id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2956 KeyError reading mmCIF dirk.fahrenkamp@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/dirk/Desktop/T3SS_Building/WT_job151_IR_C24.mrc Opened WT_job151_IR_C24.mrc, grid size 432,432,432, pixel 1.09, shown at level 0.00534, step 2, values float32 > open /Users/dirk/Desktop/T3SS_Building/WT_job151_IR_C24.cif Summary of feedback from opening /Users/dirk/Desktop/T3SS_Building/WT_job151_IR_C24.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Traceback (most recent call last): File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 628, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths])) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 723, in open session, filenames, format=format, name=name, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 503, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 456, in open_data models, status = open_func(*args, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 56, in open_file log_info=log_info, combine_sym_atoms=combine_sym_atoms) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 86, in open_mmcif for p in pointers] File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 86, in for p in pointers] File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2249, in __init__ self._set_chain_descriptions(self.session) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2449, in _set_chain_descriptions entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False) KeyError: 'A' KeyError: 'A' File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2449, in _set_chain_descriptions entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False) See log for complete Python traceback. > volume #1 level 0.0241 > open /Users/dirk/Desktop/T3SS_Building/WT_job151_IR_C24.cif Summary of feedback from opening /Users/dirk/Desktop/T3SS_Building/WT_job151_IR_C24.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Traceback (most recent call last): File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 628, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths])) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 723, in open session, filenames, format=format, name=name, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 503, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 456, in open_data models, status = open_func(*args, **kw) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 56, in open_file log_info=log_info, combine_sym_atoms=combine_sym_atoms) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 86, in open_mmcif for p in pointers] File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 86, in for p in pointers] File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2249, in __init__ self._set_chain_descriptions(self.session) File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2449, in _set_chain_descriptions entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False) KeyError: 'A' KeyError: 'A' File ""/private/var/folders/f0/_syt4qxn40zglh2dv2vvvf600000gn/T/AppTranslocation/69DC2D25-AA27-47DF- BCA5-2D9DE31FF923/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2449, in _set_chain_descriptions entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.4.23 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc. }}} " defect closed normal Input/Output 0.91 can't reproduce all ChimeraX