id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7408 Graphics crash, macOS 12.5, AMD Radeon R9 M395 chimerax-bug-report@… Tom Goddard "{{{ 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. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x000000010a47c600 (most recent call first): File ""/Applications/ChimeraX-1.4 1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 235 in swap_buffers File ""/Applications/ChimeraX-1.4 1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 496 in swap_buffers File ""/Applications/ChimeraX-1.4 1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 179 in draw File ""/Applications/ChimeraX-1.4 1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/Applications/ChimeraX-1.4 1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback 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\n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 68K 7 \nColorSync 224K 26 \nCoreAnimation 144K 10 \nCoreGraphics 12K 2 \nCoreServices 168K 1 \nCoreUI image data 2356K 20 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 3.0G 1022 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 128K 32 \nStack 159.2M 33 \nStack Guard 56.0M 1 \nVM_ALLOCATE 104.5M 99 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 58.2M 721 \n__DATA_CONST 31.0M 340 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 680.0M 183 \n__TEXT 811.4M 706 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 112.8M 41 \nshared memory 2972K 27 \n=========== ======= ======= \nTOTAL 5.4G 3521 \nTOTAL, minus reserved VM space 5.0G 3521 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000434 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jingyu/Desktop/Image > processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes_ArtiaX/myco_script_demo > copy.cxc"" > cd ""/Users/jingyu/Desktop/Image > processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes_ArtiaX"" Current working directory is: /Users/jingyu/Desktop/Image processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes_ArtiaX > artiax start > open With_AP_PE_tRNA_bin1_job216.star format star Opened Particle list With_AP_PE_tRNA_bin1_job216.star with 4721 particles. > open With_AP_PE_tRNA_shifted_right_bin1_job237.star format star Opened Particle list With_AP_PE_tRNA_shifted_right_bin1_job237.star with 2352 particles. > open With_PPtRNA_bin1_job257.star format star Opened Particle list With_PPtRNA_bin1_job257.star with 1277 particles. > open With_PPtRNA_L1_stalk_back_bin1_job267.star format star Opened Particle list With_PPtRNA_L1_stalk_back_bin1_job267.star with 765 particles. > open refine_after_no_align_with_only_60S_bin2_job052.star format star Opened Particle list refine_after_no_align_with_only_60S_bin2_job052.star with 7617 particles. > artiax particles #1.2.1 color 50,50,50,100 > artiax particles #1.2.2 color 94,64,100,100 > artiax particles #1.2.3 color 100,80,60,100 > artiax particles #1.2.4 color 0,46,86,100 > artiax particles #1.2.5 color 100,100,50,100 > artiax particles #1.2.1 originScaleFactor 2.12 > artiax particles #1.2.2 originScaleFactor 2.12 > artiax particles #1.2.3 originScaleFactor 2.12 > artiax particles #1.2.4 originScaleFactor 2.12 > artiax particles #1.2.5 originScaleFactor 2.12 > artiax view xy > open > refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216_bin4.mrc Opened refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216_bin4.mrc as #2, grid size 64,64,64, pixel 8.48, shown at level 4.46, step 1, values float32 > open > refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237_bin4.mrc Opened refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237_bin4.mrc as #3, grid size 64,64,64, pixel 8.48, shown at level 4.45, step 1, values float32 > open > refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257_bin4.mrc Opened refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257_bin4.mrc as #4, grid size 64,64,64, pixel 8.48, shown at level 4.48, step 1, values float32 > open > refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267_bin4.mrc Opened refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267_bin4.mrc as #5, grid size 64,64,64, pixel 8.48, shown at level 4.34, step 1, values float32 > open refine_after_no_align_with_only_60S_bin2_job052_bin4.mrc Opened refine_after_no_align_with_only_60S_bin2_job052_bin4.mrc as #6, grid size 64,64,64, pixel 8.48, shown at level 4.18, step 1, values float32 > artiax attach #2 toParticleList #1.2.1 Opened refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216_bin4.mrc as #1.2.1.1.1, grid size 64,64,64, pixel 8.48, shown at level 4.46, step 1, values float32 > volume #1.2.1.1.1 capFaces false > artiax attach #3 toParticleList #1.2.2 Opened refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237_bin4.mrc as #1.2.2.1.1, grid size 64,64,64, pixel 8.48, shown at level 4.45, step 1, values float32 > volume #1.2.2.1.1 capFaces false > artiax attach #4 toParticleList #1.2.3 Opened refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257_bin4.mrc as #1.2.3.1.1, grid size 64,64,64, pixel 8.48, shown at level 4.48, step 1, values float32 > volume #1.2.3.1.1 capFaces false > artiax attach #5 toParticleList #1.2.4 Opened refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267_bin4.mrc as #1.2.4.1.1, grid size 64,64,64, pixel 8.48, shown at level 4.34, step 1, values float32 > volume #1.2.4.1.1 capFaces false > artiax attach #6 toParticleList #1.2.5 Opened refine_after_no_align_with_only_60S_bin2_job052_bin4.mrc as #1.2.5.1.1, grid size 64,64,64, pixel 8.48, shown at level 4.18, step 1, values float32 > volume #1.2.5.1.1 capFaces false > artiax particles #1.2.1 surfaceLevel 3.49 > artiax particles #1.2.2 surfaceLevel 3.43 > artiax particles #1.2.3 surfaceLevel 3.03 > artiax particles #1.2.4 surfaceLevel 2.58 > artiax particles #1.2.5 surfaceLevel 3.79 > artiax hide axes > artiax hide markers > open ""/Users/jingyu/Desktop/Image > processing/RNAgranules_tomo/tiltseries/TS_001/TS_001_rec.mrc"" Opened TS_001_rec.mrc as #2, grid size 1023,1440,350, pixel 8.48,8.48,8.48, shown at level 22.1, step 1, values int16 > artiax add tomo #2 Opened TS_001_rec.mrc as #1.1.1, grid size 1023,1440,350, pixel 8.48,8.48,8.48, shown at level 22.1, step 1, values int16 > artiax tomo #1.1.1 sliceDirection 0,0,1 > artiax view xy > artiax tomo #1.1.1 pixelSize 8.48 > artiax view xy > volume #1.1.1 style image region 0,0,174,1022,1439,174 step 1 > set bgColor black > camera mono > material dull > lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1.2 > ambientIntensity 2 shadows true qualityOfShadows finer multiShadow 512 > msMapSize 1024 > artiax view xy executed myco_script_demo copy.cxc ===== Log before crash end ===== Log: Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho 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 ATI-4.8.101 OpenGL renderer: AMD Radeon R9 M395 OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: iMac Model Identifier: iMac17,1 Processor Name: Quad-Core Intel Core i7 Processor Speed: 4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 451.140.1.0.0 OS Loader Version: 540.120.3~19 SMC Version (system): 2.34f3 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 44 minutes Graphics/Displays: AMD Radeon R9 M395: Chipset Model: AMD Radeon R9 M395 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x6920 Revision ID: 0x0001 ROM Revision: 113-C905AA-799 VBIOS Version: 113-C905A1-007 EFI Driver Version: 01.00.799 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) 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-ArtiaX: 0.1 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 pandas: 1.4.3 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 starfile: 0.4.11 suds-community: 1.0.0 superqt: 0.3.3 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 typing-extensions: 4.3.0 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX