Opened 15 months ago

Closed 15 months ago

Last modified 15 months ago

#15706 closed defect (fixed)

AlphaFold database missing

Reported by: andreyf@… Owned by: Greg Couch
Priority: high Milestone:
Component: Infrastructure Version:
Keywords: Cc: Scooter Morris, Zach Pearson, Tom Goddard, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
after updating to v 1.8, I can no longer fetch AlphaFold predictions from Structure Precictions>AlphaFold menue and instead get an error:

AlphaFold sequence search web service

https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py

reported error:

Traceback (most recent call last):
File "/usr/local/projects/chimerax/www/production/cgi-bin/alphafold_search3_cgi.py", line 305, in search_database
matches = sequence_search(sequences)
File "/usr/local/projects/chimerax/www/production/cgi-bin/alphafold_search3_cgi.py", line 50, in sequence_search
seq_num, num_kmer_matches = kmer_index.search(seq, nthreads = nthreads)
File "/usr/local/projects/chimerax/www/production/cgi-bin/alphafold_search3_cgi.py", line 81, in search
self.load_index()
File "/usr/local/projects/chimerax/www/production/cgi-bin/alphafold_search3_cgi.py", line 148, in load_index
self.counts = fromfile(counts_path, dtype=uint32)
FileNotFoundError: [Errno 2] No such file or directory: '/databases/mol/AlphaFold/v4_kmer/alphafold.counts'

 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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
> MIESVWSIKIMEGVSEDFYDSGPTFQYPNPLSSIYDKSMNIDLMNHYHPSTSLITNSNNPFYESLSDTSSDDLNNEDNSNSNNNQNNNNNNNNNNNNNNQNSNNKLLGIEKQLQSINLLTNKVDWSDYHQQVYHGCSNENSQLISWSVDNQIAFTMNFNKNQFIKQEQQQIYITRVEYPHEYVVIKTSHTNSIKCLEWSTQSPSNLLLSFDQSDKLCLWKTKDNCSDDWYCLHIFPFQYLLLSKWLPLRSTYTPIFDPFNLNNTNNNNNNTTNINNNNNNNSNNSNTSTNTFKSPFESLITDNHIDNSFQTFISITKDGKIYIGYYGIVESCWKYIIGQIPLPFYHTIDCVDIFPTQEPDSLLVTIYSKNIGLALIVYHINYNIHTSEVTVTLKDKISMSNIIEQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQDVDIRSLSFRISSIQFDNSMSSLIVLMKGIDSSAIYRLEKKLISIDSPQLSIFELLSGTAPNETNQEIEEWTCTAKRLFYTPNNNNSNNNSNSNNNNNSGNNFNHYSTISSIYFSSTTGFLWLTHSNGSIEIVDRLTFESISTLKESEKPIDNIIISSNLNNENSEQSIMNSPTISGSTSPILQSTKANSPHSIKDDSMVIDPSNPTSTSTTTSSTTSQIQEQDNNNNNNNNNNFLPSTKNTTLSITSSPNGGLIACLNSDLKVTLYSLPIKSIGTSPDNQKVVSKWLAQLFQNSMLKSNDWWDILILLKIYSTSPDTRTTFHHTIIHLSSDFSCLPLTFQQTYRHCFDAIKASIYRIVSGMEVAFVDSQAKSFIYYLCDTLKSSFSPLLMQPSQQSDGTTNQQTLKERENIIILIDWAIEFSQFFLKNCYYFSFVYAKKGDISVKIPESMLDLPIKHYFPFYYSETKGNFHFPIISFLCDFNLLFVIFELMNISKLFKEKTSTSQSKVKFKKSKEIDFFLEYFTKIIKVLCKEVVSSSSSSNNNNPDEINNTLGLIDTYLSTFYGFLSEDKLDQVITPPAIECKGSHMNSIIAIMKKFDSIIPSEVIADTNDISINISYSILDLDPPLDGFLDQNPITSSSLSTIQQQQQQQQLGNSSNNNNYNNNNNNDTSGNGSVIFKYSPKSTEYMGIVHDIITRIPIAPRIDKPYKKCIRCHRITVMLRTSMFWSDRWSMACPICGGKWKSYQSSSSSYSSSSNTHDIANNFNSNFYNNNYSSNNFNSNYYNSNNNNNYNNNNYNNNKYYFNNSNNNKINKHLNKTNKHLNNIHRHHNHILINRT

AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py  
  
reported error:  
  
Traceback (most recent call last):  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 305, in search_database  
matches = sequence_search(sequences)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 50, in sequence_search  
seq_num, num_kmer_matches = kmer_index.search(seq, nthreads = nthreads)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 81, in search  
self.load_index()  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 148, in load_index  
self.counts = fromfile(counts_path, dtype=uint32)  
FileNotFoundError: [Errno 2] No such file or directory:
'/databases/mol/AlphaFold/v4_kmer/alphafold.counts'  
  

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> alphafold search
> MIESVWSIKIMEGVSEDFYDSGPTFQYPNPLSSIYDKSMNIDLMNHYHPSTSLITNSNNPFYESLSDTSSDDLNNEDNSNSNNNQNNNNNNNNNNNNNNQNSNNKLLGIEKQLQSINLLTNKVDWSDYHQQVYHGCSNENSQLISWSVDNQIAFTMNFNKNQFIKQEQQQIYITRVEYPHEYVVIKTSHTNSIKCLEWSTQSPSNLLLSFDQSDKLCLWKTKDNCSDDWYCLHIFPFQYLLLSKWLPLRSTYTPIFDPFNLNNTNNNNNNTTNINNNNNNNSNNSNTSTNTFKSPFESLITDNHIDNSFQTFISITKDGKIYIGYYGIVESCWKYIIGQIPLPFYHTIDCVDIFPTQEPDSLLVTIYSKNIGLALIVYHINYNIHTSEVTVTLKDKISMSNIIEQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQDVDIRSLSFRISSIQFDNSMSSLIVLMKGIDSSAIYRLEKKLISIDSPQLSIFELLSGTAPNETNQEIEEWTCTAKRLFYTPNNNNSNNNSNSNNNNNSGNNFNHYSTISSIYFSSTTGFLWLTHSNGSIEIVDRLTFESISTLKESEKPIDNIIISSNLNNENSEQSIMNSPTISGSTSPILQSTKANSPHSIKDDSMVIDPSNPTSTSTTTSSTTSQIQEQDNNNNNNNNNNFLPSTKNTTLSITSSPNGGLIACLNSDLKVTLYSLPIKSIGTSPDNQKVVSKWLAQLFQNSMLKSNDWWDILILLKIYSTSPDTRTTFHHTIIHLSSDFSCLPLTFQQTYRHCFDAIKASIYRIVSGMEVAFVDSQAKSFIYYLCDTLKSSFSPLLMQPSQQSDGTTNQQTLKERENIIILIDWAIEFSQFFLKNCYYFSFVYAKKGDISVKIPESMLDLPIKHYFPFYYSETKGNFHFPIISFLCDFNLLFVIFELMNISKLFKEKTSTSQSKVKFKKSKEIDFFLEYFTKIIKVLCKEVVSSSSSSNNNNPDEINNTLGLIDTYLSTFYGFLSEDKLDQVITPPAIECKGSHMNSIIAIMKKFDSIIPSEVIADTNDISINISYSILDLDPPLDGFLDQNPITSSSLSTIQQQQQQQQLGNSSNNNNYNNNNNNDTSGNGSVIFKYSPKSTEYMGIVHDIITRIPIAPRIDKPYKKCIRCHRITVMLRTSMFWSDRWSMACPICGGKWKSYQSSSSSYSSSSNTHDIANNFNSNFYNNNYSSNNFNSNYYNSNNNNNYNNNNYNNNKYYFNNSNNNKINKHLNKTNKHLNNIHRHHNHILINRT

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

> alphafold match
> MELLYMTHRKSNSVSFVETQQNFEFFSTTSTCNVLAFTTTNELTEPSPIQGWGFHIYVADLNTPWFPYRVTTSKYPVSVLEWDVLGRFLLVGDRNGNVQLFAQKGTLSEWKAVYSVRFPGENIIAAAFFHNGRKISLQMDKKEHSLYVEKFPKGKFSASVRQFGGVPVEGVVIVSATGMLGAFAIPADSNVNIMKQQEPMVLTPVTESLGITRNFYTTADICYGKSGHFMIAAGNGDTKSANSGMIQCFRVAVTVKKGCETLEIGSSALPSFFLAEGLGKDLKELRVAHIKWVSNEDADSLIVASNYAGGGSFIEQWELTEESMPIHKLFQSSKNESFKTILWTSKTKYVYNSKVVKVCSTRLNFMNCSFIYLAMSDNSIHCLQRDTFKRLTCTNIISIRDPNDHASKQIRLGVKIGAINVSYLGHLFVALDTTGQIYTYRCNFMIQDQLGTPALIVQTVNLLEFCLVTGFDCLEILLTLKPQILDNILERLTDNFNRQPPNVQQYYYVNFLTMKIALYRLSITGQQKAHDLSNLLILHSILIAFKSLLRPSDLTSHDKGPAENLAMVLSESVQDVDKVLLNLEAKDFTMERPTLQSLQQLIQWVADLALNILAKLPESRSFMSSKQGYDISKDIVALNSIRELLVMIRIWGLLNPQCLPVFSRSTDNLDILVTLFRLLTKLSLNPNEPDDLLLDECCLLPNQVLIPQLQFVPSRTMIASPLLPHVSLPVICDYGVENETLKFCPEIPIVEGGLSNDNVIDSVMYLQLGRKPPSLRRCSRCGSCSSPVSVAKTPAMKAWEQRWIDKCRPRLQSDRAELRTSSAAP

AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py  
  
reported error:  
  
Traceback (most recent call last):  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 305, in search_database  
matches = sequence_search(sequences)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 50, in sequence_search  
seq_num, num_kmer_matches = kmer_index.search(seq, nthreads = nthreads)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 81, in search  
self.load_index()  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 148, in load_index  
self.counts = fromfile(counts_path, dtype=uint32)  
FileNotFoundError: [Errno 2] No such file or directory:
'/databases/mol/AlphaFold/v4_kmer/alphafold.counts'  
  

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> help help:contact.html

> alphafold match
> MELLYMTHRKSNSVSFVETQQNFEFFSTTSTCNVLAFTTTNELTEPSPIQGWGFHIYVADLNTPWFPYRVTTSKYPVSVLEWDVLGRFLLVGDRNGNVQLFAQKGTLSEWKAVYSVRFPGENIIAAAFFHNGRKISLQMDKKEHSLYVEKFPKGKFSASVRQFGGVPVEGVVIVSATGMLGAFAIPADSNVNIMKQQEPMVLTPVTESLGITRNFYTTADICYGKSGHFMIAAGNGDTKSANSGMIQCFRVAVTVKKGCETLEIGSSALPSFFLAEGLGKDLKELRVAHIKWVSNEDADSLIVASNYAGGGSFIEQWELTEESMPIHKLFQSSKNESFKTILWTSKTKYVYNSKVVKVCSTRLNFMNCSFIYLAMSDNSIHCLQRDTFKRLTCTNIISIRDPNDHASKQIRLGVKIGAINVSYLGHLFVALDTTGQIYTYRCNFMIQDQLGTPALIVQTVNLLEFCLVTGFDCLEILLTLKPQILDNILERLTDNFNRQPPNVQQYYYVNFLTMKIALYRLSITGQQKAHDLSNLLILHSILIAFKSLLRPSDLTSHDKGPAENLAMVLSESVQDVDKVLLNLEAKDFTMERPTLQSLQQLIQWVADLALNILAKLPESRSFMSSKQGYDISKDIVALNSIRELLVMIRIWGLLNPQCLPVFSRSTDNLDILVTLFRLLTKLSLNPNEPDDLLLDECCLLPNQVLIPQLQFVPSRTMIASPLLPHVSLPVICDYGVENETLKFCPEIPIVEGGLSNDNVIDSVMYLQLGRKPPSLRRCSRCGSCSSPVSVAKTPAMKAWEQRWIDKCRPRLQSDRAELRTSSAAP

AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py  
  
reported error:  
  
Traceback (most recent call last):  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 305, in search_database  
matches = sequence_search(sequences)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 50, in sequence_search  
seq_num, num_kmer_matches = kmer_index.search(seq, nthreads = nthreads)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 81, in search  
self.load_index()  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 148, in load_index  
self.counts = fromfile(counts_path, dtype=uint32)  
FileNotFoundError: [Errno 2] No such file or directory:
'/databases/mol/AlphaFold/v4_kmer/alphafold.counts'  
  

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
      OS Loader Version: 580~2215

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 4 days, 42 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U3219Q:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 6ZWQWP2     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
        DELL U3219Q:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 7NQNWP2     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


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-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-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
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Change History (9)

comment:1 by Eric Pettersen, 15 months ago

Cc: Scooter Morris Zach Pearson Tom Goddard added
Component: Unassigned → Infrastructure
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AlphaFold database missing

Reported by Andrey Feklistov

comment:2 by Eric Pettersen, 15 months ago

Priority: normal → high

comment:3 by Zach Pearson, 15 months ago

Cc: Greg Couch added
Owner: changed from Greg Couch to Eric Pettersen

In case you do not have slack open:

scooter 12:32 PM
@Eric Pettersen Ack! I accidentally deleted /wynton/group/ferrin/databases. Can you please restore it from the latest backups? (edited)

comment:4 by Eric Pettersen, 15 months ago

Cc: Eric Pettersen added; Greg Couch removed
Owner: changed from Eric Pettersen to Greg Couch

That message was from yesterday. The database information that we backup was restored yesterday into plato-backup:/usr/local/lib/gnudump/extract/databases-backups. I don't think that's relevant here because we don't backup databases that can be reconstructed from information on the internet. Assuming the AlphaFold database information isn't in the extracted backup data (would probably need to check /usr/local/etc/periodic/scripts/mariadb10_backup-all.sh to see) then this ticket probably should be reassigned to whomever built the database the first time, since it will be needed to be rebuilt.

Version 0, edited 15 months ago by Eric Pettersen (next)

comment:5 by Zach Pearson, 15 months ago

Oh, sorry, didn't check the date.

comment:6 by Zach Pearson, 15 months ago

Related: #15704

comment:7 by Tom Goddard, 15 months ago

Are the databases really all lost?

Reconstructing the AlphaFold k-mer and ESMFold k-mer databases is going to be a pain.

Also maybe all of the BLAST databases (PDB, AlphaFold, uniref50, uniref90, uniref100, nr) are missing, ticket #15709, since none of those searches work.

Instructions for the AlphaFold k-mer database are here

​https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/alphafold/src/kmer_search/README

Similar steps for the ESMFold database after downloading the 120 GBytes of sequence data as indicated in #7970 comment 13.

comment:8 by Tom Goddard, 15 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

I restored the AlphaFold k-mer search database from a backup I had on an external drive so that is now working. I also restored the deleted AlphaFold blast database. And I am in the process of rebuilding the ESMFold k-mer search database that should be finished in the next day or two (takes a long time to recompute the index).

comment:9 by andreyf@…, 15 months ago 

Dear All,

Thanks a lot for your prompt action. I can confirm that I can fetch AF predictions now.

Have a good weekend,

Andrey
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