id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2652 ISOLDE: using deleted 'session' attribute of dead Structure jliu321@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.12.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.9 (2019-06-06) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data2/users/jliu/ccpem_project/Flex-EM_3/1_MD/final1_mdcg.pdb Chain information for final1_mdcg.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open /data2/users/jliu/Documents/J79/J79_map_invert.mrc Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level 0.294, step 2, values float32 > ui mousemode rightMode ""rotate selected models"" > select #1 10404 atoms, 10542 bonds selected > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > fitmap #1 inMap #2 Fit molecule final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404 atoms average map value = 0.4909, steps = 116 shifted from previous position = 9.65 rotated from previous position = 6.16 degrees atoms outside contour = 3741, contour level = 0.29422 Position of final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2) coordinates: Matrix rotation and translation -0.96239600 -0.04256905 0.26829437 274.52001913 -0.17241686 -0.66748987 -0.72438233 356.81491917 0.20992005 -0.74340112 0.63504992 133.05039824 Axis -0.13241463 0.40642003 -0.90404044 Axis point 134.70529547 202.88620204 0.00000000 Rotation angle (degrees) 175.88174344 Shift along axis -11.61667520 > addh Summary of feedback from adding hydrogens to final1_mdcg.pdb #1 --- warning | Unknown hybridization for atoms (C8, C3, C4, O4, C1, C7, O3, O6, C5, O5, C6, O7, C2) of residue type NAG; not adding hydrogens to them notes | No usable SEQRES records for final1_mdcg.pdb (#1) chain A; guessing termini instead No usable SEQRES records for final1_mdcg.pdb (#1) chain B; guessing termini instead No usable SEQRES records for final1_mdcg.pdb (#1) chain C; guessing termini instead No usable SEQRES records for final1_mdcg.pdb (#1) chain D; guessing termini instead No usable SEQRES records for final1_mdcg.pdb (#1) chain E; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 190, /B PRO 37, /C GLN 1, /D LYS 289, /E LEU 40 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 287, /B GLN 273, /C SER 189, /D GLN 389, /E ALA 713 Chain-final residues that are not actual C termini: 676 hydrogen bonds 10265 hydrogens added > show selAtoms > hide selAtoms > hide selAtoms > show selAtoms ribbons > hide selAtoms > show selAtoms > hide selAtoms > hide > hide HC > toolshed show ISOLDE > set selectionWidth 4 Chain information for final1_mdcg.pdb --- Chain | Description 1.3/A | No description available 1.3/B | No description available 1.3/C | No description available 1.3/D | No description available 1.3/E | No description available Done loading forcefield > select #1.3.1 2 models selected > select #1.3.2 2 models selected > ~select #1.3.3 2 models selected > ~select #1.3 Nothing selected > select #1 20669 atoms, 20807 bonds, 7 models selected > hide #!2 models > hide #!2.1 models > hide #!1.3.1 models > hide #!1.3.2 models > hide #!1.3.3 models > hide #!1.1 models > show #!1.2 models > hide #!1 models > show #!1 models > hide #!1.3 models > show #!1.3 models > select #1.3 20669 atoms, 20807 bonds, 5 models selected > clipper associate #2 toModel #1.3 > clipper spotlight radius 20.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 20.00 Setting spotlight mode for model 1.3 to True > clipper associate #2 toModel #1.3 Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1552, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Invoked getPositions() on a State which does not contain positions. Error processing trigger ""new frame"": Invoked getPositions() on a State which does not contain positions.: RuntimeError: Invoked getPositions() on a State which does not contain positions. File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. QWidget::repaint: Recursive repaint detected Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1552, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Invoked getPositions() on a State which does not contain positions. Error processing trigger ""new frame"": Invoked getPositions() on a State which does not contain positions.: RuntimeError: Invoked getPositions() on a State which does not contain positions. File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. > ~select #1.2 14 atoms, 13 bonds, 1 model selected > hide #!1.2 models > hide #!1.1.1 models > close #1.3 > close Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1015, in _update_model_list self._update_sim_control_button_states() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1117, in _update_sim_control_button_states self._selection_changed() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1052, in _selection_changed self._clear_rotamer() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2074, in _clear_rotamer rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/session_extensions.py"", line 110, in get_rotamer_restraint_mgr return Rotamer_Restraint_Mgr(model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 3189, in __init__ session=model.session File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/programs/x86_64-linux/chimerax/0.9/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 ""/programs/x86_64-linux/chimerax/0.9/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: 'Structure' object has no attribute 'session' Error processing trigger ""remove models"": 'Structure' object has no attribute 'session': AttributeError: 'Structure' object has no attribute 'session' File ""/programs/x86_64-linux/chimerax/0.9/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. Exception ignored in: Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1086, in __del__ if not self.was_deleted: AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted' > open /data2/users/jliu/ccpem_project/Flex-EM_3/1_MD/final1_mdcg.pdb Chain information for final1_mdcg.