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Opened 18 months ago
Closed 18 months ago
#15174 closed defect (limitation)
AlphaFold Prediction Requires Newer ChimeraX
| Reported by: | 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: macOS-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later.
The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024.
Log:
> color #9:73-73 lime
> color #9:144-144 magenta
> alphafold pae #9 colorDomains true
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color #9:12-148 lime
> color #9:413-571 magenta
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> alphafold pae #9 colorDomains true
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dxs516/Desktop/movie10.mp4
Movie saved to /Users/dxs516/Desktop/movie10.mp4
> show #1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file "/Users/dxs516/Desktop/AlphaFold/GMIP
> predicted_aligned_error_v4.json"
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> alphafold pae #9 colorDomains true
[Repeated 1 time(s)]
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color #1:204-204 lime
> color #1:103-103 magenta
> color #1:76-76 lime
> color #1:147-147 magenta
> color #1:73-397 lime
> color #1:250-250 lime
> color #1:383-383 magenta
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color #1:491-491 lime
> color #1:500-500 magenta
> color #1:484-662 lime
> color #1:611-611 lime
> color #1:735-735 magenta
> color #1:564-564 lime
> color #1:632-632 magenta
> alphafold pae #9 colorDomains true
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> hide #1 models
> show #1 models
> hide #9 models
> hide #1 models
> show #1 models
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color #1:274-274 lime
> color #1:254-254 magenta
> color #1:136-234 lime
> color #1:269-269 magenta
> color #1:272-272 lime
> color #1:269-269 magenta
> color #1:273-273 lime
> color #1:254-254 magenta
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> alphafold pae #9 colorDomains true
[Repeated 2 time(s)]
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color bfactor #1 palette alphafold
7506 atoms, 970 residues, atom bfactor range 20.4 to 98.7
> show #9 models
> hide #9 models
> show #9 models
> hide #1 models
> show #1 models
> alphafold pae #9 colorDomains true
[Repeated 1 time(s)]
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> alphafold pae #9 colorDomains true
> color bfactor #9 palette alphafold
4977 atoms, 618 residues, atom bfactor range 34.5 to 98.9
> hide #1 models
> hide #9 models
> show #6 models
> show #13 models
> hide #13 models
> hide #6 models
> show #8 models
> show #11 models
> hide #8 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #5 models
> show #2 models
> hide #5 models
> hide #11 models
> show #10 models
> alphafold contacts /A toResidues /B distance 8
No to residues specified for alphafold contacts
> hide #2 models
> show #5 models
> hide #5 models
> hide #10 models
> show #10 models
> show #3 models
> hide #3 models
> undo
[Repeated 9 time(s)]
> hide #5 models
> hide #11 models
> show #10 models
> alphafold contacts /A toResidues /B distance 8
No to residues specified for alphafold contacts
> alphafold contacts /A toResidues /B distance 6
No to residues specified for alphafold contacts
> alphafold contacts /A toResidues /B distance 1
No to residues specified for alphafold contacts
> alphafold contacts /A toResidues /B distance 0
No to residues specified for alphafold contacts
> alphafold contacts /A toResidues /B distance 100
No to residues specified for alphafold contacts
> show #1 models
> hide #2 models
> hide #10 models
> show #9 models
> alphafold contacts /A toResidues /B distance 8
No to residues specified for alphafold contacts
> alphafold contacts #1
> hide #9 models
> hide #!1 models
> show #6 models
> alphafold contacts #1
> hide #6 models
> show #3 models
> alphafold contacts #1
[Repeated 1 time(s)]
> alphafold contacts #3
> hide #!3 models
> show #6 models
> hide #6 models
> show #2 models
> hide #2 models
> show #2 models
> show #10 models
> alphafold contacts /2 toResidues /10 distance 8
No residues specified for alphafold contacts
> show #!1 models
> hide #2 models
> hide #10 models
> show #9 models
> alphafold contacts /2 toResidues /10 distance 8
No residues specified for alphafold contacts
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #!1 models
> contacts9
Unknown command: alphafold contacts9
> show #2 models
> hide #9 models
> show #10 models
> alphafold contacts #1
> to#10 distance 8
Unknown command: to#10 distance 8
> select add #2
7562 atoms, 7725 bonds, 971 residues, 1 model selected
> select add #10
12539 atoms, 12815 bonds, 1589 residues, 2 models selected
> hide #2 models
> hide #10 models
> select subtract #10
7562 atoms, 7725 bonds, 971 residues, 1 model selected
> select subtract #2
Nothing selected
> show #2 models
> show #10 models
> hide #2 models
> show #!1 models
> hide #10 models
> hide #!1 models
> show #!1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file "/Users/dxs516/Desktop/AlphaFold/GMIP
> predicted_aligned_error_v4.json"
> color bfactor #1 palette alphafold
7506 atoms, 970 residues, atom bfactor range 20.4 to 98.7
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
7506 atoms, 970 residues, atom bfactor range 20.4 to 98.7
> hide #!1 models
> show #!1 models
> color bfactor #1 palette alphafold
7506 atoms, 970 residues, atom bfactor range 20.4 to 98.7
> color #1:67-375 lime
> ui mousemode right "translate selected models"
> hide #!1 models
> show #!3 models
> ui mousemode right "translate selected models"
> hide #!3 models
> show #!3 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!3 models
> ui mousemode right "translate selected models"
[Repeated 2 time(s)]
> ui tool show AlphaFold
> alphafold predict #1
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold search #3
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
> alphafold predict #3
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold predict #3
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> open /Users/dxs516/Downloads/AF-Q9P107-F1-model_v4.cif
Chain information for AF-Q9P107-F1-model_v4.cif #4
---
Chain | Description | UniProt
A | GEM-interacting protein | GMIP_HUMAN 1-970
Color AF-Q9P107-F1-model_v4.cif by residue attribute pLDDT_score
> open /Users/dxs516/Downloads/AF-Q9P107-F1-model_v4.cif
Chain information for AF-Q9P107-F1-model_v4.cif #15
---
