Problem parsing mmCIF: unexpected left bracket

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-10-27)
Description
Opening the attached assembly

Log:
UCSF ChimeraX version: 0.8 (2018-10-27)  
How to cite UCSF ChimeraX  

open /Users/pett/rm/1bep_assembly.cif

open /Users/pett/rm/1bep_assembly.cif

Traceback (most recent call last):  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 542, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2563, in run  
    result = ci.function(session, **kw_args)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 583, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 461, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 416, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/__init__.py", line 52, in open_file  
    log_info=log_info)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 59, in open_mmcif  
    pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets,
atomic)  
_mmcif.error: unexpected left bracket near line 34  
  
_mmcif.error: unexpected left bracket near line 34  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 59, in open_mmcif  
pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation
File attachment: 1bep_assembly.cif

1bep_assembly.cif​

[lpravda@…]

Added by email2trac

[Eric Pettersen]

This structure is one of the entries for a protein-ligand interaction pipeline being developed by the PDB.

[Greg Couch]

That file is illegal according to the CIF standard. [ and ] are reserved for future use. See paragraph 11 of ​https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax. You need to quote the data value that starts with [.

[Greg Couch]

Did change this to say 'left square bracket' -- the unicode name for [. And made it a UserError, so no traceback is shown.