Sequence search found 1 AlphaFold id that do not have AlphaFold database models
The following bug report has been submitted:
Platform: macOS-15.6.1-x86_64-i386-64bit
ChimeraX Version: 1.11.dev202510090345 (2025-10-09 03:45:28 UTC)
Description
Hi,
I have been trying to fetch a protein from AlphaFold through ChimeraX. For some reason it does not work. The error in the log:
Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Sequence search found 1 AlphaFold id that do not have AlphaFold database models: P06865 (1 sequences)
No AlphaFold model with similar sequence for 1 sequences
Opened 0 AlphaFold model
I am unsure if it is me doing something wrong or if it is the software. I have been trying to check in different ways that there are no hidden linebreaks etc. It also gave the same error when I tried with using a UniProt code instead of the paste version. Any chance you can help me with this? Thank you in advance!
Best regards,
Käthe Dahlström
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11.dev202510090345 (2025-10-09)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show "AlphaFold Error Plot"
> ui tool show AlphaFold
> alphafold match
> MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSLHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Sequence search found 1 AlphaFold id that do not have AlphaFold database
models: P06865 (1 sequences)
No AlphaFold model with similar sequence for 1 sequences
Opened 0 AlphaFold model
> help help:contact.html
OpenGL version: 4.1 INTEL-23.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
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Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
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OS Loader Version: 583~2210
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System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
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Vendor: Intel
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![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
The closest sequence to what you were searching for has UniProt identifier P06865 and the AlphaFold Database version 3 or 4 used by ChimeraX had no structure for it, hence the message ChimeraX gave
"Sequence search found 1 AlphaFold id that do not have AlphaFold database models: P06865 "
But I see that the AlphaFold Database version 6 came out last month so I have updated so ChimeraX will now use version 6. You do not need to update ChimeraX, it will update to using version 6 automatically but it may take up to one day, because ChimeraX only checks for a new version when you do a fetch and it has not checked in the last 24 hours. You can fetch this model immediately by specifying the version using ChimeraX command
I see that Alphafold Database version 6 includes isoforms, and in fact there are two predicted models for P06865 using the reference sequence and one isoform. Previous versions of the database did not predict isoforms so ChimeraX does not handle that. So you may want to go directly to the AlphaFold database to download the isoform models if those are of interest to you.
https://alphafold.ebi.ac.uk/search/text/P06865
Here is the AlphaFold database FAQ and under "Which proteins are included?" it talks about version 6 of the database.
https://alphafold.ebi.ac.uk/faq