Opened 17 hours ago

Closed 15 hours ago

#20858 closed defect (fixed)

"alphafold search" produces no output

Reported by: Eric Pettersen Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.7.9-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
alphafold search produces no output

Tried on 1.4, 1.8, 1.10.1, 1.11, 1.12, and the daily build.  Mostly produced no output at all in the log after the command, but either 1 or 2 of them managed the "Webservice job ID:" output, but none of them produced the BLAST-related output.  To ensure that it wasn't my machine/account somehow I also tried on the Mac in the test lab with 1.12 and got the same behavior, but because I had never used ChimeraX there it did output that it was fetching compressed AlphaFold parameters from our web site, but nothing after that.


Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> alphafold search
> MAGGGGAERVRVGAAAAGLLPPSCRQPRRRESRERLSVCSKLCYAVGGAPYQTTGCALGFFLQIYLLDVAQLDPFYASIILFVGRAWDAITDPMVGFFISKTPWTRFGRLMPWIIFSTPFAVISYFLIWFVPDISTGQVMWYLIFYCIFQTLVTCFHVPYSALTMFISREQSERDSATAYRMTVEVLGTVLGTAIQGQIVGKAVTPCIENPPFLSETNFSVAIRNVNMTHYTGSLADTRNAYMVAAGVIGGLYILCAVILSVGVREKRESSELQSDEPVSFFRGLKLVMNHGAYIKLITGFLFTSLAFMLLEGNFALFCTYTLGFRNEFQNILLAIMLSATLTIPFWQWFLTRFGKKTAVYVGISSAVPFLITVVVLDSNLVVTYIVAVAAGISVAAAFLLPWSMLPDVIDDFKLQHPESRGHEAIFFSFYVFFTKFTSGVSLGISTLSLDFAGYQTRGCSQPSEVNITLKLLVSAVPVGLILLGLLLFKLYPIDEEKRRENKKALQDLREESNSSSESDSTELANIV

> open /Users/pett/src/chimerax/src/bundles/seqalign/test-data/nonassoc.fa
> format fasta

Summary of feedback from opening
/Users/pett/src/chimerax/src/bundles/seqalign/test-data/nonassoc.fa  
---  
notes | Alignment identifier is nonassoc.fa  
Showing conservation header ("seq_conservation" residue attribute) for
alignment nonassoc.fa  
  
Opened 5 sequences from nonassoc.fa  

> open 1qvc 1kaw 1eyg 3ull

1qvc title:  
Crystal structure analysis of single stranded DNA binding protein (SSB) from
E.coli [more info...]  
  
Chain information for 1qvc #1  
---  
Chain | Description | UniProt  
A B C D | SINGLE STRANDED DNA BINDING PROTEIN MONOMER | SSB_ECOLI 1-145 201-345 401-545 601-745  
  
1kaw title:  
Structure of single stranded DNA binding protein (SSB) [more info...]  
  
Chain information for 1kaw #2  
---  
Chain | Description | UniProt  
A B C D | SINGLE-STRANDED DNA BINDING PROTEIN | SSB_ECOLI 1-135  
  
1eyg title:  
Crystal structure of chymotryptic fragment of E. coli ssb bound to two 35-mer
single strand DNAS [more info...]  
  
Chain information for 1eyg #3  
---  
Chain | Description | UniProt  
A B C D | SINGLE-STRAND DNA-BINDING PROTEIN | SSB_ECOLI 1000-1115 2000-2115 3000-3115 4000-4115  
Q R | SINGLE STRANDED 28-MER OF D(C) |   
  
1eyg mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
3ull title:  
Human mitochondrial single-stranded DNA binding protein [more info...]  
  
Chain information for 3ull #4  
---  
Chain | Description | UniProt  
A B | DNA BINDING PROTEIN | SSB_HUMAN 1-132  
  
3ull mmCIF Assemblies  
---  
1| author_defined_assembly  
  
Associated 1qvc chain A to 1qvc with 0 mismatches  
Associated 1qvc chain B to 1qvc with 0 mismatches  
Associated 1qvc chain C to 1qvc with 0 mismatches  
Associated 1qvc chain D to 1qvc with 0 mismatches  
Associated 1kaw chain A to 1qvc with 0 mismatches  
Associated 1kaw chain B to 1qvc with 0 mismatches  
Associated 1kaw chain C to 1qvc with 0 mismatches  
Associated 1kaw chain D to 1qvc with 0 mismatches  
Associated 1eyg chain A to 1eyg with 0 mismatches  
Associated 1eyg chain B to 1eyg with 0 mismatches  
Associated 1eyg chain C to 1eyg with 0 mismatches  
Associated 1eyg chain D to 1eyg with 0 mismatches  
Associated 3ull chain A to 3ull with 0 mismatches  
Associated 3ull chain B to 3ull with 0 mismatches  

