id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6208 Crash deleting structure rhloring@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. I was checking the error message I was getting if I tried to bond two peptides together without first combining the chains into a single model. I was using the pdbs for the alphafold version of mu-conotoxin and mu-conotoxin from the pdb database. After successfully bonding, I closed the session and instead of just closing, the session aborted. Fatal Python error: Aborted Current thread 0x00002bf0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\molobject.py"", line 1372 in delete File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py"", line 115 in delete File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\models.py"", line 895 in close File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\models.py"", line 574 in reset_state File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\session.py"", line 535 in reset File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\close.py"", line 60 in close_session File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2856 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 680 in file_close_cb File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 1032 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== 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\rhlor\Dropbox\Research\ChimeraX data\Bond AF-mu CTX to mu- > CTX.cxs"" format session opened ChimeraX session > close session > open ""C:/Users/rhlor/Dropbox/Research/ChimeraX data/AF-mu conotoxin > P0C349.pdb"" > open ""C:/Users/rhlor/Dropbox/Research/ChimeraX data/Mu-Conotoxin P0C349.pdb"" Chain information for Mu-Conotoxin P0C349.pdb #2 --- Chain | Description A | No description available > select #2 316 atoms, 319 bonds, 22 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right rotate > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected atoms"" > undo > view > select #2 316 atoms, 319 bonds, 22 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.42999,-0.24761,0.86822,9.7454,-0.0605,0.9674,0.24593,0.97289,-0.9008,0.053219,-0.43095,0.83888 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.42999,-0.24761,0.86822,-5.8423,-0.0605,0.9674,0.24593,-1.0157,-0.9008,0.053219,-0.43095,2.4714 > select clear > select #2 316 atoms, 319 bonds, 22 residues, 1 model selected > view matrix models > #2,-0.42999,-0.24761,0.86822,-7.7728,-0.0605,0.9674,0.24593,-1.2128,-0.9008,0.053219,-0.43095,3.3709 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.29694,-0.24409,0.92317,-8.3191,-0.0095519,0.96749,0.25273,-1.462,-0.95485,0.06623,-0.28962,4.052 > view matrix models > #2,-0.68656,-0.29476,0.66464,-7.0137,-0.0044679,0.91583,0.40154,-1.1133,-0.72706,0.27271,-0.63009,2.0526 > view matrix models > #2,-0.70316,0.2295,0.67297,-6.5625,0.23158,0.96879,-0.088415,-3.6669,-0.67226,0.093677,-0.73437,1.3614 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.70316,0.2295,0.67297,-7.0729,0.23158,0.96879,-0.088415,2.8512,-0.67226,0.093677,-0.73437,2.8934 > select clear > ui mousemode right ""translate selected models"" > select #1 164 atoms, 167 bonds, 22 residues, 1 model selected > ~select #1 Nothing selected > select #2 316 atoms, 319 bonds, 22 residues, 1 model selected > view matrix models > #2,-0.70316,0.2295,0.67297,-6.003,0.23158,0.96879,-0.088415,0.10785,-0.67226,0.093677,-0.73437,5.2027 > view matrix models > #2,-0.70316,0.2295,0.67297,-5.4082,0.23158,0.96879,-0.088415,1.2332,-0.67226,0.093677,-0.73437,7.3988 > view matrix models > #2,-0.70316,0.2295,0.67297,-5.2213,0.23158,0.96879,-0.088415,1.9393,-0.67226,0.093677,-0.73437,7.0284 > bond #2/A:22@C #1/A:1@N reasonable false Cannot bond atoms in different molecules > combine #1 #2 Remapping chain ID 'A' in Mu-Conotoxin P0C349.pdb #2 to 'B' > close #1-2 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 3/A > sequence chain /B Alignment identifier is 3/B > select /A:22 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:22 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:1 26 atoms, 25 bonds, 1 residue, 1 model selected > select /B:1 26 atoms, 25 bonds, 1 residue, 1 model selected > bond #3/A:22@C #3/B:1@N reasonable false Created 1 bond > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 3/A > select /A:22 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A:1,22 55 atoms, 52 bonds, 4 residues, 1 model selected > select /A:22 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A:1,22 55 atoms, 52 bonds, 4 residues, 1 model selected > close session ===== Log before crash end ===== 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 OpenGL version: 3.3.0 - Build 27.20.100.9664 OpenGL renderer: Intel(R) HD Graphics 620 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: Inspiron 13-7378 OS: Microsoft Windows 10 Home (Build 19043) Memory: 8,453,287,936 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') 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: 2.1.11 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: 1.13.7 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 File attachment: Mu-Conotoxin P0C349.pdb }}} [attachment:""Mu-Conotoxin P0C349.pdb""] " defect closed normal Core fixed all ChimeraX