id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5709 Graphics driver crash, macOS 12.0.1, Intel Iris Plus Graphics 640, VM - Fault hit memory shortage chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3rc202111292147 (2021-11-29 21:47:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x000070001b548000 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File 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""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700019542000 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001853f000 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001753c000 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700016539000 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700015536000 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000010fe0a600 (most recent call first): File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 1626 in set_multishadow_view File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 227 in _draw_scene File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 165 in draw File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2021-11-30 22:48:07.00 -0800"",""app_version"":""1.3.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.3.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.0.1 (21A559)"",""incident_id"":""29D9CD0F-7B57-40A4-A304-42115F1FCDCC"",""name"":""ChimeraX""} { ""uptime"" : 88000, ""procLaunch"" : ""2021-11-30 13:00:54.2163 -0800"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro14,1"", ""procStartAbsTime"" : 78115769201398, ""coalitionID"" : 14990, ""osVersion"" : { ""train"" : ""macOS 12.0.1"", ""build"" : ""21A559"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2021-11-30 22:47:40.5235 -0800"", ""incident"" : ""29D9CD0F-7B57-40A4-A304-42115F1FCDCC"", ""bug_type"" : ""309"", ""pid"" : 43865, ""procExitAbsTime"" : 88062221966537, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : 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(non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 1576K 49 \nColorSync 248K 29 \nCoreAnimation 5108K 82 \nCoreGraphics 12K 2 \nCoreServices 108K 1 \nCoreUI image data 5216K 44 \nFoundation 16K 1 \nKernel Alloc Once 32K 3 \nMALLOC 2.5G 630 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 5 \nSTACK GUARD 116K 29 \nStack 251.2M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.2G 121 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__DATA 42.9M 707 \n__DATA_CONST 31.5M 342 \n__DATA_DIRTY 1641K 220 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 734.2M 171 \n__OBJC_RO 81.5M 1 \n__OBJC_RW 3120K 2 \n__TEXT 814.5M 695 \n__UNICODE 588K 1 \ndyld private memory 1024K 1 \nmapped file 514.0M 55 \nshared memory 2972K 23 \n=========== ======= ======= \nTOTAL 6.6G 3268 \nTOTAL, minus reserved VM space 6.2G 3268 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""6194416dea7ed64a7812a429"" }, ""deploymentId"" : 240000322 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000162 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""614a34c5eae97a2111628dc5"" }, ""deploymentId"" : 240000271 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000076 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3rc202111292147 (2021-11-29) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/nikolausflores/Downloads/Tbrucei_pp215fid.xyz Install the SEQCROW bundle to open ""XYZ file"" format files. Opener for format 'XYZ file' is not installed; see log for more info > open /Users/nikolausflores/Downloads/Tbrucei_pp215.3dmod Unrecognized file suffix '.3dmod' Downloading bundle SEQCROW-1.3-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/1.3/site-packages sysconfig: /Users/nikolausflores/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/1.3/site-packages sysconfig: /Users/nikolausflores/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/include/python3.9/Send2Trash sysconfig: /Users/nikolausflores/Library/Python/3.9/include/Send2Trash WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/bin sysconfig: /Users/nikolausflores/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX sysconfig: /Users/nikolausflores/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/include/python3.9/SEQCROW sysconfig: /Users/nikolausflores/Library/Python/3.9/include/SEQCROW WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/nikolausflores/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.2.4; however, version 21.3.1 is available. You should consider upgrading via the '/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/nikolausflores/Downloads/SEQCROW-1.3-py3-none-any.whl Requirement already satisfied: psutil in /private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.3) (5.8.0) Requirement already satisfied: ChimeraX-Core=1.2 in /private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.3) (1.3rc202111292147) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: scipy in /private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.3) (1.7.1) Requirement already satisfied: numpy=1.16.5 in /private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from scipy->SEQCROW==1.3) (1.21.2) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.3 Send2Trash-1.8.0 \--- Successfully installed SEQCROW-1.3 Send2Trash-1.8.0 Installed SEQCROW (1.3) > open /Users/nikolausflores/Downloads/Tbrucei_pp215.3dmod Unrecognized file suffix '.3dmod' > open /Users/nikolausflores/Downloads/Tbrucei_pp215fid.xyz Install the SEQCROW bundle to open ""XYZ file"" format files. Opener for format 'XYZ file' is not installed; see log for more info > help help:quickstart > open /Users/nikolausflores/Downloads/Tbrucei_pp215_full_rec.mrc Opened Tbrucei_pp215_full_rec.mrc as #1, grid size 960,364,928, pixel 10.2,10.2,10.2, shown at step 1, values float32 > set bgColor white > set bgColor black > volume #1 region 0,0,0,959,363,927 step 4 > set bgColor white > volume #1 change image level 0.2071,0 level 1.201,0.8 level 1.743,1 > volume #1 level 0.1766 > volume #1 level 0.8578 > volume #1 level 1.098 > volume #1 level 0.6174 > volume #1 level 0.8778 > volume #1 step 2 > volume #1 level 1.221 > volume #1 level 1.367 > volume #1 level -0.3464 > volume #1 level -3.137 > volume #1 level 0.6819 > lighting soft > lighting full > lighting soft > volume #1 level 0.7554 > volume #1 level 0.9023 > style stick Changed 0 atom styles > ui tool show ""Side View"" > lighting shadows true intensity 0.5 > volume #1 step 16 > volume #1 step 4 > volume #1 step 2 > volume #1 step 4 > view > graphics silhouettes true > select #1 3 models selected > ~select #1 Nothing selected > set bgColor gray > set bgColor black > set bgColor white > ui tool show ""Color Actions"" > ui tool show ""Surface Color"" > color cylindrical #1.2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff > center 4878.8,-20.424,4715.4 > volume #1 step 2 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3rc202111292147 (2021-11-29) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.2.10 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 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: 8 GB System Firmware Version: 447.40.12.0.0 OS Loader Version: 540.40.4~45 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 13 days 1:22 Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Family: Supported, Metal GPUFamily macOS 2 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 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: 2.0.8 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: 1.3rc202111292147 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: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 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: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 Send2Trash: 1.8.0 SEQCROW: 1.3 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