> ui tool show "Modeller Comparative"

Populating font family aliases took 183 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> modeller comparative nonassoc.fa:4 numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false directory
> /Users/pett/rm

Webservices job id: 5CLNCC1KEKXYIZHI  
Webservices job finished: 5CLNCC1KEKXYIZHI  
Modeller job (ID 5CLNCC1KEKXYIZHI) finished  
Parameters  
---  
Chain pairing | ss  
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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment
score = 198.9  
Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment
score = 225.9  
Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment
score = 208.7  
Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment
score = 194.8  
RMSD between 249 pruned atom pairs is 0.774 angstroms; (across all 545 pairs:
9.039)  
  
Parameters  
---  
Chain pairing | ss  
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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment
score = 169.9  
Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment
score = 221.5  
Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment
score = 196  
Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment
score = 203.1  
RMSD between 242 pruned atom pairs is 0.751 angstroms; (across all 540 pairs:
9.499)  
  
Parameters  
---  
Chain pairing | ss  
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 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment
score = 189.6  
Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment
score = 218.7  
Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment
score = 208.7  
Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment
score = 204.3  
RMSD between 254 pruned atom pairs is 0.688 angstroms; (across all 547 pairs:
8.841)  
  
Associated T0151 chain A to T0151 with 0 mismatches  
Associated T0151 chain B to T0151 with 0 mismatches  
Associated T0151 chain C to T0151 with 0 mismatches  
Associated T0151 chain D to T0151 with 0 mismatches  
Associated T0151 chain A to T0151 with 0 mismatches  
Associated T0151 chain B to T0151 with 0 mismatches  
Associated T0151 chain C to T0151 with 0 mismatches  
Associated T0151 chain D to T0151 with 0 mismatches  
Associated T0151 chain A to T0151 with 0 mismatches  
Associated T0151 chain B to T0151 with 0 mismatches  
Associated T0151 chain C to T0151 with 0 mismatches  
Associated T0151 chain D to T0151 with 0 mismatches  
Chain information for T0151  
---  
Chain | Description  
5.1/A 5.2/A 5.3/A 5.1/B 5.2/B 5.3/B 5.1/C 5.2/C 5.3/C 5.1/D 5.2/D 5.3/D | No description available  
  

> close

> alphafold search
> MAGGGGAERVRVGAAAAGLLPPSCRQPRRRESRERLSVCSKLCYAVGGAPYQTTGCALGFFLQIYLLDVAQLDPFYASIILFVGRAWDAITDPMVGFFISKTPWTRFGRLMPWIIFSTPFAVISYFLIWFVPDISTGQVMWYLIFYCIFQTLVTCFHVPYSALTMFISREQSERDSATAYRMTVEVLGTVLGTAIQGQIVGKAVTPCIENPPFLSETNFSVAIRNVNMTHYTGSLADTRNAYMVAAGVIGGLYILCAVILSVGVREKRESSELQSDEPVSFFRGLKLVMNHGAYIKLITGFLFTSLAFMLLEGNFALFCTYTLGFRNEFQNILLAIMLSATLTIPFWQWFLTRFGKKTAVYVGISSAVPFLITVVVLDSNLVVTYIVAVAAGISVAAAFLLPWSMLPDVIDDFKLQHPESRGHEAIFFSFYVFFTKFTSGVSLGISTLSLDFAGYQTRGCSQPSEVNITLKLLVSAVPVGLILLGLLLFKLYPIDEEKRRENKKALQDLREESNSSSESDSTELANIV




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac13,1
      Model Number: Z14J0008FLL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: mBoot-18000.161.10
      OS Loader Version: 11881.140.96.701.1

Software:

    System Software Overview:

