id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8513 self.structure is None chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-10) Description (Describe the actions that caused this problem to occur here) Log: Startup Errors --- error | Bundle 'ChimeraX-Registration' custom initialization failed warning | 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/toolshed/info.py"", line 432, in initialize api._api_caller.initialize(api, session, self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1624, in initialize return cls._get_func(api, ""initialize"")(session, bi) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/registration/__init__.py"", line 41, in initialize nag(session) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 28, in nag if not check_registration(logger=session.logger): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 49, in check_registration return _check_expiration(param, logger) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 140, in _check_expiration logger.warning(""Registration file %r has expired"" % reg_file) NameError: name 'reg_file' is not defined UCSF ChimeraX version: 0.91 (2019-12-10) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yizhang_n/Documents/Facility/Projects/WuXD/volume-for- > mask-J115-box384.mrc Opened volume-for-mask-J115-box384.mrc, grid size 384,384,384, pixel 1.06, shown at level 2.44e-05, step 2, values float32 > volume #1 step 1 Updating list of available bundles failed: name 'reg_file' is not defined > toolshed show Toolbar > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > set bgColor white > volume #1 level 0.1144 > volume #1 color #b2b2b2fe > volume #1 color #b2b2b2fa > volume #1 color #b2b2b2ee > volume #1 color #b2b2b2de > volume #1 color #b2b2b2d7 > volume #1 color #b2b2b2d3 > volume #1 color #b2b2b2c8 > volume #1 color #b2b2b2c2 > volume #1 color #b2b2b2ba > volume #1 color #b2b2b2b7 > volume #1 color #b2b2b2b6 > volume #1 color #b2b2b2b5 > volume #1 color #b2b2b2b2 > volume #1 color #b2b2b2af > volume #1 color #b2b2b2ab > volume #1 color #b2b2b2a9 > volume #1 color #b2b2b2a8 > volume #1 color #b2b2b2a6 > volume #1 color #b2b2b2a1 > volume #1 color #b2b2b29c > volume #1 color #b2b2b295 > volume #1 color #b2b2b291 > volume #1 color #b2b2b28f > volume #1 color #b2b2b28b > volume #1 color #b2b2b288 > volume #1 color #b2b2b287 > volume #1 color #b2b2b286 > volume #1 color #b2b2b285 > volume #1 color #b2b2b284 > volume #1 color #b2b2b283 > volume #1 color #b2b2b282 > volume #1 color #b2b2b281 > volume #1 color #b2b2b280 > open > /Users/yizhang_n/Documents/Facility/Projects/WuXD/AF-Q9DBS2-F1-model_v4.pdb AF-Q9DBS2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for tumor protein P63-regulated gene 1-like protein (Q9DBS2) [more info...] Chain information for AF-Q9DBS2-F1-model_v4.pdb #2 --- Chain | Description A | tumor protein P63-regulated gene 1-like protein AF-Q9DBS2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for tumor protein P63-regulated gene 1-like protein (Q9DBS2) [more info...] Chain information for AF-Q9DBS2-F1-model_v4.pdb --- Chain | Description 2.1/A | tumor protein P63-regulated gene 1-like protein > ui mousemode rightMode translate > ui mousemode rightMode translate > select #1 2 models selected > ~select #1 Nothing selected > select #2.1 2099 atoms, 2146 bonds, 5 models selected > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode rotate > ui mousemode rightMode translate > close #2.1 > toolshed show ""Side View"" 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. 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/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1385, in _box_moved_cb self._update_box() File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""/Users/yizhang_n/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/clipper/symmetry.py"", line 1398, in _update_box atoms = self.structure.atoms See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.31 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. }}} " defect closed normal Third Party duplicate all ChimeraX