id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1920	Sequence icon using probably-not-ready-for-primetime 'sequence' command	Elaine Meng	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-08)
Description
open 6cmn
show Molecule Display icons, click Sequence icon

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 6cmn format mmCIF fromDatabase pdb

Summary of feedback from opening 6cmn fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for G #18 in chain D  
  
6cmn title:  
Co-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7 [more
info...]  
  
Chain information for 6cmn #1  
---  
Chain | Description  
A | TAR-Binding Protein 6.7  
D | Trans-Activation Response RNA Element  
  
  

> sequence chain selAtoms

Traceback (most recent call last):  
File
""/Users/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/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/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/logger.py)  
  
File
""/Users/meng/Desktop/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 INTEL-12.8.38
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

}}}
"	defect	closed	normal		General Controls		fixed		Eric Pettersen				all	ChimeraX