id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1443 Clipper: cannot import name 'ArrayGridData' chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-11-06) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.8 (2018-11-06) How to cite UCSF ChimeraX > toolshed show Shell QLineEdit::setSelection: Invalid start position (-1) Unknown command: install ChimeraX- ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl QLineEdit::setSelection: Invalid start position (-1) QLineEdit::setSelection: Invalid start position (-1) > toolshed show ISOLDE before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 126, in invoke return self._func(self._name, data) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 1020, in _update_model_list self._change_selected_model(model=current_model, force=True) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2311, in _change_selected_model get_symmetry_handler(m, create=True) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 145, in get_symmetry_handler return Symmetry_Manager(structure) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 396, in __init__ radius = spotlight_radius, live = spotlight_mode, debug=debug) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 798, in __init__ self.live_scrolling = live File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 228, in __setattr__ super(Drawing, self).__setattr__(key, value) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 965, in live_scrolling self._update_box() File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1021, in _update_box from .crystal import find_box_params File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/crystal.py"", line 25, in from chimerax.map.data import ArrayGridData ImportError: cannot import name 'ArrayGridData' Error processing trigger ""add models"": cannot import name 'ArrayGridData': ImportError: cannot import name 'ArrayGridData' File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/crystal.py"", line 25, in from chimerax.map.data import ArrayGridData See log for complete Python traceback. Traceback (most recent call last): File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 3219, in load_demo_data sym_handler = symmetry.get_symmetry_handler(before_struct, create=True) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 145, in get_symmetry_handler return Symmetry_Manager(structure) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 396, in __init__ radius = spotlight_radius, live = spotlight_mode, debug=debug) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 798, in __init__ self.live_scrolling = live File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 228, in __setattr__ super(Drawing, self).__setattr__(key, value) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 965, in live_scrolling self._update_box() File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1021, in _update_box from .crystal import find_box_params File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/crystal.py"", line 25, in from chimerax.map.data import ArrayGridData ImportError: cannot import name 'ArrayGridData' ImportError: cannot import name 'ArrayGridData' File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/crystal.py"", line 25, in from chimerax.map.data import ArrayGridData See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 126, in invoke return self._func(self._name, data) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1171, in _model_changed_cb self._update_sym_coords() File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1176, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) TypeError: 'NoneType' object is not subscriptable Error processing trigger ""changes"": 'NoneType' object is not subscriptable: TypeError: 'NoneType' object is not subscriptable File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1176, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 126, in invoke return self._func(self._name, data) File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1171, in _model_changed_cb self._update_sym_coords() File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1176, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) TypeError: 'NoneType' object is not subscriptable Error processing trigger ""changes"": 'NoneType' object is not subscriptable: TypeError: 'NoneType' object is not subscriptable File ""/Users/rgk680/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/symmetry.py"", line 1176, in _update_sym_coords res = atom_and_bond_sym_transforms_from_sym_atoms(*focal_set[0:3]) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.2.17 OpenGL renderer: Intel(R) Iris(TM) Graphics 650 OpenGL vendor: Intel Inc. }}} " defect closed normal Third Party fixed Tom Goddard all ChimeraX