mmCIF bad _struct_conn table written by CCP4

[Tom Goddard]

Oliver Clarke provided the attached mmCIF file written by CCP4 which has a _struct_conn table that is missing required fields.

Probably ChimeraX should give a warning and not use the _struct_conn table. Currently it gives an error. It would be useful to have it continue with the file to see what other problems are present, and to allow the user to open the model if the missing data is not critical.

open 1bl8_ccp4.cif

Summary of problems opening /Users/goddard/ucsf/people/clarke/1bl8_ccp4.cif:

Warnings:
Skipping atom "?" on line 1774: missing coordinates
Skipping atom "?" on line 2483: missing coordinates
Skipping atom "?" on line 3190: missing coordinates
Skipping atom "?" on line 3897: missing coordinates
Traceback (most recent call last):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 120, in on_enter
cmd.run(cmd_text)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2122, in run
results.append(ci.function(session, kw_args))
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 76, in open
models = session.models.open(paths, format=format, name=name)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 289, in open
format=format, name=name, kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 554, in open_multiple_data
models, status = open_data(session, fspec, format=format, name=name, kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 513, in open_data
models, status = open_func(session, stream, dname, kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/mmcif.py", line 33, in open_mmcif
pointers = _mmcif.parse_mmCIF_file(filename, _additional_categories, session.logger)
_mmcif.error: Missing tag ptnr1_label_asym_id in category struct_conn on line 956

[Tom Goddard]

mmCIF written by CCP4 with bad _struct_conn table.

[Greg Couch]

Log warning saying table was skipped, instead of failing.

[Eric Pettersen]

reducing # of categories, so lumping into I/O category