERSONAL FOLDERS\Barney\Projects\BGW10 - MRC
> RIPR\02 Sequences\AF predictions Pv\fold_pvpcr_tail_trunc_model_0.cif"
> format mmcif

Chain information for fold_pvpcr_tail_trunc_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  

> alphafold contacts

Missing or invalid "atoms" argument: empty atom specifier  

> alphafold contacts /B toAtoms /A

Structure fold_pvpcr_tail_trunc_model_0.cif #1 does not have PAE data opened  

> open "F:/Draper Group Share/PERSONAL FOLDERS/Barney/Projects/BGW10 - MRC
> RIPR/02 Sequences/AF predictions Pv/fold_pvpcr_tail_trunc_full_data_0.json"

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open F:/Draper Group Share/PERSONAL FOLDERS/Barney/Projects/BGW10 - MRC
RIPR/02 Sequences/AF predictions Pv/fold_pvpcr_tail_trunc_full_data_0.json
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> toolshed show

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "F:\\\Draper Group Share\\\PERSONAL
> FOLDERS\\\Barney\\\Projects\\\BGW10 - MRC RIPR\\\02 Sequences\\\AF
> predictions Pv\\\fold_pvpcr_tail_trunc_full_data_0.json"

> alphafold contacts /B toAtoms /A

Found 7 residue or atom pairs within distance 3  

> alphafold contacts /B toAtoms /A outputFile contact_pae.txt

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'contact_pae.txt'  
  
PermissionError: [Errno 13] Permission denied: 'contact_pae.txt'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> alphafold contacts /B toAtoms /A outputFile contact.txt

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'contact.txt'  
  
PermissionError: [Errno 13] Permission denied: 'contact.txt'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> interfaces select /A & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0 bothSides true

29 contacting residues  

> select add #1

8540 atoms, 8700 bonds, 7 pseudobonds, 1090 residues, 2 models selected  

> select subtract #1

Nothing selected  

> alphafold contacts /B toAtoms /A outputFile contact.txt

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'contact.txt'  
  
PermissionError: [Errno 13] Permission denied: 'contact.txt'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> alphafold contacts /B toAtoms /A

Found 7 residue or atom pairs within distance 3  

> alphafold contacts /B toAtoms /A select

Expected a keyword  

> alphafold contacts /B toAtoms /A selectS

Expected a keyword  

> alphafold contacts /B toAtoms /A Select

Expected a keyword  

> select ((/A & ::polymer_type>0 ) & ((/B & ::polymer_type>0 ) :<3)) | ((/B & ::polymer_type>0 ) & ((/A & ::polymer_type>0 ) :<3))

93 atoms, 85 bonds, 7 pseudobonds, 11 residues, 2 models selected  

> select ((/A & ::polymer_type>0 ) & ((/B & ::polymer_type>0 ) :<3)) | ((/B & ::polymer_type>0 ) & ((/A & ::polymer_type>0 ) :<3))

93 atoms, 85 bonds, 7 pseudobonds, 11 residues, 2 models selected  

> show sel atoms

> alphafold contacts /B toAtoms /A outputFile

Missing "outputFile" keyword's argument  

> alphafold contacts /B toAtoms /A outputFile

Missing "outputFile" keyword's argument  

> alphafold contacts /B toAtoms /A outputFile page

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'page'  
  
PermissionError: [Errno 13] Permission denied: 'page'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> outputFile Contacts.txt

Unknown command: outputFile Contacts.txt  

> output contacts.txt

Unknown command: output contacts.txt  

> alphafold contacts /B toAtoms /C outputFile contact.txt

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'contact.txt'  
  
PermissionError: [Errno 13] Permission denied: 'contact.txt'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 131, in alphafold_contacts  
with open(output_file, 'w') as f:  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.6078
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 7440
OS: Microsoft Windows 11 Education (Build 22631)
Memory: 16,479,051,776
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i7-1365U
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    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: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    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-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
    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: 1.2.6
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    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: 1.5.18
    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-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-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    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
    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: 1.41
    ChimeraX-Umap: 1.0
    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
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    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
    numexpr: 2.10.2
    numpy: 2.2.4
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    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
    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-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 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
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    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
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (3)

comment:1 by barnabas.williams@…, 4 months ago 

Never mind - it was a permission error on my computer. I moved the directory and it works fine. \U0001f60a

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: 13 June 2025 15:40
To: Barnabas Williams <barnabas.williams@paediatrics.ox.ac.uk>
Subject: Re: [ChimeraX] #17979: ChimeraX bug report submission

#17979: ChimeraX bug report submission
---------------------------------+-----------------------------
 Reporter:  barnabas.williams@\u2026  |                Type:  defect
   Status:  new                  |            Priority:  normal
Component:  Unassigned           |          Blocked By:
 Blocking:                       |  Notify when closed:
---------------------------------+-----------------------------

comment:2 by pett, 4 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → alphafold contacts: Permission denied

comment:3 by pett, 4 months ago

Resolution: → nonchimerax
Status: assigned → closed
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