Opened 13 months ago

Closed 13 months ago

Last modified 13 months ago

#16027 closed defect (fixed)

alphafold match failure with UniProt ID

Reported by: phil.cruz@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Eric Pettersen, Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-12.7.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
In this session, trying to Fetch from the AlphaFold DB fails from the AlphaFold window, no structure in the graphics window:

Missing or invalid "sequences" argument: Sequences argument "EGFR_HUMAN" is not a chain specifier, alignment id, UniProt id, or sequence characters

But doing it from the command line works: 
open uniprot:EGFR_HUMAN

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold match EGFR_HUMAN

Missing or invalid "sequences" argument: Sequences argument "EGFR_HUMAN" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold match EGFR_HUMAN

Missing or invalid "sequences" argument: Sequences argument "EGFR_HUMAN" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold fetch EGFR_HUMAN

Chain information for AlphaFold EGFR_HUMAN #1  
---  
Chain | Description | UniProt  
A | Epidermal growth factor receptor | EGFR_HUMAN 1-1210  
  
Color AlphaFold EGFR_HUMAN by residue attribute pLDDT_score  

> alphafold match EGFR_HUMAN

Missing or invalid "sequences" argument: Sequences argument "EGFR_HUMAN" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold match P00533

Missing or invalid "sequences" argument: Sequences argument "P00533" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> close session

> alphafold match EGFR_HUMAN

Missing or invalid "sequences" argument: Sequences argument "EGFR_HUMAN" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold fetch EGFR_HUMAN

Chain information for AlphaFold EGFR_HUMAN #1  
---  
Chain | Description | UniProt  
A | Epidermal growth factor receptor | EGFR_HUMAN 1-1210  
  
Color AlphaFold EGFR_HUMAN by residue attribute pLDDT_score  

> ui tool show AlphaFold

> alphafold match EGFR_HUMAN

Missing or invalid "sequences" argument: Sequences argument "EGFR_HUMAN" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> open uniport: EGFR_HUMAN

No such database 'uniport'  

> open uniprot: EGFR_HUMAN

'EGFR_HUMAN' has no suffix  

> open uniprot:EGFR_HUMAN

Summary of feedback from opening EGFR_HUMAN fetched from uniprot  
---  
note | UniProt identifier EGFR_HUMAN maps to entry P00533  
  
Fetching url https://www.uniprot.org/uniprot/P00533.xml failed:  
<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed:
self signed certificate in certificate chain (_ssl.c:1002)>  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 7459.141.1.701.1

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 12 days 1:14

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Thunderbolt Display:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BenQ GW2750H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NIHPresets: 1.2.5
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-ScholAR: 0.4
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (7)

comment:1 by phil.cruz@…, 13 months ago

I was running the NIH VPN when I saw this issue. Shutting down the VPN resolved the error, so the problem was on my end.

Phil

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, September 26, 2024 at 4:56 PM
To: Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #16027: ChimeraX bug report submission
#16027: ChimeraX bug report submission
-------------------------+-----------------------------
 Reporter:  phil.cruz@…  |                Type:  defect
   Status:  new          |            Priority:  normal
Component:  Unassigned   |          Blocked By:
 Blocking:               |  Notify when closed:
-------------------------+-----------------------------
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Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F16027&data=05%7C02%7Cphil.cruz%40nih.gov%7Cf76841b9bb784087c13508dcde6dbd99%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638629810161587502%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=s9%2FtMI8A5pAxUYN0TdMskN8EryG4MpcK3bgBn7522wM%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16027>>
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comment:2 by Eric Pettersen, 13 months ago

Cc: Eric Pettersen Elaine Meng added
Component: UnassignedStructure Prediction
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionalphafold match failure with UniProt ID

comment:3 by Eric Pettersen, 13 months ago

This problem apparently occurred because of the NIH VPN, so not a ChimeraX problem per se, but it sure would be nice if the response from "alphafold match" indicated a failure contacting UniProt rather than the misleading message it currently gives.

comment:4 by Tom Goddard, 13 months ago

The error message is indeed horrible. I see why it does that. It test the argument to see if it is any of "chain specifier, alignment id, UniProt id, or sequence characters" and if none of those work it gives the error. If it is a UniProt id and it can't reach the uniprot web site then it says the uniprot check failed. But that needs to be handled differently -- if it looks like a uniprot id and can't reach the web site it should give a different error. I'll fix that error message next week. Giving informative error messages is key to the usability of ChimeraX.

comment:5 by Tom Goddard, 13 months ago

Resolution: fixed
Status: assignedclosed

Fixed.

If you are not connected to the internet and you try to lookup a Uniprot sequence by accession code (P00533) or name (EGFR_HUMAN) it now gives a clearer error message.

The message is still pretty bad. It says the sequences argument is missing or invalid which isn't really true, but that is what the generic ChimeraX command argument parsing is saying, and I don't want to tamper with that.

Also the Python urllib library that makes the request for the Uniprot sequence gives a pretty unintelligible error "<urlopen error [Errno 8] nodename nor servname provided, or not known>" and I did not attempt to translate that into English ("you have no internet connection") because it is unclear what other types of networking errors might produce this message (it is saying DNS failed to convert a host name to IP address). But I think the resulting message is adequate to point the user in the right direction.

alphafold match EGFR_HUMAN

Missing or invalid "sequences" argument: Could not lookup UniProt accession code for "EGFR_HUMAN".
Request url https://rest.uniprot.org/idmapping/run failed: <urlopen error [Errno 8] nodename nor servname provided, or not known>
alphafold match p00533

Missing or invalid "sequences" argument: Could not fetch sequence for UniProt id "p00533".
Fetching url https://www.uniprot.org/uniprot/p00533.xml failed:
<urlopen error [Errno 8] nodename nor servname provided, or not known>

comment:6 by Elaine Meng, 13 months ago

A minor pedantic note on the following error message.  Should be "look up" rather than "lookup"  (the latter is used when "lookup" is a noun).  Feel free to ignore :-)

Elaine

comment:7 by goddard@…, 13 months ago

Thanks, lookup will be look up in tomorrow's daily build.

	Tom
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