id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18049 Graphics hardware encountered an error and was reset noha.elhuseiny@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-11.7.10-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. I was visualizing a big model of 15 protomers in a 1.2 MDa cryoEM map Fatal Python error: Aborted Current thread 0x000000010b16be00 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1689 in set_multishadow_view File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 250 in _draw_scene File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55) Process: ChimeraX [5073] Path: /Applications/ChimeraX-1.7.app/Contents/MacOS/ChimeraX Identifier: ChimeraX Version: 1.7.0 (1.7.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [5073] User ID: 501 Date/Time: 2025-06-20 20:58:50.093 +0300 OS Version: macOS 11.7.10 (20G1427) Report Version: 12 Anonymous UUID: 65BD8C37-22F7-C783-9511-41061272B6D5 Sleep/Wake UUID: 95BB5F3B-75F0-4497-A7DE-96CD2554A74C Time Awake Since Boot: 25000 seconds Time Since Wake: 2000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Application Specific Information: abort() called Application Specific Signatures: Graphics hardware encountered an error and was reset: 0x00008013 Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff2066a90e __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff206995bd pthread_kill + 263 2 libsystem_c.dylib 0x00007fff2057dbd5 raise + 26 3 org.python.python 0x0000000107a315d4 faulthandler_fatal_error + 388 4 libsystem_platform.dylib 0x00007fff206ded7d _sigtramp + 29 5 ??? 000000000000000000 0 + 0 6 libsystem_c.dylib 0x00007fff205ee406 abort + 125 7 libGPUSupportMercury.dylib 0x00007fff46605096 gpusGenerateCrashLog.cold.1 + 95 8 libGPUSupportMercury.dylib 0x00007fff465fc21c gpusGenerateCrashLog + 89 9 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff66161bb8 gpusKillClientExt + 9 10 libGPUSupportMercury.dylib 0x00007fff465fd72d gpusSubmitDataBuffers + 490 11 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff65d2b3c4 IntelCommandBuffer::getNew(GLDContextRec*) + 48 12 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff65d2b1db intelSubmitCommands + 178 13 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff65d318ec glrWriteBufferData + 1336 14 GLEngine 0x00007fff6be2013f glBufferSubData_Exec + 608 15 libffi.dylib 0x00007fff2dc818f5 ffi_call_unix64 + 85 16 libffi.dylib 0x00007fff2dc8122d ffi_call_int + 699 17 libffi.dylib 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libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011ab987bf 0x116ca5000 + 66009023 4 QtWebEngineCore 0x000000011ab9926c 0x116ca5000 + 66011756 5 QtWebEngineCore 0x000000011ab98e6d 0x116ca5000 + 66010733 6 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 7 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 6:: CompositorTileWorker1 0 libsystem_kernel.dylib 0x00007fff20666cbe __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20699e49 _pthread_cond_wait + 1298 2 QtWebEngineCore 0x000000011abcbd1b 0x116ca5000 + 66219291 3 QtWebEngineCore 0x000000011cc9992d 0x116ca5000 + 100616493 4 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 5 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 6 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 7:: Chrome_InProcGpuThread 0 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QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 10 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 11 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 13:: ThreadPoolSingleThreadForegroundBlocking0 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011ab987bf 0x116ca5000 + 66009023 4 QtWebEngineCore 0x000000011ab9926c 0x116ca5000 + 66011756 5 QtWebEngineCore 0x000000011ab98ecd 0x116ca5000 + 66010829 6 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 7 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 14:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011abd3bef 0x116ca5000 + 66251759 4 QtWebEngineCore 0x000000011ab091c9 0x116ca5000 + 65421769 5 QtWebEngineCore 0x000000011ab82a5c 0x116ca5000 + 65919580 6 QtWebEngineCore 0x000000011ab3a998 