id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1152	open pdbdev:4 gives error	Elaine Meng	Tom Goddard	"
UCSF ChimeraX version: 0.7 (2018-06-03)

open pdbdev:4

Summary of feedback from opening 4 fetched from pdbdev
warnings	Found disconnected atom H1 that is not in residue template for MET #1 in chain A
Found disconnected atom H1 that is not in residue template for MET #1 in chain B
Warning: ihm_model_id in atom_site table currently ignored. Assuming ihm model ids in atom_site table are 1,2,3,...
notes	Fetching IHM 00000004 from https://pdb-dev.wwpdb.org/static/cif/PDBDEV_00000004.cif
Fetching compressed mmCIF 1ubq from http://files.rcsb.org/download/1ubq.cif
No PDBx fixed column width tables
No PDBx keywords
Traceback (most recent call last):
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py"", line 205, in execute
    cmd.run(cmd_text)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2646, in run
    result = ci.function(session, **kw_args)
  File ""/Users/meng/Desktop/ChimeraX.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/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 81, in open
    filename, format=format, name=name, ignore_cache=ignore_cache, **kw)
  File ""/Users/meng/Desktop/ChimeraX.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/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/fetch.py"", line 433, in fetch_from_database
    models, status = df.fetch(session, id, format=format, ignore_cache=ignore_cache, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/fetch.py"", line 496, in fetch
    return fetch(session, database_id, ignore_cache=ignore_cache, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py"", line 327, in fetch_cb
    return fetch_shim(session, identifier, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py"", line 325, in fetch_shim
    return f(session, identifier, database_name=database_name, format_name=format_name, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/__init__.py"", line 37, in fetch_from_database
    return fetch_ihm(session, identifier, ignore_cache=ignore_cache)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/fetch_ihm.py"", line 41, in fetch_ihm
    models, status = io.open_data(session, filename, format = 'ihm', name = name, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"", line 404, in open_data
    models, status = open_func(*args, **kw)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/__init__.py"", line 24, in open_file
    return ihm.read_ihm(session, path, file_name, load_ensembles = ensembles)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 38, in read_ihm
    show_atom_crosslinks = show_atom_crosslinks)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 128, in __init__
    self.group_result_models(smodels, emodels, amodels, lmaps, mgroup)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 691, in group_result_models
    group_models = self.make_model_groups()
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 740, in make_model_groups
    ml = mlt.fields(ml_fields)
  File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/mmcif.py"", line 477, in fields
    have))
ValueError: Field model_group_name is not in table ""ihm_model_list"", have fields ordinal_id, model_id, model_group_id, model_name, assembly_id, protocol_id, and representation_id

ValueError: Field model_group_name is not in table ""ihm_model_list"", have fields ordinal_id, model_id, model_group_id, model_name, assembly_id, protocol_id, and representation_id

File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/mmcif.py"", line 477, in fields
have))
"	defect	closed	moderate		Input/Output		fixed						all	ChimeraX