id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1924	cannot import name 'user_error_format'	tic20@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-05-07)
Description
Typo when trying to open a model from the PDB (I wanted to open 5u8q) on starting ChimeraX causes a crash back to the Bash prompt.

ChimeraX u8q

Traceback (most recent call last):
  File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py"", line 31, in run
    results = command.run(text, log=log)
  File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py"", line 2631, in run
    result = ci.function(session, **kw_args)
  File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py"", line 37, in open
    db_fetches, paths = _db_fetches_and_paths(filename, format, from_database)
  File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py"", line 92, in _db_fetches_and_paths
    p = _expand_path(path)
  File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py"", line 134, in _expand_path
    raise UserError('File not found: %s' % path)
chimerax.core.errors.UserError: File not found: u8q

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/ChimeraX_main.py"", line 711, in init
    commands.run(sess, 'open %s' % arg)
  File ""/opt/UCSF/ChimeraX-daily/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' (/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/logger.py)


Log:
UCSF ChimeraX version: 0.9 (2019-05-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5u8q

Summary of feedback from opening 5u8q fetched from pdb  
---  
notes | Fetching compressed mmCIF 5u8q from
http://files.rcsb.org/download/5u8q.cif  
Fetching CCD MLT from http://ligand-expo.rcsb.org/reports/M/MLT/MLT.cif  
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif  
  
5u8q title:  
Structure of the ectodomain of the human Type 1 insulin-like growth factor
receptor in complex with IGF-I [more info...]  
  
Chain information for 5u8q #1  
---  
Chain | Description  
A | Insulin-like growth factor 1 receptor  
B | Insulin-like growth factor I  
H | Fv 24-60 heavy chain  
L | Fv 24-60 light chain  
  
Non-standard residues in 5u8q #1  
---  
MAN — α-D-mannose  
MLT — D-malate ((2R)-2-hydroxybutanedioic acid; 2-hydroxy-succinic acid)  
NAG — N-acetyl-D-glucosamine  
SO4 — sulfate ion  
  
5u8q mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	normal		Logging		fixed						all	ChimeraX