Context Navigation

← Previous Ticket
Next Ticket →

#5399 closed defect (fixed)

AlphaFold failure due to blast reorganization

Reported by:	juliingaramo.98@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Structure Prediction	Version:
Keywords:		Cc:	Zach Pearson
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202110120902 (2021-10-12 09:02:44 UTC)
Description
(Describe the actions that caused this problem to occur here)
I am here because i need to make a alphafold of an enzime and it didnt work, i receive these message:
RuntimeError: delayed command registration for 'alphafold search' failed (register_command() failed for command alphafold search in bundle ChimeraX-AlphaFold:
No module named 'chimerax.blastprotein.databases')

File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2176, in lazy_register
raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))

See log for complete Python traceback

Log:
UCSF ChimeraX version: 1.3.dev202110120902 (2021-10-12)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 314, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1267, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\\__init__.py", line 37, in register_command  
blast.register_alphafold_search_command(logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\blast.py", line 36, in
register_alphafold_search_command  
from chimerax.blastprotein.databases import AvailableMatrices  
ModuleNotFoundError: No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2174, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2105, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 304, in cb  
s._register_cmd(ci, l)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 316, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
alphafold search in bundle ChimeraX-AlphaFold:  
No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 182, in _search  
self._run_command('search')  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 209, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2791, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2527, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  

> open C:\Users\Usuario\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Usuario\Downloads\sequence.fasta  
---  
note | Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

> open C:\Users\Usuario\Downloads\sequence.fasta format fasta

Summary of feedback from opening C:\Users\Usuario\Downloads\sequence.fasta  
---  
notes | Destroying pre-existing alignment with identifier sequence.fasta  
Alignment identifier is sequence.fasta  
  
Opened 1 sequences from sequence.fasta  

No sequence chosen for AlphaFold search  

> save "C:/Users/Usuario/Desktop/fasta tiorredoxina" format fasta alignment
> sequence.fasta

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 314, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1267, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\\__init__.py", line 37, in register_command  
blast.register_alphafold_search_command(logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\blast.py", line 36, in
register_alphafold_search_command  
from chimerax.blastprotein.databases import AvailableMatrices  
ModuleNotFoundError: No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2174, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2105, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 304, in cb  
s._register_cmd(ci, l)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 316, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
alphafold search in bundle ChimeraX-AlphaFold:  
No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 182, in _search  
self._run_command('search')  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 209, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2791, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2527, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 314, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1267, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\\__init__.py", line 37, in register_command  
blast.register_alphafold_search_command(logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\blast.py", line 36, in
register_alphafold_search_command  
from chimerax.blastprotein.databases import AvailableMatrices  
ModuleNotFoundError: No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2174, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2105, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 304, in cb  
s._register_cmd(ci, l)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 316, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
alphafold search in bundle ChimeraX-AlphaFold:  
No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 182, in _search  
self._run_command('search')  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 209, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2791, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2527, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 314, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1267, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\\__init__.py", line 37, in register_command  
blast.register_alphafold_search_command(logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\blast.py", line 36, in
register_alphafold_search_command  
from chimerax.blastprotein.databases import AvailableMatrices  
ModuleNotFoundError: No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2174, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2105, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 304, in cb  
s._register_cmd(ci, l)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 316, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
alphafold search in bundle ChimeraX-AlphaFold:  
No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 182, in _search  
self._run_command('search')  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 209, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2791, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2527, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 314, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1267, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\\__init__.py", line 37, in register_command  
blast.register_alphafold_search_command(logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\blast.py", line 36, in
register_alphafold_search_command  
from chimerax.blastprotein.databases import AvailableMatrices  
ModuleNotFoundError: No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2174, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2105, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 304, in cb  
s._register_cmd(ci, l)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 316, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
alphafold search in bundle ChimeraX-AlphaFold:  
No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 182, in _search  
self._run_command('search')  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 209, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2791, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2527, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 314, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1267, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\\__init__.py", line 37, in register_command  
blast.register_alphafold_search_command(logger)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\blast.py", line 36, in
register_alphafold_search_command  
from chimerax.blastprotein.databases import AvailableMatrices  
ModuleNotFoundError: No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2174, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2105, in call  
return self.proxy()  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 304, in cb  
s._register_cmd(ci, l)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 316, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
alphafold search in bundle ChimeraX-AlphaFold:  
No module named 'chimerax.blastprotein.databases'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 182, in _search  
self._run_command('search')  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 209, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2791, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2527, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
RuntimeError: delayed command registration for 'alphafold search' failed
(register_command() failed for command alphafold search in bundle ChimeraX-
AlphaFold:  
No module named 'chimerax.blastprotein.databases')  
  
File "C:\Program Files\ChimeraX 1.3.dev202110120902\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2176, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 23.20.16.4973
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 13-7359
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 3,971,710,976
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
OSLanguage: es-MX
Locale: ('es_AR', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110120902
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.3
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.4
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 4 years ago

Cc:	Zach Pearson added
Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → AlphaFold failure due to blast reorganization

Perhaps blast needs a publicly declared API?

comment:2 by pett, 4 years ago

Reported by Julia Ingaramo

comment:3 by Zach Pearson, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed in this commit; I organized the BLAST bundle so that there's nothing useful that can't be imported from chimerax.blastprotein.

Note: See TracTickets for help on using tickets.

Download in other formats: