id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8060 crash running modal dialog chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. 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unallocated=8.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 3520K 4 \nCG image 176K 8 \nColorSync 608K 26 \nCoreAnimation 288K 15 \nCoreGraphics 32K 2 \nCoreUI image data 2528K 16 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 6.1G 246 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 616.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 51 \nStack 207.2M 51 \nVM_ALLOCATE 224.7M 550 \nVM_ALLOCATE (reserved) 512.0M 2 reserved VM address space (unallocated)\n__AUTH 2609K 308 \n__AUTH_CONST 20.6M 506 \n__CTF 756 1 \n__DATA 25.0M 694 \n__DATA_CONST 28.0M 694 \n__DATA_DIRTY 1804K 216 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 612.6M 187 \n__OBJC_CONST 3646K 279 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 754.1M 712 \n__UNICODE 592K 1 \ndyld private memory 1216K 3 \nmapped file 191.5M 51 \nshared memory 5824K 27 \n=========== ======= ======= \nTOTAL 9.7G 4687 \nTOTAL, minus reserved VM space 8.2G 4687 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""6112dda2fc54bc3389840642"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""631730a28520965d1cba0681"" }, ""deploymentId"" : 240000145 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5.dev202208060049 (2022-08-06) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/clemens.plaschka/Library/CloudStorage/OneDrive- > VBC/papers/2022_Pacheco-Fiallos- > Vorlaender/figures/scripts/Fig3e_TREX_EJC_overview_surface_thinRNA_T2_colors.cxc > open ../../../../lab/coot/TREX-mRNP/hTREX_mRNA_nB_new.pdb Chain information for hTREX_mRNA_nB_new.pdb #1 --- Chain | Description 2 4 | No description available A a | No description available B b | No description available C K c k | No description available E | No description available F N n | No description available G g | No description available H h | No description available I i | No description available J j | No description available L l | No description available M m | No description available O o | No description available P p | No description available e | No description available f | No description available > open ../../../../lab/coot/TREX-mRNP/models/HsUAP56_5suq_conf.pdb Chain information for HsUAP56_5suq_conf.pdb #2 --- Chain | Description H | No description available Y | No description available > open ../../../../lab/coot/TREX-mRNP/models/HsUAP56_5suq_conf.pdb Chain information for HsUAP56_5suq_conf.pdb #3 --- Chain | Description H | No description available Y | No description available > open ../pdbs/refine_run4_chainA-E-a-e_EJC-ALY_fit_to_TREX.pdb Chain information for refine_run4_chainA-E-a-e_EJC-ALY_fit_to_TREX.pdb #4 --- Chain | Description A a | No description available B b | No description available C c | No description available D d | No description available E e | No description available > open ../../../../lab/coot/TREX-mRNP/hTREX_mRNA_nB_new.pdb Chain information for hTREX_mRNA_nB_new.pdb #5 --- Chain | Description 2 4 | No description available A a | No description available B b | No description available C K c k | No description available E | No description available F N n | No description available G g | No description available H h | No description available I i | No description available J j | No description available L l | No description available M m | No description available O o | No description available P p | No description available e | No description available f | No description available > open ../../../../lab/coot/TREX-mRNP/hTREX_mRNA_nB_new.pdb Chain information for hTREX_mRNA_nB_new.pdb #6 --- Chain | Description 2 4 | No description available A a | No description available B b | No description available C K c k | No description available E | No description available F N n | No description available G g | No description available H h | No description available I i | No description available J j | No description available L l | No description available M m | No description available O o | No description available P p | No description available e | No description available f | No description available > hide > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 275695 atom styles > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2.2 sides 24 thickness 1.2 > cartoon style nucleic xsection round width 2 thickness 2 > nucleotides stubs > lighting shadows false > lighting simple > camera ortho > lighting soft intensity 0.2 fillIntensity 0.5 ambientIntensity 1 > windowsize 800 800 > size #1 pseudobondRadius 0.5 Changed 196 pseudobond radii > select #1 minimumLength 1 196 pseudobonds, 1 model selected > hide sel > ~cartoon #2/H > ~cartoon #3/H > align #2/H toAtoms #1/H RMSD between 1398 atom pairs is 0.760 angstroms > align #5/j:500-2000 toAtoms #1/B:500-2000 RMSD between 4186 atom pairs is 0.001 angstroms > align #3/H toAtoms #1/h RMSD between 1398 atom pairs is 0.760 angstroms > align #6/j:500-2000 toAtoms #1/b:500-2000 RMSD between 4186 atom pairs is 0.001 angstroms > nucleotides #1,12#!8-9,13 fill > style nucleic & #1,12#!8-9,13 stick Changed 160 atom styles > nucleotides #4,12#!8-9,13 fill > style nucleic & #4,12#!8-9,13 stick Changed 234 atom styles > graphics silhouettes true > set bgColor white > ~cartoon > hide #1-6 atoms > surface #1 > ~surface #1/H,P,h,p,L,l,2,4 > cartoon #1/P,p,L,l,2,4 #4 #5/4,p,l #6/4,p,l > show #1/2,4 #4/e,E #5/4 #6/4 atoms > color #1/A,I,a,i lime green target abcspf ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Processor Name: Unknown Processor Speed: 2,4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 64 GB Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 12 days 1:20 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX