BLAST AlphaFold database version 3: Bad Request

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.5-arm64-arm-64bit
ChimeraX Version: 1.5.dev202207311904 (2022-07-31 19:04:24 UTC)
Description
I changed the blastprotein/job.py code to set the AlphaFold database version to "3" (was "2").  And I added a v3 directory on plato in /databases/mol/AlphaFold.  But it gives this error immediately (within 1 second) when I try to do a BLAST search of the AlphaFold database.

Log:
UCSF ChimeraX version: 1.5.dev202207311904 (2022-07-31)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> alphafold search
> MITLASGVFIDWEQLTGQSKFVVDLISFPIFAGIAGWLTNWTGVLMLFWPLRFRGVRVPGLKVLYPYLPRRVQVLPVFSEDGSRFGFQGFIPARAEKMASICVDKALLRIGSPRDFIHELDLDGIADYVAEMAHKQVQSIVDDVMYRENPELWGSLPRAMKQLVYQRVDRELPALCRRAFESLGDNVDQLIDVKGFVIRYLQDNPIILKDLTTTIAAPELRFMVRIGLLGAPFGLLLALYLHVHPNIPVLGWVPAWVIVLLVSAGIGVLVNLIAIKMVFEPGDPQPRYKYLWRQALLAKRQPQAAVDLARILAYQVLTLPNLSKELLEGPNGDKTRQLLERLISDEIHRQLGRTTSVVRAAFGRRQFDNLKVGAAGAAVGLAPTLVEDAEFTEEQAKKIDEFAARKLKQLTPGEFMEMFYASVEQDAWLLYVHGGLLGLVVGGVHLLLFGW

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 114, in run  
result = self.chimerax_api.submit_job(  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 1712, in submit_job  
(data) = self.submit_job_with_http_info(params, filepaths, job_type, **kwargs)
# noqa: E501  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 1787, in
submit_job_with_http_info  
return self.api_client.call_api(  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 358, in request  
return self.rest_client.POST(url,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 263, in POST  
return self.request("POST", url,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Tue, 09 Aug 2022 00:18:13
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '72', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "unknown
AlphaFold version"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 214, in _run_thread  
self.run(*args, **kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 122, in run  
raise JobLaunchError(str(e))  
chimerax.core.tasks.JobLaunchError: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Tue, 09 Aug 2022 00:18:13
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '72', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "unknown
AlphaFold version"}'  
  
  
Exception in thread:  
chimerax.core.tasks.JobLaunchError: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Tue, 09 Aug 2022 00:18:13
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '72', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "unknown
AlphaFold version"}'  
  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 122, in run  
raise JobLaunchError(str(e))  
  
See log for complete Python traceback.  
  




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

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
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      OS Loader Version: 7459.141.1

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      Time since boot: 8 days 18:40

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[Tom Goddard]

The http response headers give "description" as "unknown AlphaFold version". So I guess the server-side code only accepts AlphaFold database versions 1 and 2. Could you update it to accept "3" also?

HTTP response headers: HTTPHeaderDict({'Date': 'Tue, 09 Aug 2022 00:18:13
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '72', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "unknown
AlphaFold version"}' 

[Zach Pearson]

On it, thanks for letting me know!

[Zach Pearson]

Bumped the allowable database versions on webservices; should be good to test now.

[Tom Goddard]

Thanks. It is working. I am fixing the parsing of the sequence description which has changed in AlphaFold database version 3.