id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4122 End of simulation: 'PositionRestraintMgr' object has no attribute '_c_pointer' rmccool@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ISOLDE > set selectionWidth 4 Done loading forcefield > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Summary of feedback from opening 20205 fetched from emdb --- note | Fetching compressed map 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > clipper associate #2 toModel #1 > isolde start > set selectionWidth 4 Done loading forcefield > isolde start > set selectionWidth 4 Done loading forcefield > isolde restrain ligands #1 > select #1 11505 atoms, 11622 bonds, 1720 residues, 14 models selected > isolde sim start sel > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > close > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > clipper associate #2 toModel #1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | capsid protein VP1 > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > hide HC > isolde restrain ligands #1 Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1.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/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1017, in _sim_end_cb self._pr_sim_end_cb() File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1074, in _pr_sim_end_cb restraints = self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms) File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 2329, in get_restraints return self._get_restraints(atoms) File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 2282, in _get_restraints num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret)) AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer' Error processing trigger ""sim terminated"": AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer' File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 2282, in _get_restraints num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1.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/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/validation/ramaplot.py"", line 197, in _sim_end_cb self._mode_change_cb() File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/validation/ramaplot.py"", line 233, in _mode_change_cb self.selection_mode = mode File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/validation/ramaplot.py"", line 288, in selection_mode self.set_target_residues(self.current_model.residues) File ""/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 ""/Applications/ChimeraX-1.1.1.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-1.1.1.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(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'residues' property raised AttributeError Error processing trigger ""simulation terminated"": AttributeError: Execution of 'Structure' object's 'residues' property raised AttributeError File ""/Applications/ChimeraX-1.1.1.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(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > isolde start > set selectionWidth 4 Done loading forcefield > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 1205 hydrogen bonds /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 0 hydrogens added > hide HC > isolde restrain ligands #1 > select #1 22945 atoms, 23062 bonds, 1720 residues, 14 models selected > select #1 22945 atoms, 23062 bonds, 1720 residues, 14 models selected > isolde sim start sel Undo failed, probably because structures have been modified. reverting to start Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1.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/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/delayed_reaction.py"", line 79, in callback if self.tf is None or self.tf(): File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 245, in thread_finished return f(self._c_pointer) AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' Error processing trigger ""new frame"": AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 245, in thread_finished return f(self._c_pointer) See log for complete Python traceback. > cview /A:57 reverting to start Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1.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/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/delayed_reaction.py"", line 79, in callback if self.tf is None or self.tf(): File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 245, in thread_finished return f(self._c_pointer) AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' Error processing trigger ""new frame"": AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 245, in thread_finished return f(self._c_pointer) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1.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/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/delayed_reaction.py"", line 79, in callback if self.tf is None or self.tf(): File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 245, in thread_finished return f(self._c_pointer) AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' Error processing trigger ""new frame"": AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' File ""/Users/McCool/Library/Application Support/ChimeraX/1.1/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 245, in thread_finished return f(self._c_pointer) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.8 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro12,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.7 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 192.0.0.0.0 SMC Version (system): 2.28f7 Software: System Software Overview: System Version: macOS 10.15.7 (19H2) Kernel Version: Darwin 19.6.0 Time since boot: 46 days 23:18 Graphics/Displays: Intel Iris Graphics 6100: Chipset Model: Intel Iris Graphics 6100 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x162b Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 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tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Third Party fixed all ChimeraX