id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7964 Crash in event loop after ISOLDE sim start chimerax-bug-report@… Eric Pettersen "{{{ 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. Chimera crashes all the time when trying to run Isolde. 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reserved VM address space (unallocated)\nMach message 24K 5 \nObjC additional data 15K 1 \nOpenCL 1.1G 96 \nOpenCL (reserved) 6372K 4 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 56.1M 35 \nStack 137.8M 35 \nVM_ALLOCATE 327.6M 149 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 45.2M 766 \n__DATA_CONST 32.5M 340 \n__DATA_DIRTY 1641K 214 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 753.3M 218 \n__TEXT 894.0M 744 \n__UNICODE 592K 1 \ndyld private memory 1056K 2 \nmapped file 480.9M 60 \nshared memory 2976K 25 \n=========== ======= ======= \nTOTAL 7.3G 4520 \nTOTAL, minus reserved VM space 6.8G 4520 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""queue"" : ""opencl_runtime"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112dda2fc54bc3389840642"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""620aec83b02b354d3afd2f50"" }, ""deploymentId"" : 240000145 }, { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 } ], ""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/butryna/Desktop/124_5RA/j229/229-coot_fixed.pdb format pdb Chain information for 229-coot_fixed.pdb #1 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available M | No description available N | No description available > select ::name=""AGS"" 186 atoms, 198 bonds, 6 residues, 1 model selected > delete atoms sel > delete bonds sel > save /Users/butryna/Desktop/124_5RA/j229/229-coot_fixed.pdb relModel #1 > open /Users/butryna/Desktop/124_5RA/223_-40/postprocess.mrc Opened postprocess.mrc as #2, grid size 440,440,440, pixel 0.95, shown at level 0.00553, step 2, values float32 > volume #2 step 1 > clipper associate #2 toModel #1 Opened postprocess.mrc as #1.1.1.1, grid size 440,440,440, pixel 0.95, shown at level 0.0113, step 1, values float32 Chain information for 229-coot_fixed.pdb --- Chain | Description 1.2/2 | No description available 1.2/3 | No description available 1.2/4 | No description available 1.2/5 | No description available 1.2/6 | No description available 1.2/7 | No description available 1.2/8 | No description available 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/M | No description available 1.2/N | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 321 residues in model #1.2 to IUPAC-IUB standards. Done loading forcefield > addh Summary of feedback from adding hydrogens to 229-coot_fixed.pdb #1.2 --- warnings | Not adding hydrogens to /6 CYS 311 CB because it is missing heavy- atom bond partners Not adding hydrogens to /6 CYS 314 CB because it is missing heavy-atom bond partners Not adding hydrogens to /6 CYS 333 CB because it is missing heavy-atom bond partners Not adding hydrogens to /6 CYS 338 CB because it is missing heavy-atom bond partners Not adding hydrogens to /7 LYS 217 CB because it is missing heavy-atom bond partners 15 messages similar to the above omitted notes | No usable SEQRES records for 229-coot_fixed.pdb (#1.2) chain 2; guessing termini instead No usable SEQRES records for 229-coot_fixed.pdb (#1.2) chain 3; guessing termini instead No usable SEQRES records for 229-coot_fixed.pdb (#1.2) chain 4; guessing termini instead No usable SEQRES records for 229-coot_fixed.pdb (#1.2) chain 5; guessing termini instead No usable SEQRES records for 229-coot_fixed.pdb (#1.2) chain 6; guessing termini instead 10 messages similar to the above omitted Chain-initial residues that are actual N termini: /2 PRO 201, /3 PRO 17, /4 ARG 178, /5 ILE 27, /6 VAL 103, /7 ALA 4, /8 LEU 13, /A ASN 787, /B LYS 258, /C ALA 16, /D ASP 46, /E ASN 2, /F SER 271 Chain-initial residues that are not actual N termini: /2 THR 380, /2 PHE 447, /2 SER 475, /2 GLN 737, /3 ILE 91, /3 HIS 151, /3 SER 273, /3 LEU 314, /3 ASP 344, /3 VAL 651, /4 ASN 218, /4 LEU 456, /4 LYS 854, /5 ASN 130, /5 GLN 253, /5 SER 319, /5 LYS 365, /5 GLY 408, /5 GLY 591, /6 GLU 260, /6 ASP 447, /6 ARG 499, /6 THR 902, /7 LYS 59, /7 ASP 101, /7 GLU 190, /7 LEU 393, /8 VAL 87, /8 GLU 184, /8 SER 436, /8 ASN 459, /B VAL 355, /B GLY 506, /C GLU 55, /C ASP 180, /C LEU 509, /D THR 171, /D ILE 207, /E SER 319, /E ASN 372, /E SER 412, /F ARG 393 Chain-final residues that are actual C termini: /D LEU 529 Chain-final residues that are not actual C termini: /2 TYR 864, /2 LEU 334, /2 TYR 434, /2 ARG 459, /2 HIS 707, /3 LEU 738, /3 ALA 53, /3 HIS 141, /3 MET 264, /3 ASN 310, /3 LEU 329, /3 ARG 570, /4 ARG 928, /4 GLU 214, /4 PRO 443, /4 ASP 846, /5 SER 693, /5 ALA 110, /5 LEU 172, /5 GLY 306, /5 ILE 342, /5 GLY 395, /5 GLY 578, /6 HIS 978, /6 SER 200, /6 ASP 406, /6 GLY 463, /6 SER 834, /7 SER 723, /7 ASP 31, /7 GLY 96, /7 SER 163, /7 LYS 386, /8 LEU 595, /8 PHE 77, /8 ASN 157, /8 ILE 415, /8 THR 449, /A GLU 907, /B GLY 506, /B LEU 343, /B MET 498, /C GLY 615, /C PRO 27, /C HIS 159, /C PRO 499, /D HIS 158, /D SER 190, /E ASP 476, /E LEU 299, /E LYS 353, /E PRO 395, /F ALA 430, /F PHE 389 4401 hydrogen bonds Adding 'H' to /2 THR 380 Adding 'H' to /2 PHE 447 Adding 'H' to /2 SER 475 Adding 'H' to /2 GLN 737 Adding 'H' to /3 ILE 91 37 messages similar to the above omitted /2 TYR 864 is not terminus, removing H atom from 'C' /3 LEU 738 is not terminus, removing H atom from 'C' /4 ARG 928 is not terminus, removing H atom from 'C' /5 SER 693 is not terminus, removing H atom from 'C' /6 HIS 978 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 50767 hydrogens added > select #1 101671 atoms, 102701 bonds, 42 pseudobonds, 6233 residues, 13 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Populating font family aliases took 352 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-18.8.4 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 i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0) OS Loader Version: 540.120.3~19 Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 2:16 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 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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 Core can't reproduce Tom Goddard all ChimeraX