Opened 3 years ago

Closed 3 years ago

#8172 closed defect (fixed)

Read MOLE format: KeyError: 'Channels'

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold match
> MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> alphafold search
> MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Webservices job id: XN6ICFTRP8ITV6W2  

> alphafold fetch A0A1B6FCL0 version 4

Fetching compressed AlphaFold A0A1B6FCL0 from
https://alphafold.ebi.ac.uk/files/AF-A0A1B6FCL0-F1-model_v4.cif  
Chain information for AlphaFold A0A1B6FCL0 #1  
---  
Chain | Description | UniProt  
A | Neur_chan_LBD domain-containing protein | A0A1B6FCL0_9HEMI  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A1B6FCL0 | MGHNI...IMLIV | 22.1 | 58.8  

> alphafold fetch A0A1B6LFJ7 version 4

Fetching compressed AlphaFold A0A1B6LFJ7 from
https://alphafold.ebi.ac.uk/files/AF-A0A1B6LFJ7-F1-model_v4.cif  
| Chain information for AlphaFold A0A1B6LFJ7 #2  
---  
Chain | Description | UniProt  
A | Neur_chan_LBD domain-containing protein | A0A1B6LFJ7_9HEMI  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A1B6LFJ7 | MGHNI...IMLIV | 25.6 | 67.0  

> alphafold fetch A0A023EY00 version 4

Fetching compressed AlphaFold A0A023EY00 from
https://alphafold.ebi.ac.uk/files/AF-A0A023EY00-F1-model_v4.cif  
| Chain information for AlphaFold A0A023EY00 #3  
---  
Chain | Description | UniProt  
A | Putative nicotinic acetylcholine receptor alpha9 subunit |
A0A023EY00_TRIIF  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A023EY00 | MGHNI...IMLIV | 21.2 | 50.6  

> hide #3 models

> hide #2 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #2 models

> show #1 models

> hide #2 models

> alphafold predict
> MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> alphafold predict
> MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV

Running AlphaFold prediction  
[Repeated 4 time(s)]AlphaFold prediction finished  
Results in C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

| Chain information for best_model.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "C:/Users/ferna/OneDrive/Área de
> Trabalho/Euschistus/nAchR_euschistus_prediction_1/best_model_nAchR_euschistus_1.pdb"

Chain information for best_model_nAchR_euschistus_1.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #5 models

> show #5 models

> hide #4 models

> show #4 models

> hide #5 models

> show #5 models

> hide #4 models

> hide #1 models

> show #1 models

> show #2 models

> hide #1 models

> hide #5 models

> hide #2 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 target m

> show #4 models

> hide #4 models

> alphafold predict
> MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV

Running AlphaFold prediction  

> show #5 models

> select add #5

3253 atoms, 3329 bonds, 403 residues, 1 model selected  

> select subtract #5

Nothing selected  

> hide #5 models

> show #4 models

> select add #4

3253 atoms, 3329 bonds, 403 residues, 1 model selected  

> alphafold fetch A0A1B6FCL0 version 4

Chain information for AlphaFold A0A1B6FCL0 #6  
---  
Chain | Description | UniProt  
A | Neur_chan_LBD domain-containing protein | A0A1B6FCL0_9HEMI  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A1B6FCL0 | MGHNI...IMLIV | 22.1 | 58.8  

> select subtract #4

Nothing selected  

> matchmaker #1 to #4

| Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain A (#4) with AlphaFold A0A1B6FCL0, chain A
(#1), sequence alignment score = 928  
RMSD between 217 pruned atom pairs is 1.140 angstroms; (across all 403 pairs:
9.785)  
  

> matchmaker #1 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain A (#4) with AlphaFold A0A1B6FCL0, chain A
(#1), sequence alignment score = 928  
RMSD between 217 pruned atom pairs is 1.140 angstroms; (across all 403 pairs:
9.785)  
  

> hide #6 models

> hide #4 models

> show #1 models

> hide #1 atoms

> style #1 stick

Changed 3571 atom styles  

> style #1 stick

Changed 3571 atom styles  

> ui tool show "Color Actions"

> color cyan

> show #4 models

> hide #1 models

> color bfactor #4 palette alphafold

3253 atoms, 403 residues, atom bfactor range 29.5 to 98.1  

> show #1 models

> show #1,4 atoms

> hide #1,4 atoms

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 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

  

> hide #4 models

> hide #1 models

AlphaFold prediction finished  
Results in C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

Chain information for best_model.pdb #7  
---  
Chain | Description  
A | No description available  
  

> show #4 models

> open C:/Users/ferna/Downloads/thiamethoxam_Conformer3D_CID_5821911.json

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mole\\__init__.py", line 27, in open  
return mole.read_mole_json(session, data, file_name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
KeyError: 'Channels'  
  
KeyError: 'Channels'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) HD Graphics 530
OpenGL vendor: Intel

Python: 3.9.11
Locale: pt_BR.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7040
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 17,061,920,768
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
OSLanguage: pt-BR

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Read MOLE format: KeyError: 'Channels'

comment:2 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

The user tried to open a PubChem 3D structure file in JSON format. ChimeraX tried to open that as MoleOnline format and of course failed. ChimeraX does not read PubChem JSON format.

I've made the MoleOnline json reader warn that the file does not look like the right format.

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