AlphaFold JSON vs. MOLE JSON

[isaphan@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
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  

> open
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_001.pdb
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_001.pdb

Chain information for
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_001.pdb
#1  
---  
Chain | Description  
A | No description available  
  
Chain information for
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
  
Chain information for
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
  
Chain information for
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_001.pdb
#4  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_U1_c99f5/is00.pdb

Summary of feedback from opening
/Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_U1_c99f5/is00.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 4 4 PRO A 157
SER A 159 1 3  
Start residue of secondary structure not found: HELIX 5 5 GLY A 185 ARG A 196
1 12  
Start residue of secondary structure not found: SHEET 6 6 1 PHE A 172 ILE A
175 0  
Start residue of secondary structure not found: SHEET 7 7 1 THR A 201 ALA A
203 0  
  
Chain information for is00.pdb #5  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #1-4 to #5

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 is00.pdb, chain A (#5) with
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_001.pdb,
chain A (#1), sequence alignment score = 970.3  
RMSD between 118 pruned atom pairs is 0.327 angstroms; (across all 118 pairs:
0.327)  
  
Matchmaker is00.pdb, chain A (#5) with
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#2), sequence alignment score = 964.9  
RMSD between 118 pruned atom pairs is 0.313 angstroms; (across all 118 pairs:
0.313)  
  
Matchmaker is00.pdb, chain A (#5) with
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#3), sequence alignment score = 964.9  
RMSD between 118 pruned atom pairs is 0.273 angstroms; (across all 118 pairs:
0.273)  
  
Matchmaker is00.pdb, chain A (#5) with
af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_001.pdb,
chain A (#4), sequence alignment score = 964.9  
RMSD between 118 pruned atom pairs is 0.270 angstroms; (across all 118 pairs:
0.270)  
  

> open
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_scores_rank_005_alphafold2_ptm_model_3_seed_001.json
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_scores_rank_006_alphafold2_ptm_model_4_seed_000.json
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_scores_rank_007_alphafold2_ptm_model_4_seed_001.json
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_scores_rank_008_alphafold2_ptm_model_3_seed_000.json
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_scores_rank_009_alphafold2_ptm_model_5_seed_000.json
> /Users/iphan/Documents/ssgcid/HVT_19_BasCongo/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d/af2_mmseq2_beta_af2ptm_template_run1_U1_9dd4d_scores_rank_010_alphafold2_ptm_model_5_seed_001.json

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/__init__.py", line 27, in open  
return mole.read_mole_json(session, data, file_name, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 16 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.6.2 (21G320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 9 days 5:06

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    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-Clipper: 0.19.0
    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-ISOLDE: 1.5
    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
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    ChimeraX-ModelSeries: 1.0.1
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    ChimeraX-Neuron: 1.0
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    ChimeraX-OpenCommand: 1.9.1
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    ChimeraX-PDBBio: 1.0
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    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
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    ChimeraX-PubChem: 2.1
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    ChimeraX-RNALayout: 1.0
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    ChimeraX-SDF: 2.0
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
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    ChimeraX-SwapAA: 2.0.1
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    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

Reported by Isabelle Phan

[Tom Goddard]

ChimeraX does not use the open command to AlphaFold PAE error estimates. You should use menu Tools / Structure Prediction / AlphaFold Error Plot to open and display that data. The error is because the open command is assuming from the file .json suffix that it is another file type that contain protein channel data.

The reason the open command does not handle the PAE data is because the PAE data is just an attribute of another model, the AlphaFold predicted structure. So it only makes sense to open it and associate it with the already open AlphaFold structure. I guess it might be sensible to allow something like "open paedata.json associateTo #3" where model #3 is the AlphaFold model.