id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1921	chimera.core.logger.user_error_format missing	goddard@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-08)
Description
Error importing user_error_format after commands open 5cd4 ; seq chain selAtoms.

Log:
UCSF ChimeraX version: 0.9 (2019-05-08)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5cd4 format mmCIF fromDatabase pdb

5cd4 title:  
The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the
asymmetric unit arranged back-to-back [more info...]  
  
Chain information for 5cd4 #1  
---  
Chain | Description  
A M | CRISPR system Cascade subunit CasE  
B C D E F G N O P Q R S | CRISPR system Cascade subunit CasC  
H T | CRISPR system Cascade subunit CasD  
I U | CRISPR system Cascade subunit CasA  
J K V W | CRISPR system Cascade subunit CasB  
L X | crRNA  
  
Non-standard residues in 5cd4 #1  
---  
23G — guanosine-5'-phosphate-2',3'-cyclic phosphate  
ZN — zinc ion  
  
5cd4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> sequence chain selAtoms

Traceback (most recent call last):  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py"", line 31, in run  
results = command.run(text, log=log)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2631, in run  
result = ci.function(session, **kw_args)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py"", line 127, in seqalign_chain  
raise UserError(""Chains must have same sequence"")  
chimerax.core.errors.UserError: Chains must have same sequence  
  
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/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py"", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py"", line 89, in handle_scheme  
shortcuts.keyboard_shortcuts(self.session).run_shortcut(value)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py"", line 388, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py"", line 285, in run  
commands.run(s, f)  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py"", line 38, in run  
from ..logger import user_error_format  
ImportError: cannot import name 'user_error_format' from
'chimerax.core.logger'
(/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/logger.py)  
  
ImportError: cannot import name 'user_error_format' from
'chimerax.core.logger'
(/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/logger.py)  
  
File
""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py"", line 38, in run  
from ..logger import user_error_format  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.8.38
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	defect	closed	normal		Logging		fixed						all	ChimeraX