id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6983 Graphics crash, macOS 12.2.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad"" }, ""deploymentId"" : 240000414 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000370 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000149 } ], ""experiments"" : [ ] } } ===== 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 > /Users/fli05/Documents/Phenix/CB1_Fab52515/RealSpaceRefine_11/J883_real_space_refined_011-coot-0.pdb > format pdb Chain information for J883_real_space_refined_011-coot-0.pdb #1 --- Chain | Description A | No description available H | No description available L | No description available > open /Users/fli05/Library/CloudStorage/OneDrive- > Amgen/CB1/EM/CB1_Fab52515/FinalMap/cryosparc_P11_J883_010_volume_map_sharp.mrc > format mrc Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 0.813, shown at level 0.0332, step 2, values float32 > ui tool show ISOLDE > set selectionWidth 4 Removed all altlocs in #1 and reset associated occupancies to 1. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 35 residues in model #1 to IUPAC-IUB standards. Chain information for J883_real_space_refined_011-coot-0.pdb --- Chain | Description 1.2/A | No description available 1.2/H | No description available 1.2/L | No description available Done loading forcefield > clipper associate #2 toModel #1 Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #1.1.1.1, grid size 400,400,400, pixel 0.813, shown at step 1, values float32 > set bgColor white > addh Summary of feedback from adding hydrogens to J883_real_space_refined_011-coot-0.pdb #1.2 --- warnings | Not adding hydrogens to /A GLU 100 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LEU 117 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 183 CB because it is missing heavy-atom bond partners 4 messages similar to the above omitted notes | No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2) chain H; guessing termini instead No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2) chain L; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 100, /H GLN 1, /L ASP 128 Chain-initial residues that are not actual N termini: /A ASN 112, /A ALA 335 Chain-final residues that are actual C termini: /H SER 127, /L ARG 235 Chain-final residues that are not actual C termini: /A PHE 412, /A MET 103, /A SER 303 404 hydrogen bonds Adding 'H' to /A ASN 112 Adding 'H' to /A ALA 335 /A PHE 412 is not terminus, removing H atom from 'C' 4026 hydrogens added > hide HC > select up 453 atoms, 454 bonds, 30 residues, 1 model selected > select up 4465 atoms, 4524 bonds, 275 residues, 1 model selected Loading residue template for ZDG from internal database ISOLDE: stopped sim > select clear > select up 61 atoms, 64 bonds, 1 residue, 1 model selected > isolde parameterise sel Residue name ZDG already corresponds to template MC_ZDG in the amber14 forcefield. If you wish to replace that template, re-run this command with override=True > select up 61 atoms, 64 bonds, 1 residue, 1 model selected > select up 4465 atoms, 4524 bonds, 275 residues, 1 model selected > select down 61 atoms, 64 bonds, 1 residue, 1 model selected > delete atoms (#!1.2 & sel) > delete bonds (#!1.2 & sel) > select up 18 atoms, 17 bonds, 1 residue, 1 model selected > select up 534 atoms, 544 bonds, 30 residues, 1 model selected > select up 4404 atoms, 4458 bonds, 274 residues, 1 model selected ISOLDE: stopped sim > save /Users/fli05/Desktop/CB1.pdb > close session Fetching CCD LEU_LL from http://ligand- expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif Fetching CCD LEU_LEO2 from http://ligand- expo.rcsb.org/reports/L/LEU_LEO2/LEU_LEO2.cif Fetching CCD LEU_LFZW from http://ligand- expo.rcsb.org/reports/L/LEU_LFZW/LEU_LFZW.cif Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif Traceback (most recent call last): File ""/Users/fli05/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/validation/unparameterised.py"", line 180, in _show_selected_unparameterised_residue residue.atoms.displays = True File ""atomic_cpp/cymol.pyx"", line 994, in chimerax.atomic.cymol.CyResidue.atoms.__get__ RuntimeError: Residue already deleted RuntimeError: Residue already deleted File ""atomic_cpp/cymol.pyx"", line 994, in chimerax.atomic.cymol.CyResidue.atoms.__get__ See log for complete Python traceback. > open > /Users/fli05/Documents/Phenix/CB1_Fab52515/RealSpaceRefine_11/J883_real_space_refined_011-coot-0.pdb > format pdb Chain information for J883_real_space_refined_011-coot-0.pdb #1 --- Chain | Description A | No description available H | No description available L | No description available Removed all altlocs in #1 and reset associated occupancies to 1. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 35 residues in model #1 to IUPAC-IUB standards. Chain information for J883_real_space_refined_011-coot-0.pdb --- Chain | Description 1.2/A | No description available 1.2/H | No description available 1.2/L | No description available > open /Users/fli05/Library/CloudStorage/OneDrive- > Amgen/CB1/EM/CB1_Fab52515/FinalMap/cryosparc_P11_J883_010_volume_map_sharp.mrc > format mrc Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 0.813, shown at level 0.0332, step 2, values float32 > volume #2 step 1 > volume #2 level 0.2481 Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #1.1.1.1, grid size 400,400,400, pixel 0.813, shown at step 1, values float32 > addh Summary of feedback from adding hydrogens to J883_real_space_refined_011-coot-0.pdb #1.2 --- warnings | Not adding hydrogens to /A GLU 100 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LEU 117 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 183 CB because it is missing heavy-atom bond partners 4 messages similar to the above omitted notes | No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2) chain H; guessing termini instead No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2) chain L; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 100, /H GLN 1, /L ASP 128 Chain-initial residues that are not actual N termini: /A ASN 112, /A ALA 335 Chain-final residues that are actual C termini: /H SER 127, /L ARG 235 Chain-final residues that are not actual C termini: /A PHE 412, /A MET 103, /A SER 303 404 hydrogen bonds Adding 'H' to /A ASN 112 Adding 'H' to /A ALA 335 /A PHE 412 is not terminus, removing H atom from 'C' 4026 hydrogens added > hide HC > select #1 8050 atoms, 8158 bonds, 2 pseudobonds, 510 residues, 13 models selected ISOLDE: stopped sim Fetching CCD ZDG from http://ligand-expo.rcsb.org/reports/Z/ZDG/ZDG.cif > select up 453 atoms, 454 bonds, 30 residues, 1 model selected > select up 4465 atoms, 4524 bonds, 275 residues, 1 model selected ISOLDE: stopped sim Deleted the following atoms from residue ZDG A2110: HBB1, HAU, HBG2, HAV, HBD, HBI1, HBK1, HAD1, HBI2, HBB3, HAD2, HAK, HAJ, HBJ1, HAM, HBB2, HBK2, HAX, HAE, HAN, HBH1, HBJ2, HBH2, HBG1 > close session > open /Users/fli05/Desktop/CB1.pdb format pdb Chain information for CB1.pdb #1 --- Chain | Description A | No description available H | No description available L | No description available ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for CB1.pdb --- Chain | Description 1.2/A | No description available 1.2/H | No description available 1.2/L | No description available > open /Users/fli05/Library/CloudStorage/OneDrive- > Amgen/CB1/EM/CB1_Fab52515/FinalMap/cryosparc_P11_J883_010_volume_map_sharp.mrc > format mrc Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 0.813, shown at level 0.0332, step 2, values float32 Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #1.1.1.1, grid size 400,400,400, pixel 0.813, shown at step 1, values float32 > addh Summary of feedback from adding hydrogens to CB1.pdb #1.2 --- warnings | Not adding hydrogens to /A GLU 100 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LEU 117 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 183 CB because it is missing heavy-atom bond partners 4 messages similar to the above omitted notes | No usable SEQRES records for CB1.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for CB1.pdb (#1.2) chain H; guessing termini instead No usable SEQRES records for CB1.pdb (#1.2) chain L; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 100, /H GLN 1, /L ASP 128 Chain-initial residues that are not actual N termini: /A ASN 112, /A ALA 335 Chain-final residues that are actual C termini: /H SER 127, /L ARG 235 Chain-final residues that are not actual C termini: /A PHE 412, /A MET 103, /A SER 303 386 hydrogen bonds /A PHE 412 is not terminus, removing H atom from 'C' 2 hydrogens added > hide HC > select up 453 atoms, 454 bonds, 30 residues, 1 model selected > select up 4406 atoms, 4460 bonds, 274 residues, 1 model selected Populating font family aliases took 386 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. ISOLDE: started sim ===== 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: 4.1 INTEL-18.4.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0) OS Loader Version: 540.80.2~11 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 2 days 29 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 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-Clipper: 0.17.0 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-ISOLDE: 1.3 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 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: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 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 ptyprocess: 0.7.0 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 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 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 }}} " defect closed normal Graphics nonchimerax all ChimeraX