id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17053 Graphics crash, macOS 12.2.1, Intel HD Graphics 6000 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.2.1-x86_64-i386-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description PrograLast time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics. Fatal Python error: Aborted Thread 0x000070001aa9e000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700019a9b000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700018a98000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700017a95000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700016a92000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700015a8f000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700014a8c000 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000011848e600 (most recent call first): File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2859 in draw_elements File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1749 in draw File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 852 in _draw_geometry File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 794 in draw_self File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780 in draw File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567 in _draw_multiple File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1624 in draw_highlight_outline File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 273 in _draw_scene File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 288 in render File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 113 in _redraw File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.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 ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/private/var/folders/67/n3yz466x0hn7c3dmd6bbrmmm0000gn/T/AppTranslocation/7F55DE4E-6A78-41B5-B790-AAF0DA0B094A/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-10 11:44:07.00 +0100"",""app_version"":""1.9.0"",""slice_uuid"":""079d39d3-a489-3e56-92d8-c781f5a4bb98"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.2.1 (21D62)"",""incident_id"":""9A600435-3A3E-4EA5-8149-6D6D5257B208"",""name"":""ChimeraX""} { ""uptime"" : 60000, ""procLaunch"" : ""2025-03-07 15:26:21.5158 +0100"", ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir7,2"", ""procStartAbsTime"" : 45865405010555, ""coalitionID"" : 1900, ""osVersion"" : { ""train"" : ""macOS 12.2.1"", ""build"" : ""21D62"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-10 11:43:24.5563 +0100"", ""incident"" : ""9A600435-3A3E-4EA5-8149-6D6D5257B208"", ""bug_type"" : ""309"", ""pid"" : 29278, ""procExitAbsTime"" : 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VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 544K 4 \nCG image 272K 43 \nColorSync 240K 28 \nCoreAnimation 200K 27 \nCoreGraphics 12K 2 \nCoreUI image data 2056K 29 \nFoundation 48K 2 \nIOKit 7940K 1 \nKernel Alloc Once 404K 4 \nMALLOC 318.5M 390 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 132K 33 \nStack 298.3M 34 \nStack Guard 56.0M 1 \nVM_ALLOCATE 140.5M 191 \n__CTF 759 1 \n__DATA 38.7M 709 \n__DATA_CONST 40.7M 434 \n__DATA_DIRTY 1784K 238 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 672.5M 159 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 828.1M 715 \n__UNICODE 588K 1 \ndyld private memory 1064K 3 \nmapped file 199.5M 45 \nshared memory 3100K 28 \n=========== ======= ======= \nTOTAL 3.0G 3149 \nTOTAL, minus reserved VM space 2.6G 3149 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""6193d03f2171a2330e561dfc"" }, ""deploymentId"" : 240000305 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad"" }, ""deploymentId"" : 240000416 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000614 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000083 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000460 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | QCoreApplication::postEvent: Unexpected null receiver note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/clara/Downloads/3g2a.pdb 3g2a.pdb title: Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 [more info...] Chain information for 3g2a.pdb #1 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' Computing secondary structure > sequence chain #1/A Alignment identifier is 1/A > style stick Changed 264 atom styles > style sphere Changed 264 atom styles > style sphere Changed 264 atom styles > style ball Changed 264 atom styles > nucleotides atoms > style nucleic stick Changed 240 atom styles > color byhetero > color bychain > color bypolymer > rainbow > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 3g2a.pdb_A SES surface #1.1: minimum, -18.90, mean -7.58, maximum -0.39 Coulombic values for 3g2a.pdb_B SES surface #1.2: minimum, -17.46, mean -7.35, maximum -0.04 To also show corresponding color key, enter the above coulombic command and add key true > mlp mlp: no amino acids specified > show atoms > hide atoms > show atoms > hide atoms > show atoms > hide atoms > show atoms > show cartoons > hide cartoons > hide atoms > hide cartoons > hide surfaces > show surfaces > hide surfaces > show cartoons > hide cartoons > show atoms > ui tool show ""Side View"" > undo > redo > open /Users/clara/Downloads/3g2a.pdb 