id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6552 Graphics driver crash, macOS 12.2.1, Intel Iris Plus Graphics mmasse@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x0000700015fc6000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1284 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000147c0000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000137bd000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000127ba000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000117b7000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000107b4000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070000f7b1000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070000e7ae000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070000d7ab000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070000c7a8000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070000b7a5000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070000a7a2000 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000010bde1600 (most recent call first): File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 2676 in update_buffer_data File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1847 in update_buffers File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1859 in activate_bindings File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 786 in _draw_geometry File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 759 in draw_self File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 752 in draw File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1512 in _draw_multiple File ""/private/var/folders/kj/5hrdcy3j55335fxpxdm9rtkw0000gn/T/AppTranslocation/D659FD7B-95E4-405D-A8C1-178CCBB09816/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1499 in draw_opaque File 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""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad"" }, ""deploymentId"" : 240000416 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000128 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000014 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000313 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/merandamasse/Desktop/CryoEM > ApoMb153+EDC/20220120_conf_1.mrc.zip"" Unrecognized file suffix '.zip' > open ""/Users/merandamasse/Desktop/CryoEM ApoMb153+EDC/20220208_Conf_2.mrc"" Opened 20220208_Conf_2.mrc as #1, grid size 512,512,512, pixel 0.947, shown at level 0.292, step 2, values float32 Drag select of 1 20220208_Conf_2.mrc > select #1 2 models selected > select clear > show atoms > style stick Changed 0 atom styles > set bgColor black > set bgColor white > lighting simple > lighting soft > lighting full > lighting soft > volume #1 level 0.1693 > volume #1 level 0.2061 > volume #1 level 0.2491 > lighting full > lighting simple > volume #1 level 0.2859 > lighting soft > lighting full Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > transparency 50 > transparency 0 > volume style image > volume style mesh > volume style surface > volume step 2 > volume step 1 > volume #1 orthoplanes xyz positionPlanes 256,256,256 style image region all > mousemode rightMode ""move planes"" > volume #1 orthoplanes xyz positionPlanes 256,256,256 style image region all > mousemode rightMode ""move planes"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 242.4 tiltedSlabSpacing 0.947 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume show > undo > open ""/Users/merandamasse/Desktop/CryoEM ApoMb153+EDC/20220208_Conf_2.mrc"" Opened 20220208_Conf_2.mrc as #2, grid size 512,512,512, pixel 0.947, shown at level 0.292, step 2, values float32 > close #1 > volume #2 color #87fff6 > volume #2 color #b6fff9 > surface dust #2 size 9.47 > volume #2 level 0.1693 > surface dust #2 size 9.47 > volume #2 region 0,0,0,511,511,511 > surface dust #2 size 9.47 > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > save /Users/merandamasse/Desktop/20220405_Conformation_2_map_157_EDC.jpg > width 866 height 723 supersample 4 > open ""/Users/merandamasse/Desktop/CryoEM ApoMb153+EDC/20220120_conf_1.mrc"" Opened 20220120_conf_1.mrc as #1, grid size 512,512,512, pixel 0.947, shown at level 0.29, step 2, values float32 > volume #1 color #a4fea5 > volume #1 color #fae7fe > volume #1 color #fed4b1 > volume #1 color #fe9991 > volume #1 color #a9feb9 > volume #1 color #cdfec4 > volume #1 level 0.2464 > surface dust #1 size 9.47 > volume #1 step 1 > volume #2 step 1 > volume #1 region 0,0,0,511,511,511 Drag select of 1 20220120_conf_1.mrc > select clear > save /Users/merandamasse/Desktop/20220405_conformation_2_157EDC.jpg width > 866 height 723 supersample 3 > volume #2 style image > volume #2 style surface > save /Users/merandamasse/Desktop/20220405_Conformation_2_real_157EDC.jpg > width 866 height 723 supersample 3 No map chosen to save > volume #2 change image level -0.1102,0 level 0.2919,0.8 level 2.441,1 > save /Users/merandamasse/Desktop/conformation_2_EDC.png width 866 height 723 > supersample 3 > save Missing or invalid ""fileName"" argument: Expected a file name > save /Users/merandamasse/Desktop/20220405_Conformation_2_157EDC.png width > 390 height 359 supersample 3 transparentBackground true > volume #!2 style surface > lighting soft > lighting full > lighting soft No atomic structure models chosen > volume show > volume hide > volume show > volume #!2 showOutlineBox true > volume #!2 showOutlineBox false > surface dust #2 size 9.47 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > movie record > turn y 2 180 > wait 180 > movie encode /Users/merandamasse/Desktop/movie1.mp4 Movie saved to /Users/merandamasse/Desktop/movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/merandamasse/Desktop/movie2.mp4 Movie saved to /Users/merandamasse/Desktop/movie2.mp4 > volume #2 level 0.06297 > volume #2 level 0.2131 > movie record > turn y 2 180 > wait 180 > movie encode /Users/merandamasse/Desktop/movie1.mp4 Movie saved to /Users/merandamasse/Desktop/movie1.mp4 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.4.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0) OS Loader Version: 540.80.2~11 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 40 days 20:23 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 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 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX