id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7025 Attempt to log command for deleted bond rotation chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.25131 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/zhgwa/Desktop/3TX9_ds-12.pdbqt Summary of feedback from opening C:/Users/zhgwa/Desktop/3TX9_ds-12.pdbqt --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 15 messages similar to the above omitted Chain information for 3TX9_ds-12.pdb #1 --- Chain | Description A | No description available Opened 3TX9_ds-12.pdbqt containing 1 structures (3948 atoms, 4032 bonds) > ui mousemode right ""bond rotation"" > torsion /d:1@C13,C12,C4,C3 163.09 Must specify exactly 4 atoms for 'torsion' command; you specified 7 > torsion /d:1@C13,C12,C4,C3 163.09 Must specify exactly 4 atoms for 'torsion' command; you specified 7 > torsion /d:1@C13,C12,C4,C3 163.09 Must specify exactly 4 atoms for 'torsion' command; you specified 7 > save C:/ProgramData/ChimeraX/dd.pdb relModel #1 > save C:/Users/zhgwa/Desktop/dd.pdb relModel #1 > torsion /d:1@C13,C12,C4,C3 163.09 Must specify exactly 4 atoms for 'torsion' command; you specified 7 > torsion /d:1@C13,C12,C4,C3 167.09 Must specify exactly 4 atoms for 'torsion' command; you specified 7 > close session > open C:\Users\zhgwa\Desktop\dd.pdb format pdb Chain information for dd.pdb #1 --- Chain | Description A | No description available Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 637, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 531, in _dispatch_mouse_event lm.mouse_up(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 38, in mouse_up self._log_command() File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 44, in _log_command log_torsion_command(br) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 123, in log_torsion_command fs_atom = bond.other_atom(ms_atom) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 169, in other_atom o = f(self._c_pointer, atom._c_pointer) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\attributes.py"", line 57, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\attributes.py"", line 85, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Bond' object has no attribute '_c_pointer' AttributeError: 'Bond' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\attributes.py"", line 85, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 34, in mouse_drag br.angle += dy File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\bond_rot.py"", line 80, in set_angle moving, fixed = self.moving_side.coord, self.bond.other_atom(self.moving_side).coord File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 34, in mouse_drag br.angle += dy File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\bond_rot.py"", line 80, in set_angle moving, fixed = self.moving_side.coord, self.bond.other_atom(self.moving_side).coord File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 34, in mouse_drag br.angle += dy File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\bond_rot.py"", line 80, in set_angle moving, fixed = self.moving_side.coord, self.bond.other_atom(self.moving_side).coord File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 34, in mouse_drag br.angle += dy File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\bond_rot.py"", line 80, in set_angle moving, fixed = self.moving_side.coord, self.bond.other_atom(self.moving_side).coord File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 34, in mouse_drag br.angle += dy File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\bond_rot.py"", line 80, in set_angle moving, fixed = self.moving_side.coord, self.bond.other_atom(self.moving_side).coord File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp\cymol.pyx"", line 219, in chimerax.atomic.cymol.CyAtom.coord.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 639, in gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_up"") File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\mouse_modes\mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 38, in mouse_up self._log_command() File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 44, in _log_command log_torsion_command(br) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\bond_rot\mouse_rot.py"", line 123, in log_torsion_command fs_atom = bond.other_atom(ms_atom) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 169, in other_atom o = f(self._c_pointer, atom._c_pointer) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\attributes.py"", line 57, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\attributes.py"", line 85, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Bond' object has no attribute '_c_pointer' AttributeError: 'Bond' object has no attribute '_c_pointer' File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\attributes.py"", line 85, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 512.20 OpenGL renderer: NVIDIA GeForce GT 1030/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: HP Model: HP Slim Desktop S01-pF0xxx OS: Microsoft Windows 11 专业版 Insider Preview (Build 25131) Memory: 17,071,575,040 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9400 CPU @ 2.90GHz OSLanguage: zh-CN Locale: ('zh_CN', 'cp936') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.1 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Editing fixed Eric Pettersen all ChimeraX