0x116ca5000 + 65624472 7 QtWebEngineCore 0x000000011aba4eb8 0x116ca5000 + 66059960 8 QtWebEngineCore 0x000000011aba504a 0x116ca5000 + 66060362 9 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 10 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 11 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 15:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011ab987bf 0x116ca5000 + 66009023 4 QtWebEngineCore 0x000000011ab9926c 0x116ca5000 + 66011756 5 QtWebEngineCore 0x000000011ab98ddd 0x116ca5000 + 66010589 6 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 7 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 16:: MemoryInfra 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011abd3bef 0x116ca5000 + 66251759 4 QtWebEngineCore 0x000000011ab091c9 0x116ca5000 + 65421769 5 QtWebEngineCore 0x000000011ab82a5c 0x116ca5000 + 65919580 6 QtWebEngineCore 0x000000011ab3a998 0x116ca5000 + 65624472 7 QtWebEngineCore 0x000000011aba4eb8 0x116ca5000 + 66059960 8 QtWebEngineCore 0x000000011aba504a 0x116ca5000 + 66060362 9 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 10 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 11 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011ab987bf 0x116ca5000 + 66009023 4 QtWebEngineCore 0x000000011ab98f9a 0x116ca5000 + 66011034 5 QtWebEngineCore 0x000000011ab98e0d 0x116ca5000 + 66010637 6 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 7 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 18:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff20791ebf __CFRunLoopServiceMachPort + 316 3 com.apple.CoreFoundation 0x00007fff2079059f __CFRunLoopRun + 1328 4 com.apple.CoreFoundation 0x00007fff2078f9ac CFRunLoopRunSpecific + 563 5 com.apple.AppKit 0x00007fff2311fb7a _NSEventThread + 124 6 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 19:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011ab987bf 0x116ca5000 + 66009023 4 QtWebEngineCore 0x000000011ab9926c 0x116ca5000 + 66011756 5 QtWebEngineCore 0x000000011ab98e6d 0x116ca5000 + 66010733 6 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 7 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 20:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff2066429a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2066460c mach_msg + 60 2 QtWebEngineCore 0x000000011abd3e26 0x116ca5000 + 66252326 3 QtWebEngineCore 0x000000011ab987bf 0x116ca5000 + 66009023 4 QtWebEngineCore 0x000000011ab9926c 0x116ca5000 + 66011756 5 QtWebEngineCore 0x000000011ab98ddd 0x116ca5000 + 66010589 6 QtWebEngineCore 0x000000011abcc908 0x116ca5000 + 66222344 7 libsystem_pthread.dylib 0x00007fff206998fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff20695443 thread_start + 15 Thread 21: 0 libsystem_pthread.dylib 0x00007fff20695420 start_wqthread + 0 Thread 22: 0 libsystem_pthread.dylib 0x00007fff20695420 start_wqthread + 0 Thread 23: 0 libsystem_pthread.dylib 0x00007fff20695420 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010b16be00 rcx: 0x00007fd65c5dd9e8 rdx: 0x0000000000000000 rdi: 0x0000000000000103 rsi: 0x0000000000000006 rbp: 0x00007fd65c5dda10 rsp: 0x00007fd65c5dd9e8 r8: 0x0000000000000002 r9: 0xcccccccccccccccd r10: 0x000000010b16be00 r11: 0x0000000000000246 r12: 0x0000000000000103 r13: 0x00007fd65f1e7101 r14: 0x0000000000000006 r15: 0x0000000000000016 rip: 0x00007fff2066a90e rfl: 0x0000000000000246 cr2: 0x00000001079fa630 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Thread 0 instruction stream not available. Thread 0 last branch register state not available. 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0x7fff3dd66fff com.apple.sidecar-ui (1.0 - 231.0.3) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI 0x7fff3e389000 - 0x7fff3e3ebfff com.apple.ImageCaptureCore (1711.5.2.1 - 1711.5.2.1) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore 0x7fff3e3ec000 - 0x7fff3e411fff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters 0x7fff3e5f0000 - 0x7fff3e65cfff com.apple.Safari.Core (16611 - 16611.3.10.1.19) /System/Library/PrivateFrameworks/SafariCore.framework/Versions/A/SafariCore 0x7fff3e65d000 - 0x7fff3e7bffff com.apple.MediaPlayer (1.0 - 