id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5134	Blastprotein Qt GUI breaks alphafold search	Zach Pearson	Zach Pearson	"blocks #5133 

AlphaFold tries to register a command and can't because of the way the Blastprotein tool has changed. 

{{{
Traceback (most recent call last):
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 312, in _register_cmd
    api._api_caller.register_command(api, self, ci, logger)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py"", line 1271, in register_command
    return cls._get_func(api, ""register_command"")(ci.name, logger)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/__init__.py"", line 37, in register_command
    blast.register_alphafold_search_command(logger)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/blast.py"", line 33, in register_alphafold_search_command
    from chimerax.blastprotein.cmd import Matrices
ImportError: cannot import name 'Matrices' from 'chimerax.blastprotein.cmd' (/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/blastprotein/cmd.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2174, in lazy_register
    deferred.call()
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2105, in call
    return self.proxy()
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 302, in cb
    s._register_cmd(ci, l)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 314, in _register_cmd
    raise ToolshedError(
chimerax.core.toolshed.ToolshedError: register_command() failed for command alphafold search in bundle ChimeraX-AlphaFold:
cannot import name 'Matrices' from 'chimerax.blastprotein.cmd' (/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/blastprotein/cmd.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 297, in execute
    cmd.run(cmd_text)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2791, in run
    self._find_command_name(final, used_aliases=_used_aliases)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2527, in _find_command_name
    what.lazy_register(cmd_name)
  File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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:
cannot import name 'Matrices' from 'chimerax.blastprotein.cmd' (/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/blastprotein/cmd.py))

RuntimeError: delayed command registration for 'alphafold search' failed (register_command() failed for command alphafold search in bundle ChimeraX-AlphaFold:
cannot import name 'Matrices' from 'chimerax.blastprotein.cmd' (/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/blastprotein/cmd.py))

File ""/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.
}}}"	defect	closed	moderate		Sequence		fixed						all	ChimeraX