id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2002 No spacegroup of name i 4 goddard@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-06-05) Description Trying new open command structureFactors option produced this error. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.9 (2019-06-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1a0m structureFactors true Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 249, in symmetry_from_model_metadata_mmcif spgr_descr = Spgr_descr(spgr_str) RuntimeError: Spgr_descr: No such SG number During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 43, in open db_models = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 144, in _fetch_from_database ignore_cache=ignore_cache, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py"", line 434, in fetch_from_database models, status = df.fetch(session, id, format=format, ignore_cache=ignore_cache, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py"", line 497, in fetch return fetch(session, database_id, ignore_cache=ignore_cache, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 383, in fetch_cb return fetch_shim(session, identifier, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 381, in fetch_shim return f(session, identifier, database_name=database_name, format_name=format_name, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 45, in fetch_from_database return fetcher(session, identifier, ignore_cache=ignore_cache, **kw) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 330, in fetch_mmcif mmgr = get_map_mgr(models[0], create=True) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 149, in get_map_mgr sh = get_symmetry_handler(structure, create=create) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 145, in get_symmetry_handler return Symmetry_Manager(structure) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 433, in __init__ self.cell, self.spacegroup, self.grid, self._has_symmetry = f(*args) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 166, in symmetry_from_model_metadata return symmetry_from_model_metadata_mmcif(model) File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 251, in symmetry_from_model_metadata_mmcif raise RuntimeError('No spacegroup of name {}!'.format(spgr_str)) RuntimeError: No spacegroup of name i 4! RuntimeError: No spacegroup of name i 4! File ""/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/clipper/symmetry.py"", line 251, in symmetry_from_model_metadata_mmcif raise RuntimeError('No spacegroup of name {}!'.format(spgr_str)) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data 0.9 invalid all ChimeraX