id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7627 ChimeraX/ISOLDE version problems mille153@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.14.6-x86_64-i386-64bit ChimeraX Version: 1.5.dev202209140201 (2022-09-14 02:01:28 UTC) Description opening ISOLDE Log: UCSF ChimeraX version: 1.5.dev202209140201 (2022-09-14) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde start > set selectionWidth 4 Failed to extract font properties from /System/Library/Fonts/Apple Color Emoji.ttc: In FT2Font: Could not set the fontsize (error code 0x17) Failed to extract font properties from /Library/Fonts/NISC18030.ttf: In FT2Font: Could not set the fontsize (error code 0x17) Failed to extract font properties from /System/Library/Fonts/LastResort.otf: tuple indices must be integers or slices, not str generated new fontManager Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/tool.py"", line 42, in _launch_main_gui tw = self.tool_window = IsoldeMainWin(self) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/main_win.py"", line 56, in __init__ self.restraints_tab = RestraintsTab(self.session, self.isolde, self, tabw) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/ui_base.py"", line 226, in __init__ self.populate() File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/__init__.py"", line 20, in populate self.addWidget(ReferenceModelPanel(session, isolde, parent, gui)) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 16, in __init__ cd = self.content = ReferenceModelDialog(session, isolde, gui, self) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 85, in __init__ opt = self.options = ReferenceModelOptions(self.session, gui, options_frame) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 464, in __init__ drfi = self.distance_fuzziness_indicator = DistanceRestraintFuzzinessIndicator(session, dsl, dfl) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 636, in __init__ self._create_dummy_model() File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 704, in _create_dummy_model dr = self._dummy_restraint = drm.add_restraint(a1, a2) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 2864, in _get_restraints return self._plural_restraint_getter(ret[:num]) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 97, in _adaptive_distance_restraints return AdaptiveDistanceRestraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger ""new frame"": TypeError: __init__() takes 3 positional arguments but 4 were given File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, See log for complete Python traceback. Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 1790, in _get_and_process_changes return self._process_changes(changes) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 1775, in _process_changes changed_obj = class_funcs[1](changed_ptrs) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 97, in _adaptive_distance_restraints return AdaptiveDistanceRestraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger ""new frame"": TypeError: __init__() takes 3 positional arguments but 4 were given File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, See log for complete Python traceback. > 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 | UniProt A | capsid protein VP1 | CAPSD_NVN68 B | capsid protein VP1 | CAPSD_NVN68 C | capsid protein VP1 | CAPSD_NVN68 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB standards. 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 | UniProt 1.2/A | capsid protein VP1 | CAPSD_NVN68 1.2/B | capsid protein VP1 | CAPSD_NVN68 1.2/C | capsid protein VP1 | CAPSD_NVN68 Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/cmd/cmd.py"", line 240, in _load_demo load_fn(session, **kwargs) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 1483, in load_cryo_em_demo session.isolde.selected_model = m File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 433, in selected_model self.change_selected_model(model) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 771, in change_selected_model self._change_selected_model(self, model=model, force=True) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 823, in _change_selected_model sx.get_rota_annotator(m) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/session_extensions.py"", line 216, in get_rota_annotator return RotamerAnnotator(model) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 74, in __init__ self.track_whole_model = True File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 255, in __setattr__ super(Drawing, self).__setattr__(key, value) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 109, in track_whole_model self._selected_rotamers = self._mgr.get_rotamers(res) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 1602, in get_rotamers return _rotamers(f(self._c_pointer, residues._c_pointers, n)) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 78, in _rotamers return Rotamers(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 306, in __init__ super().__init__(c_pointers, Rotamer, Rotamers) TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger ""new frame"": TypeError: __init__() takes 3 positional arguments but 4 were given File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 306, in __init__ super().__init__(c_pointers, Rotamer, Rotamers) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 4043, in _model_changes_cb self.update_graphics(update_visibility) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 4087, in update_graphics self._last_visibles = self.visible_restraints File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 3980, in visible_restraints return self._ARRAY_GETTER(f(self._c_pointer)) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 3627, in _ARRAY_GETTER return _proper_dihedral_restraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 132, in _proper_dihedral_restraints return ProperDihedralRestraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 835, in __init__ super().__init__(c_pointers, ProperDihedralRestraint, ProperDihedralRestraints) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 732, in __init__ super().__init__(c_pointers, singular_py_class, array_py_class) TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger ""changes"": TypeError: __init__() takes 3 positional arguments but 4 were given File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 732, in __init__ super().__init__(c_pointers, singular_py_class, array_py_class) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 4043, in _model_changes_cb self.update_graphics(update_visibility) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 4087, in update_graphics self._last_visibles = self.visible_restraints File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 3980, in visible_restraints return self._ARRAY_GETTER(f(self._c_pointer)) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 3627, in _ARRAY_GETTER return _proper_dihedral_restraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 132, in _proper_dihedral_restraints return ProperDihedralRestraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 835, in __init__ super().__init__(c_pointers, ProperDihedralRestraint, ProperDihedralRestraints) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 732, in __init__ super().__init__(c_pointers, singular_py_class, array_py_class) TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger ""changes"": TypeError: __init__() takes 3 positional arguments but 4 were given File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 732, in __init__ super().__init__(c_pointers, singular_py_class, array_py_class) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 4043, in _model_changes_cb self.update_graphics(update_visibility) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 4087, in update_graphics self._last_visibles = self.visible_restraints File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 3980, in visible_restraints return self._ARRAY_GETTER(f(self._c_pointer)) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 3627, in _ARRAY_GETTER return _proper_dihedral_restraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 132, in _proper_dihedral_restraints return ProperDihedralRestraints(p) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 835, in __init__ super().__init__(c_pointers, ProperDihedralRestraint, ProperDihedralRestraints) File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 732, in __init__ super().__init__(c_pointers, singular_py_class, array_py_class) TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger ""changes"": TypeError: __init__() takes 3 positional arguments but 4 were given File ""/Users/mille153/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py"", line 732, in __init__ super().__init__(c_pointers, singular_py_class, array_py_class) See log for complete Python traceback. OpenGL version: 4.1 ATI-2.11.20 OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,1 Processor Name: Intel Core i9 Processor Speed: 3.6 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 220.270.93.0.0 SMC Version (system): 2.46f12 Software: System Software Overview: System Version: macOS 10.14.6 (18G95) Kernel Version: Darwin 18.7.0 Time since boot: 118 days 2:49 Graphics/Displays: Radeon Pro 575X: Chipset Model: Radeon Pro 575X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c4 ROM Revision: 113-D0008A-042 VBIOS Version: 113-D0008A14GP-003 EFI Driver Version: 01.01.042 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 5120 x 2880 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.1 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.2 ChimeraX-AtomicLibrary: 7.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0 ChimeraX-CheckWaters: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0.2 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5.dev202209140201 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.7 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.7 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.1 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.0.0 filelock: 3.7.1 fonttools: 4.37.1 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 4.12.0 ipykernel: 6.15.1 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.1 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.5 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.3 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.1 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.1 python-dateutil: 2.8.2 pytz: 2022.2.1 pyzmq: 23.2.1 qtconsole: 5.3.1 QtPy: 2.2.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.5.0 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.8.1 }}} " defect closed normal Third Party fixed all ChimeraX