id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6465 Crash showing ribbons 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. {""app_name"":""ChimeraX"",""timestamp"":""2022-03-25 10:58:14.00 +0000"",""app_version"":"""",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":"""",""platform"":1,""share_with_app_devs"":0,""is_first_party"":1,""bug_type"":""309"",""os_version"":""macOS 12.1 (21C52)"",""incident_id"":""9C61AF21-D398-4544-A983-7F308E8C01E7"",""name"":""ChimeraX""} { ""uptime"" : 120000, ""procLaunch"" : ""2022-03-24 16:32:11.9530 +0000"", ""procRole"" : ""Unspecified"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,2"", ""procStartAbsTime"" : 113135685321376, ""coalitionID"" : 8391, ""osVersion"" : { ""train"" : ""macOS 12.1"", ""build"" : ""21C52"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-03-25 10:58:14.5511 +0000"", ""incident"" : ""9C61AF21-D398-4544-A983-7F308E8C01E7"", ""bug_type"" : ""309"", ""pid"" : 48512, ""procExitAbsTime"" : 122845919074579, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""DE3E0CEC-2671-665D-0F23-CF4242532BCB"", ""responsiblePid"" : 48500, ""wakeTime"" : 2786, ""bridgeVersion"" : {""build"":""19P647"",""train"":""6.1""}, ""sleepWakeUUID"" : ""AA5D0A4D-976B-400F-B38F-9241068296E3"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x108614160 is in 0x108444000-0x1086a9000; bytes after start: 1900896 bytes before end: 609951\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 108422000-10843c000 [ 104K] r--\/rwx SM=COW ...t_id=f4dbe1cf\n GAP OF 0x8000 BYTES\n---> mapped file 108444000-1086a9000 [ 2452K] r-x\/rwx SM=COW ...t_id=f3e99dcf\n mapped file 1086a9000-1086e3000 [ 232K] rw-\/rwx SM=COW ...t_id=fba8b1cf"", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x000000000000000a, 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""usedImages"" : [ { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 140703338172416, ""size"" : 15216738304, ""uuid"" : ""40432a03-88d3-305f-9c0c-e7549e71d927"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=628K resident=0K(0%) swapped_out_or_unallocated=628K(100%)\nWritable regions: Total=1.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nKernel Alloc Once 8K 1 \nMALLOC 256.1M 32 \nMALLOC guard page 24K 5 \nMALLOC_MEDIUM (reserved) 840.0M 7 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nSTACK GUARD 12K 3 \nStack 9752K 4 \nStack Guard 56.0M 1 \nVM_ALLOCATE 96.3M 9 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__DATA 16K 1 \n__DATA_CONST 80K 1 \n__LINKEDIT 208K 2 \n__TEXT 432K 1 \ndyld private memory 1024K 1 \nmapped file 81.6M 141 \nshared memory 12K 2 \n=========== ======= ======= \nTOTAL 1.7G 213 \nTOTAL, minus reserved VM space 501.3M 213 \n"", ""legacyInfo"" : { ""threadTriggered"" : { } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""6193d03f2171a2330e561dfc"" }, ""deploymentId"" : 240000303 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""621d4d0f680160486b9e1c98"" }, ""deploymentId"" : 240000412 }, { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000123 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000295 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- notes | available bundle cache has not been initialized yet Updating list of available bundles failed: Internal Server Error 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/hannahdoherty/Downloads/PA14_05600_a6fa2.result/PA14_05600_a6fa2_unrelaxed_rank_5_model_4.pdb Chain information for PA14_05600_a6fa2_unrelaxed_rank_5_model_4.pdb #1 --- Chain | Description A | No description available > open /Users/hannahdoherty/Downloads/6z3n.cif Summary of feedback from opening /Users/hannahdoherty/Downloads/6z3n.cif --- notes | Fetching CCD ACT from http://ligand- expo.rcsb.org/reports/A/ACT/ACT.cif Fetching CCD NI from http://ligand-expo.rcsb.org/reports/N/NI/NI.cif Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif 6z3n.cif title: Apo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1 [more info...] Chain information for 6z3n.cif #2 --- Chain | Description | UniProt AAA BBB CCC DDD | Hydrolase | Q9I686_PSEAE Non-standard residues in 6z3n.cif #2 --- ACT — acetate ion GOL — glycerol (glycerin; propane-1,2,3-triol) NI — nickel (II) ion 6z3n.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > view #2 clip false > show atoms > hide atoms > show cartoons > hide cartoons > show cartoons > style stick Changed 7669 atom styles > style stick Changed 7669 atom styles > ui tool show ""Selection Inspector"" > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PA14_05600_a6fa2_unrelaxed_rank_5_model_4.pdb, chain A (#1) with 6z3n.cif, chain AAA (#2), sequence alignment score = 942.6 RMSD between 174 pruned atom pairs is 0.578 angstroms; (across all 177 pairs: 0.744) > select #2 6216 atoms, 5767 bonds, 14 pseudobonds, 1281 residues, 2 models selected > show #!2 target m > select #2/AAA:8-184 1408 atoms, 1439 bonds, 177 residues, 1 model selected > select #2/BBB:8-184 1408 atoms, 1439 bonds, 177 residues, 1 model selected > hide sel cartoons > select #2/CCC:8-184 1408 atoms, 1439 bonds, 177 residues, 1 model selected > hide sel cartoons > select #2/DDD:8-184 1408 atoms, 1439 bonds, 177 residues, 1 model selected > hide sel cartoons > select #1 1453 atoms, 1484 bonds, 184 residues, 1 model selected > hide #!2 models > show #!2 models > show #1 target m > view #1 clip false > color #2 #ec57cc transparency 0 > color #1 #54d7a8 transparency 0 > hide #1 models > select #2/BBB:8-184 1408 atoms, 1439 bonds, 177 residues, 1 model selected > show sel cartoons ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet 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-18.3.5 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: 32 GB System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0) OS Loader Version: 540.60.2~89 Software: System Software Overview: System Version: macOS 12.1 (21C52) Kernel Version: Darwin 21.2.0 Time since boot: 10 days 4:13 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-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 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 Depiction can't reproduce all ChimeraX