3g2a.pdb title: Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 [more info...] Chain information for 3g2a.pdb #2 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' Computing secondary structure > hide atoms > show atoms > show cartoons > hide cartoons > show cartoons > hide cartoons > show cartoons > hide #!1 models > hide #2 models > show #!1 models > show #2 models > hide #!1 models > hide #2 models > show #!1 models > close #1 > close > open /Users/clara/Downloads/3g2a.pdb format pdb 3g2a.pdb title: Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 [more info...] Chain information for 3g2a.pdb #1 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' Computing secondary structure > log metadata #1 Metadata for 3g2a.pdb #1 --- Title | Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 Citation | Crystal structures of D(cacgcg).D(cgcgtg) cocrystallizedwith MNCL2 Experimental method | X-ray diffraction Resolution | 2.00Å > log chains #1 Chain information for 3g2a.pdb #1 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' > nucleotides atoms > style nucleic stick Changed 240 atom styles > hide (protein|nucleic) target a > cartoon hide > show backbone target ab > show sidechain target ab > ui tool show Distances > ui mousemode right select Exactly two atoms must be selected! > ui mousemode right zoom > ui mousemode right translate > ui mousemode right ""move picked models"" > ui mousemode right zoom > open /Users/clara/Downloads/3g2a.pdb 3g2a.pdb title: Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 [more info...] Chain information for 3g2a.pdb #2 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' Computing secondary structure > close session > open /Users/clara/Downloads/3g2a.pdb format pdb 3g2a.pdb title: Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 [more info...] Chain information for 3g2a.pdb #1 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' Computing secondary structure > nucleotides atoms > style nucleic stick Changed 240 atom styles > hide (protein|nucleic) target a > cartoon hide > show backbone target ab > show sidechain target ab > ui tool show Distances > ui mousemode right select > select /A:2@P 1 atom, 1 residue, 1 model selected > select /A:2@P 1 atom, 1 residue, 1 model selected Drag select of 25 atoms, 28 bonds Drag select of 20 atoms, 25 bonds Drag select of 1 atoms, 1 bonds > ui tool show Distances > select add /A:1@O5' 2 atoms, 1 bond, 2 residues, 1 model selected > select add /A:6@O3' 3 atoms, 1 bond, 3 residues, 1 model selected Exactly two atoms must be selected! No distances to delete! > close session > open /Users/clara/Downloads/3g2a.pdb format pdb 3g2a.pdb title: Crystal structure of D(cacgcg).D(cgcgtg) grown In presence of 1MM MNCL2 [more info...] Chain information for 3g2a.pdb #1 --- Chain | Description A | 5'-D(*CP*ap*CP*GP*CP*G)-3' B | 5'-D(*CP*GP*CP*GP*TP*G)-3' Computing secondary structure > nucleotides atoms > style nucleic stick Changed 240 atom styles Drag select of 2 residues, 1 bonds > undo > select clear > show sidechain target ab > hide (protein|nucleic) target a > cartoon hide > show backbone target ab > show sidechain target ab > ui tool show Distances > select /A:2@P 1 atom, 1 residue, 1 model selected > select subtract /A:2@P Nothing selected > ui mousemode right select > select add /A:2@P 1 atom, 1 residue, 1 model selected > select subtract /A:2@P Nothing selected > select /A:2@P 1 atom, 1 residue, 1 model selected > select /A:2@P 1 atom, 1 residue, 1 model selected > select add /A:2@OP1 2 atoms, 1 residue, 1 model selected > select add /A:6@O3' 3 atoms, 2 residues, 1 model selected Exactly two atoms must be selected! > select ::name=""DA""::name=""DC""::name=""DG""::name=""DT"" 240 atoms, 268 bonds, 12 residues, 1 model selected > select ::name=""DA"" 21 atoms, 23 bonds, 1 residue, 1 model selected > select ::name=""DC"" 89 atoms, 94 bonds, 5 residues, 1 model selected > select ::name=""DG"" 110 atoms, 120 bonds, 5 residues, 1 model selected > select ::name=""DT"" 20 atoms, 21 bonds, 1 residue, 1 model selected > select ::name=""HOH"" 24 atoms, 24 residues, 1 model selected > select ::name=""HOH"" 24 atoms, 24 residues, 1 model selected > select ::name=""DA"" 21 atoms, 23 bonds, 1 residue, 1 model selected > hide sel target a > show sel target ab > style sel stick Changed 21 atom styles > style sel ball Changed 21 atom styles > style sel sphere Changed 21 atom styles Drag select of 3 atoms, 3 bonds > select clear Drag select of 5 atoms, 5 bonds Drag select of 6 atoms, 4 bonds > select ::name=""DC"" 89 atoms, 94 bonds, 5 residues, 1 model selected > select ::name=""DG"" 110 atoms, 120 bonds, 5 residues, 1 model selected > select ::name=""DT"" 20 atoms, 21 bonds, 1 residue, 1 model selected > ui tool show ""Side View"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.4.6 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1,8 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 428.60.3.0.0 OS Loader Version: 540.80.2~11 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 6 days 1:53 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: LCD Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus) UI Looks like: 1440 x 900 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Graphics nonchimerax all ChimeraX