Chain | Description | UniProt
A | GEM-interacting protein | GMIP_HUMAN 1-970
Color AF-Q9P107-F1-model_v4.cif by residue attribute pLDDT_score
> hide #15 models
> hide #5 models
> hide #4 models
> show #15 models
> alphafold predict #3
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold match #1
Fetching compressed AlphaFold A0A024R7N1 from
https://alphafold.ebi.ac.uk/files/AF-A0A024R7N1-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A024R7N1 (chain
A)
AlphaFold prediction matching
GMIP_13077_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A024R7N1 | A0A024R7N1_HUMAN | 45.26 | 970 | 970 | 100
Opened 1 AlphaFold model
> hide #15 models
> hide #!16 models
> hide #16.1 models
> show #16.1 models
> select add #16
7507 atoms, 7692 bonds, 970 residues, 2 models selected
> select subtract #16.1
1 model selected
> select add #16
7507 atoms, 7692 bonds, 970 residues, 2 models selected
> hide #!16 models
> show #!16 models
> hide #16.1 models
> show #16.1 models
> select subtract #16
Nothing selected
> select add #16.1
7507 atoms, 7692 bonds, 970 residues, 1 model selected
> select subtract #16.1
Nothing selected
> hide #!16 models
> hide #16.1 models
> show #9 models
> alphafold match #1
1 AlphaFold model found using sequence similarity searches: A0A024R7N1 (chain
A)
AlphaFold prediction matching
GMIP_13077_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A024R7N1 | A0A024R7N1_HUMAN | 45.26 | 970 | 970 | 100
Opened 1 AlphaFold model
> alphafold search #1
[Repeated 1 time(s)]
> alphafold search #17.1
[Repeated 2 time(s)]
> hide #!17 models
> hide #17.1 models
> show #!1 models
> hide #!1 models
> hide #9 models
> show #8 models
> hide #8 models
> show #9 models
> alphafold match #17.1
1 AlphaFold model found using UniProt identifier: A0A024R7N1 (chain A)
AlphaFold prediction matching AlphaFold A0A024R7N1_HUMAN chain A
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A024R7N1 | A0A024R7N1_HUMAN | 0.00 | 970 | 970 | 100
Opened 1 AlphaFold model
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #18.1 models
> show #18.1 models
> hide #18.1 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #9 models
> show #9 models
> alphafold match #9
Fetching compressed AlphaFold Q8IXI2 from
https://alphafold.ebi.ac.uk/files/AF-Q8IXI2-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: Q8IXI2 (chain A)
AlphaFold prediction matching
Miro1_800e8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q8IXI2 | MIRO1_HUMAN | 2.62 | 618 | 618 | 100
Opened 1 AlphaFold model
> hide #!19 models
> hide #19.1 models
> show #!19 models
> show #19.1 models
> hide #!19 models
> hide #19.1 models
> show #!19 models
> hide #!19 models
> close #19.1
> close #19
> close #18.1
> close #18
> close #17.1
> close #17
> close #16.1
> close #16
> close #15
> show #14 models
> hide #14 models
> close #14
> hide #9 models
> alphafold match #3
1 AlphaFold model found using sequence similarity searches: A0A024R7N1 (chain
A)
AlphaFold prediction matching
GMIP_13077_unrelaxed_rank_002_alphafold2_ptm_model_2_seed_000.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A024R7N1 | A0A024R7N1_HUMAN | 40.24 | 970 | 970 | 100
Opened 1 AlphaFold model
> alphafold match #9
1 AlphaFold model found using sequence similarity searches: Q8IXI2 (chain A)
AlphaFold prediction matching
Miro1_800e8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q8IXI2 | MIRO1_HUMAN | 2.62 | 618 | 618 | 100
Opened 1 AlphaFold model
> alphafold contacts /A toResidues /B distance 8
No to residues specified for alphafold contacts
> alphafold contacts /A toResidues /A distance 8
Interface PAE pseudobonds can only be computed for a single structure, got 15.
> ui mousemode right "translate selected models"
> open
> /Users/dxs516/Desktop/AlphaFold/GMIP_13077/GMIP_13077_scores_rank_001_alphafold2_ptm_model_3_seed_000.json
Failed opening file
/Users/dxs516/Desktop/AlphaFold/GMIP_13077/GMIP_13077_scores_rank_001_alphafold2_ptm_model_3_seed_000.json:
GMIP_13077_scores_rank_001_alphafold2_ptm_model_3_seed_000.json does not look
like Mole Online json file, does not contain Channels.
> alphafold match #1
1 AlphaFold model found using sequence similarity searches: A0A024R7N1 (chain
A)
AlphaFold prediction matching
GMIP_13077_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A024R7N1 | A0A024R7N1_HUMAN | 45.26 | 970 | 970 | 100
Opened 1 AlphaFold model
> alphafold predict #1
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> help help:contact.html
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.2
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: Mac14,9
Model Number: MPHE3CH/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 13天4小时47分钟
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
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: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.10.5
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: 1.3.2
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: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
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: 1.1.8
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: 1.5.14
ChimeraX-ModelPanel: 1.4
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-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: 1.1
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
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: 1.12.4
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: 1.33.3
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
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: 0.38
imagecodecs: 2023.9.18
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: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
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: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
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: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
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: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
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
Change History (2)
comment:1 by , 18 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → AlphaFold Prediction Requires Newer ChimeraX |
comment:2 by , 18 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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To run AlphaFold predictions you need a newer ChimeraX version. This is clearly explained in the error message you get: