ChimeraX bug report submission

[Greg Couch]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.7 (2018-07-26)
Description
Try to open 1tqn-assembly-1.cif from #1180.  Is this related to the recent chain changes?

Log:
UCSF ChimeraX version: 0.7 (2018-07-26)  
OpenGL version: 3.3.0 NVIDIA 391.24  
OpenGL renderer: GeForce GTX 970/PCIe/SSE2  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open C:/Users/gregc/Downloads/1tqn-assembly-1.cif

Summary of feedback from opening C:/Users/gregc/Downloads/1tqn-assembly-1.cif  
---  
notes | No PDBx fixed column width tables  
No PDBx keywords  
  
Traceback (most recent call last):  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\ui\gui.py", line 517, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\open.py", line 111, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\models.py", line 508, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 50, in open_file  
    log_info=log_info)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 63, in open_mmcif  
    for p in pointers]  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 63, in <listcomp>  
    for p in pointers]  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2157, in __init__  
    self._set_chain_descriptions(self.session)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2333, in _set_chain_descriptions  
    mmcif_cid = ch.existing_residues.mmcif_chain_ids[0]  
IndexError: index 0 is out of bounds for axis 0 with size 0  
  

IndexError: index 0 is out of bounds for axis 0 with size 0  
  
File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2333, in _set_chain_descriptions  
mmcif_cid = ch.existing_residues.mmcif_chain_ids[0]  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 3.3.0 NVIDIA 391.24
OpenGL renderer: GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Greg Couch]

So num_chains is one, the chain_id is '', and len(ch.existing_residues) is zero.

[Greg Couch]

Bad data. mmcif file has entity_poly but not entity_poly_seq

[Greg Couch]

Changed logic for detecting missing entity_poly_seq table. Structure opens.