id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1733 Sequence headers session-restore problem boschdu@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-06) Description attempting to load a recently saved ChimeraX session Log: UCSF ChimeraX version: 0.9 (2019-02-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/dustinbosch/OneDrive - UW/N_fowleri_project/SSGCID_structures/NfGalpha12.cxs"" Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 594, in restore obj = sm.restore_snapshot(self, data) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 590, in restore_snapshot inst.seq_canvas.restore_state(session, data['seq canvas']) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1120, in restore_state headers.append(header_class.session_restore(session, self.sv, header_state)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/headers/header_sequence.py"", line 164, in session_restore inst = HeaderSequence(alignment) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 229, in _actually_resize self._reformat() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1027, in _reformat self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps()) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1602, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2244, in layout_lines self._layout_line(line, label_color, bli, end) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2194, in _layout_line font=self._label_font(line)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2134, in _label_font if self.has_associated_structures(line): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2072, in has_associated_structures and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]: File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2072, in and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]: File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Sequence' object has no attribute 'structure' AttributeError: 'Sequence' object has no attribute 'structure' File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > open ""/Users/dustinbosch/OneDrive - UW/N_fowleri_project/SSGCID_structures/NfGalpha10.cxs"" opened ChimeraX session > open ""/Users/dustinbosch/OneDrive - UW/N_fowleri_project/SSGCID_structures/NfGalpha12.cxs"" Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 594, in restore obj = sm.restore_snapshot(self, data) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 590, in restore_snapshot inst.seq_canvas.restore_state(session, data['seq canvas']) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1120, in restore_state headers.append(header_class.session_restore(session, self.sv, header_state)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/headers/header_sequence.py"", line 164, in session_restore inst = HeaderSequence(alignment) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 229, in _actually_resize self._reformat() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1027, in _reformat self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps()) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 1602, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2244, in layout_lines self._layout_line(line, label_color, bli, end) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2194, in _layout_line font=self._label_font(line)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2134, in _label_font if self.has_associated_structures(line): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2072, in has_associated_structures and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]: File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/seq_canvas.py"", line 2072, in and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]: File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Sequence' object has no attribute 'structure' AttributeError: 'Sequence' object has no attribute 'structure' File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.10 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Sequence fixed all ChimeraX