1.0) /System/Library/Frameworks/MediaPlayer.framework/Versions/A/MediaPlayer 0x7fff3e7c0000 - 0x7fff3eaa1fff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud 0x7fff3eacd000 - 0x7fff3ebf5fff com.apple.AnnotationKit (1.0 - 383.6.1) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit 0x7fff3ebf6000 - 0x7fff3f096fff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer 0x7fff3f097000 - 0x7fff3f17ffff com.apple.PDFKit (1.0 - 950.40.3) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit 0x7fff3fec6000 - 0x7fff3ff43fff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput 0x7fff410df000 - 0x7fff410e2fff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz 0x7fff41507000 - 0x7fff41525fff libCGInterfaces.dylib (544.6) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff42ba5000 - 0x7fff43905fff libfaceCore.dylib (4.3.2) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib 0x7fff43906000 - 0x7fff43a19fff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition 0x7fff43a1a000 - 0x7fff43a32fff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark 0x7fff43a33000 - 0x7fff43a92fff com.apple.DifferentialPrivacy (1.0 - 1) /System/Library/PrivateFrameworks/DifferentialPrivacy.framework/Versions/A/DifferentialPrivacy 0x7fff43a93000 - 0x7fff43aacfff com.apple.SafariFoundation (16611 - 16611.3.10.1.19) /System/Library/PrivateFrameworks/SafariFoundation.framework/Versions/A/SafariFoundation 0x7fff43aad000 - 0x7fff43ab3fff com.apple.SafariPlatformSupport.framework (16611 - ???) /System/Library/PrivateFrameworks/SafariPlatformSupport.framework/Versions/A/SafariPlatformSupport 0x7fff43ab4000 - 0x7fff43d27fff com.apple.RawCamera.bundle (9.10.0 - 1450.3.1) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff44590000 - 0x7fff44594fff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit 0x7fff45f0b000 - 0x7fff45f0efff libpmenergy.dylib (227.140.1) /usr/lib/libpmenergy.dylib 0x7fff465fa000 - 0x7fff46605fff libGPUSupportMercury.dylib (18.5.9) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib 0x7fff47c2f000 - 0x7fff47c70fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics 0x7fff484be000 - 0x7fff484d9fff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics 0x7fff516c2000 - 0x7fff516effff com.apple.HelpData (2.3 - 201.1) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData 0x7fff516f0000 - 0x7fff5170afff com.apple.shortcut (2.16 - 118) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut 0x7fff5170b000 - 0x7fff517aafff com.apple.Symbolication (12.5 - 64544.70.3) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication 0x7fff5199a000 - 0x7fff5199dfff libpmsample.dylib (227.140.1) /usr/lib/libpmsample.dylib 0x7fff54032000 - 0x7fff54068fff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit 0x7fff55662000 - 0x7fff55665fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback 0x7fff61e0c000 - 0x7fff61e83fff com.apple.driver.AppleIntelHD5000GraphicsMTLDriver (16.5.14 - 16.0.5) /System/Library/Extensions/AppleIntelHD5000GraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsMTLDriver 0x7fff65d13000 - 0x7fff66226fff com.apple.driver.AppleIntelHD5000GraphicsGLDriver (16.5.14 - 16.0.5) /System/Library/Extensions/AppleIntelHD5000GraphicsGLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsGLDriver 0x7fff6975a000 - 0x7fff6975efff libmetal_timestamp.dylib (31001.192.1) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib 0x7fff6bba5000 - 0x7fff6bbabfff libCoreFSCache.dylib (200.12) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib 0x7fff6bbac000 - 0x7fff6bbb0fff libCoreVMClient.dylib (200.12) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x7fff6bbb1000 - 0x7fff6bbc0fff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff6bbc1000 - 0x7fff6bbc3fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib 0x7fff6bbc4000 - 0x7fff6bbccfff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff6bbcd000 - 0x7fff6bc00fff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6bc01000 - 0x7fff6bc3dfff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6bc3e000 - 0x7fff6bdd1fff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x7fff6bdd2000 - 0x7fff6bddcfff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6bddd000 - 0x7fff6bf5afff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine 0x7fff6bf5b000 - 0x7fff6bf83fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x7fff6d21c000 - 0x7fff6d274fff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6e31e000 - 0x7fff6e325fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff6e326000 - 0x7fff6e40dfff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio 0x7fff6f993000 - 0x7fff6f9a5fff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging 0x7fff73cc3000 - 0x7fff73ccefff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics 0x7fff73ee4000 - 0x7fff73efcfff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed 0x7fff7780b000 - 0x7fff77812fff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%) Writable regions: Total=3.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 2880K 6 CG image 200K 19 CoreAnimation 276K 18 CoreGraphics 12K 2 CoreUI image data 3608K 29 Foundation 16K 1 Kernel Alloc Once 8K 1 MALLOC 2.1G 619 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Mach message 16K 2 OpenGL GLSL 384K 4 STACK GUARD 92K 23 Stack 154.7M 24 Stack Guard 56.0M 1 VM_ALLOCATE 352.4M 242 __DATA 38.4M 647 __DATA_CONST 26.9M 319 __DATA_DIRTY 1729K 221 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 532.2M 261 __OBJC_RO 70.3M 1 __OBJC_RW 2496K 2 __TEXT 658.9M 634 __UNICODE 588K 1 mapped file 271.6M 51 shared memory 2960K 23 =========== ======= ======= TOTAL 4.6G 3167 TOTAL, minus reserved VM space 4.3G 3167 System Profile: Network Service: Wi-Fi, AirPort, en0 Thunderbolt Bus: MacBook Pro, Apple Inc., 17.2 Boot Volume File System Type: apfs Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 USB Device: USB 3.0 Bus USB Device: SSD-SCTU3A USB Device: Apple Internal Keyboard / Trackpad USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller Serial ATA Device: APPLE SSD SD0128F, 121.33 GB Model: MacBookPro11,1, BootROM 478.0.0.0.0, 2 processors, Dual-Core Intel Core i7, 2.8 GHz, 16 GB, SMC 2.16f68 Graphics: kHW_IntelIrisItem, Intel Iris, spdisplays_builtin AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x112), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1680.11) Bluetooth: Version 8.0.5d7, 3 services, 19 devices, 1 incoming serial ports ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Volumes/Noha-data2-GspD/Phenix Tanaka > lab/Class2-J544/RealSpaceRefine_9/Pentadecamer_fromC_coot_19_real_space_refined.pdb"" Chain information for Pentadecamer_fromC_coot_19_real_space_refined.pdb #1 --- Chain | Description A B C D E F G H I J K L M N O | No description available > show cartoons > show atoms > hide atoms > ui tool show ""Side View"" > open ""/Volumes/Noha-data2-GspD/Phenix Tanaka > lab/Class0-J542/RealSpaceRefine_7/Class0-J542-Ref7-15mer.pdb"" Chain information for Class0-J542-Ref7-15mer.pdb #2 --- Chain | Description A B C D E F G H I J K L M N O | No description available > hide atoms > show atoms > show cartoons > hide atoms > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > 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 Pentadecamer_fromC_coot_19_real_space_refined.pdb, chain A (#1) with Class0-J542-Ref7-15mer.pdb, chain A (#2), sequence alignment score = 2297.9 RMSD between 304 pruned atom pairs is 0.485 angstroms; (across all 482 pairs: 3.705) > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Volumes/Noha- > data2-GspD/GspD/NE240312/3Dand3DVA/Combined/Class0/cryosparc_P62_J515_004_volume_map_sharp.mrc Opened cryosparc_P62_J515_004_volume_map_sharp.mrc as #1, grid size 540,540,540, pixel 0.788, shown at level 0.0512, step 4, values float32 OpenGL version: 4.1 INTEL-16.5.14 OpenGL renderer: Intel Iris OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro11,1 Processor Name: Dual-Core Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 478.0.0.0.0 SMC Version (system): 2.16f68 Software: System Software Overview: System Version: macOS 11.7.10 (20G1427) Kernel Version: Darwin 20.6.0 Time since boot: 40 minutes Graphics/Displays: Intel Iris: Chipset Model: Intel Iris Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0a2e Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Graphics limitation all ChimeraX