      System Version: macOS 15.7.9 (24G830)
      Kernel Version: Darwin 24.6.0
      Time since boot: 6 hours, 34 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 279P1:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.7.0
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-ChopChopMF: 1.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DAQplugin: 0.13.60
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Gamepad: 0.3.0
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SelTools: 0.1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.1
    colorama: 0.4.6
    coloredlogs: 15.0.1
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    flatbuffers: 25.12.19
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    geomdl: 5.4.0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    humanfriendly: 10.0
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    mpmath: 1.3.0
    mrcfile: 1.5.4
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.13.0
    narwhals: 2.22.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 2.2.6
    numpy: 1.26.4
    onnxruntime: 1.23.2
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    pandas: 2.3.3
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.5.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    protobuf: 6.33.4
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 25.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.8.4
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt5: 5.15.11
    PyQt5-Qt5: 5.15.18
    PyQt5_sip: 12.17.2
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
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Change History (10)

comment:1 by Eric Pettersen, 17 hours ago

Cc: Zach Pearson added
Component: Unassigned → Structure Prediction
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "alphafold search" produces no output

comment:2 by Eric Pettersen, 17 hours ago

Another data point: blastprotein against the AlphaFold database behaves similarly, whereas against the pdb database works fine.

comment:3 by Eric Pettersen, 17 hours ago

Nope, I'm wrong about blastprotein -- it just takes a *long* time (several minutes) to search the AlphaFold database (and it does report a job ID fairly quickly). Pretty sure I waited at least as long for "alphafold search" (and I got no job ID there), but could try another test (tomorrow -- I have to get to the shuttle now).

Last edited 17 hours ago by Eric Pettersen (previous) (diff)

comment:4 by Tom Goddard, 16 hours ago

The alphafold search command simply runs blastprotein and relies on that command to Log any status and return results. It does that via Python call

    from chimerax.blastprotein import BlastProteinJob
    BlastProteinJob(session, sequence.ungapped(), chain_spec, database='alphafold',
                    version=version, cutoff=cutoff, matrix=matrix, max_seqs=max_sequences,
                    sequence_name = seq_name)

Maybe the blastprotein bundle has change. I know Blast searches of the 200 million sequence AlphaFold database take a long time.

comment:5 by Tom Goddard, 16 hours ago

If your aim is to get the most similar AlphaFold database sequence I always use alphafold match which uses a k-mer sequence search that takes maybe 10 seconds, not Blast which takes minutes and returns many results in addition to the top hit.

comment:6 by Zach Pearson, 16 hours ago 

I see this in the logs for *a* blast job, but not necessarily *your* blast job:

exception raised while executing (cxservices.task_runners.blast.run_job)\nTraceback (most recent call last):\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/.venv/lib64/python3.8/site-packages/rq/worker.py\", line 1418, in perform_job\n    rv = job.perform()\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/cxservices/worker.py\", line 39, in perform\n    result = super().perform()\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/.venv/lib64/python3.8/site-packages/rq/job.py\", line 1225, in perform\n    self._result = self._execute()\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/.venv/lib64/python3.8/site-packages/rq/job.py\", line 1262, in _execute\n    result = self.func(*self.args, **self.kwargs)\n  File \"/usr/local/www/webservices/wsgi-scripts/cxservices/task_runners/blast.py\", line 75, in run_job\n    raise RuntimeError(job.stderr.decode(\"utf-8\"))\nRuntimeError: BLAST Database error: Database memory map file error\n\n", "level": "error", "timestamp": "2026-08-20T22:49:19.499833Z"}

comment:7 by Zach Pearson, 16 hours ago

That traceback is from a job that requests database version 2, but we only host version 4 now. Separately I see that the default version in the alphafold source code is 6, and I think that gets passed to the BlastProteinJob code if no version is given. On the server side I don't force the requested version to 4, it'll just fail input validation if the version isn't between 1 and 4 inclusive. One thing we could do is force all versions to 4 on the backend, but it feels like misleading the user to set the version to something different behind their backs.

I'm sure that's the issue. I tried a couple of alphafold searches and then tailed the logs of the live workers and saw similar errors without any corresponding lines that say what the input parameters were, so it looks like a blast job can fail input validation and then ChimeraX gets no notification of what the job id would have been or that something was wrong *and* it doesn't get logged.

comment:8 by Zach Pearson, 15 hours ago 

The alphafold bundle does not call the start() method of the BlastProteinJob it creates in the “alphafold search” command

I’ve always meant to rework the task subsystem to have fewer footguns like that

comment:9 by Tom Goddard, 15 hours ago

Seems this commit in September 2023 removed the start() call from the BlastProteinJob constructor

​https://github.com/RBVI/ChimeraX/commit/dd7750092003333502e3e377828d707146fd3122

I guess it is so slow almost no one has tried it, and those that did maybe gave up thinking it just takes forever.

comment:10 by Tom Goddard, 15 hours ago

Resolution: → fixed
Status: assigned → closed

Fixed.

I added the start() call needed after the September 2023 change and made the default AFDB version 4 for Blast searches. The "alphafold search" command has a version option and it was defaulting to the current AFDB version which is version 6.

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