BLAST Protein failing: 'NoneType' object has no attribute 'keys'

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Blast Protein on the AlphaFold database fails.  Could be because the AlphaFold sequence database was deleted on plato, related to ticket #15706 which is about the AlphaFold k-mer search database missing.

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  

> open 8fse format mmcif fromDatabase pdb

8fse title:  
Crystal structure of integrin beta-2 tail bound to the FERM-folded talin head
domain [more info...]  
  
Chain information for 8fse #1  
---  
Chain | Description | UniProt  
A B | Integrin beta-2,Talin-1 | ITB2_MOUSE -9-0, TLN1_MOUSE 1-430  
  
8fse mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show "Blast Protein"

> blastprotein /A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version 4 name bp1

Webservices job id: H5A8P4EG9AT56SY5  
BlastProtein failed: 'bytes' object has no attribute 'items'  
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'  

> help help:contact.html




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
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: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 43 days, 19 hours, 21 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
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    aiohttp: 3.9.5
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    alabaster: 0.7.16
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    build: 1.2.1
    certifi: 2023.11.17
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    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
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    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-AlphaFold: 1.0
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    ChimeraX-Atomic: 1.57.1
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    ChimeraX-BILD: 1.0
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    ChimeraX-Crystal: 1.0
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[Tom Goddard]

BLAST of both the AlphaFold and PDB databases fails with this same error. Not sure where those sequence databases exist on plato. Maybe they got deleted as in #15706.

[Tom Goddard]

All of the Blast Protein database searches fail including: PDB, AlphaFold, nr and uniref. Also the AlphaFold and ESMFold k-mer sequence searches fail, ticket #15706.

[Zach Pearson]

Related also: #15704

[Tom Goddard]

I updated AlphaFold BLAST database and I believe Scooter updated PDB and NR. So only the Uniref BLAST databases are missing now.

[Zach Pearson]

This has been fixed for a while.