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1015, in _update_model_list self._update_sim_control_button_states() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1117, in _update_sim_control_button_states self._selection_changed() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1052, in _selection_changed self._clear_rotamer() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2074, in _clear_rotamer rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/session_extensions.py"", line 110, in get_rotamer_restraint_mgr return Rotamer_Restraint_Mgr(model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 3189, in __init__ session=model.session File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/programs/x86_64-linux/chimerax/0.9/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 ""/programs/x86_64-linux/chimerax/0.9/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: 'Structure' object has no attribute 'session' Error processing trigger ""add models"": 'Structure' object has no attribute 'session': AttributeError: 'Structure' object has no attribute 'session' File ""/programs/x86_64-linux/chimerax/0.9/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. Exception ignored in: Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1086, in __del__ if not self.was_deleted: AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted' > hide selAtoms > show selAtoms ribbons > open /data2/users/jliu/Documents/J79/J79_map_invert.mrc Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level 0.294, step 2, values float32 Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1015, in _update_model_list self._update_sim_control_button_states() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1117, in _update_sim_control_button_states self._selection_changed() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1052, in _selection_changed self._clear_rotamer() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2074, in _clear_rotamer rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/session_extensions.py"", line 110, in get_rotamer_restraint_mgr return Rotamer_Restraint_Mgr(model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 3189, in __init__ session=model.session File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/programs/x86_64-linux/chimerax/0.9/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 ""/programs/x86_64-linux/chimerax/0.9/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: 'Structure' object has no attribute 'session' Error processing trigger ""add models"": 'Structure' object has no attribute 'session': AttributeError: 'Structure' object has no attribute 'session' File ""/programs/x86_64-linux/chimerax/0.9/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. Exception ignored in: Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1086, in __del__ if not self.was_deleted: AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted' Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1015, in _update_model_list self._update_sim_control_button_states() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1117, in _update_sim_control_button_states self._selection_changed() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1052, in _selection_changed self._clear_rotamer() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2074, in _clear_rotamer rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/session_extensions.py"", line 110, in get_rotamer_restraint_mgr return Rotamer_Restraint_Mgr(model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 3189, in __init__ session=model.session File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/programs/x86_64-linux/chimerax/0.9/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 ""/programs/x86_64-linux/chimerax/0.9/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: 'Structure' object has no attribute 'session' Error processing trigger ""add models"": 'Structure' object has no attribute 'session': AttributeError: 'Structure' object has no attribute 'session' File ""/programs/x86_64-linux/chimerax/0.9/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. Exception ignored in: Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1086, in __del__ if not self.was_deleted: AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted' Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1015, in _update_model_list self._update_sim_control_button_states() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1117, in _update_sim_control_button_states self._selection_changed() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1052, in _selection_changed self._clear_rotamer() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2074, in _clear_rotamer rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/session_extensions.py"", line 110, in get_rotamer_restraint_mgr return Rotamer_Restraint_Mgr(model) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 3189, in __init__ session=model.session File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/programs/x86_64-linux/chimerax/0.9/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 ""/programs/x86_64-linux/chimerax/0.9/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: 'Structure' object has no attribute 'session' Error processing trigger ""add models"": 'Structure' object has no attribute 'session': AttributeError: 'Structure' object has no attribute 'session' File ""/programs/x86_64-linux/chimerax/0.9/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. Exception ignored in: Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1086, in __del__ if not self.was_deleted: AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted' OpenGL version: 3.3.0 NVIDIA 410.79 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party fixed all ChimeraX