id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3945 Error saving settings s1960571@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-03-12) Description Trying to find contacts Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-03-12) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6zgi format mmCIF fromDatabase pdb Summary of feedback from opening 6zgi fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""NAG"" near line 28731 6zgi title: Furin Cleaved Spike Protein of SARS-CoV-2 in Closed Conformation [more info...] Chain information for 6zgi #1 --- Chain | Description A B C | Spike glycoprotein Non-standard residues in 6zgi #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > set bgColor white > select up Nothing selected > select up Nothing selected > name s1 :27-676 > name s2 :689-1147 > color s1 green > color s2 red > hide atoms > show :614:854 > select :614:854 51 atoms, 45 bonds, 1 model selected > color byatom > toolshed show Clashes > toolshed show Contacts Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 359, in __setattr__ self._session, value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 488, in convert_to_string new_value = self.convert_from_string(session, str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 482, in convert_from_string return self.from_str(str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 91, in literal_eval return _convert(node_or_string) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 90, in _convert return _convert_signed_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 63, in _convert_signed_num return _convert_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 55, in _convert_num raise ValueError('malformed node or string: ' + repr(node)) ValueError: malformed node or string: <_ast.Call object at 0x12e31e090> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 179, in __getattr__ return self._cur_settings[name] KeyError: '_name' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/gui.py"", line 570, in get_command self.settings.save(settings=saveables) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 218, in save ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 362, in __setattr__ (self._name, name)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) AttributeError: _name AttributeError: _name File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) See log for complete Python traceback. > select :854 27 atoms, 24 bonds, 1 model selected > toolshed show Contacts Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 359, in __setattr__ self._session, value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 488, in convert_to_string new_value = self.convert_from_string(session, str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 482, in convert_from_string return self.from_str(str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 91, in literal_eval return _convert(node_or_string) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 90, in _convert return _convert_signed_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 63, in _convert_signed_num return _convert_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 55, in _convert_num raise ValueError('malformed node or string: ' + repr(node)) ValueError: malformed node or string: <_ast.Call object at 0x12df05c90> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 179, in __getattr__ return self._cur_settings[name] KeyError: '_name' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/gui.py"", line 570, in get_command self.settings.save(settings=saveables) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 218, in save ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 362, in __setattr__ (self._name, name)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) AttributeError: _name AttributeError: _name File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) See log for complete Python traceback. > select ~sel 26826 atoms, 27552 bonds, 12 pseudobonds, 2 models selected > select clear > select /C:854 9 atoms, 8 bonds, 1 model selected > toolshed show Contacts Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 359, in __setattr__ self._session, value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 488, in convert_to_string new_value = self.convert_from_string(session, str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 482, in convert_from_string return self.from_str(str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 91, in literal_eval return _convert(node_or_string) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 90, in _convert return _convert_signed_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 63, in _convert_signed_num return _convert_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 55, in _convert_num raise ValueError('malformed node or string: ' + repr(node)) ValueError: malformed node or string: <_ast.Call object at 0x12e43de90> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 179, in __getattr__ return self._cur_settings[name] KeyError: '_name' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/gui.py"", line 570, in get_command self.settings.save(settings=saveables) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 218, in save ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 362, in __setattr__ (self._name, name)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) AttributeError: _name AttributeError: _name File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) See log for complete Python traceback. > set bgColor black > toolshed show Contacts Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 359, in __setattr__ self._session, value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 488, in convert_to_string new_value = self.convert_from_string(session, str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 482, in convert_from_string return self.from_str(str_value) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 91, in literal_eval return _convert(node_or_string) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 90, in _convert return _convert_signed_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 63, in _convert_signed_num return _convert_num(node) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py"", line 55, in _convert_num raise ValueError('malformed node or string: ' + repr(node)) ValueError: malformed node or string: <_ast.Call object at 0x12edca190> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 179, in __getattr__ return self._cur_settings[name] KeyError: '_name' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/gui.py"", line 570, in get_command self.settings.save(settings=saveables) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 218, in save ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 362, in __setattr__ (self._name, name)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) AttributeError: _name AttributeError: _name File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/settings.py"", line 181, in __getattr__ raise AttributeError(name) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.8 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. }}} " defect closed normal Core duplicate all ChimeraX