open pdbdev:4 gives error

[Elaine Meng]

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))

[Tom Goddard]

Fixed.

This IHM model had missing model group names. Added code to handle missing group names.