id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18771 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070002bc8e000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070002ac8b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700029c88000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700028c85000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700027c82000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700026c7f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700025c7c000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700024c79000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700023c76000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700022c73000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700021c70000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700020c6d000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001fc6a000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001ec67000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001dc64000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001cc61000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001bc5e000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001ac5b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700019c58000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff848cb4dc0 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mask._mask (total: 54) {""app_name"":""ChimeraX"",""timestamp"":""2025-09-12 09:40:20.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.5 (24F74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""F45FA137-8915-4D3B-808F-21ADE3F90FCC""} { ""uptime"" : 6900000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 573055, ""deployVersion"" : 210, ""modelCode"" : ""iMac20,2"", ""coalitionID"" : 2030561, ""osVersion"" : { ""train"" : ""macOS 15.5"", ""build"" : ""24F74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-09-12 09:39:48.9961 +0200"", ""codeSigningMonitor"" : 0, ""incident"" : ""F45FA137-8915-4D3B-808F-21ADE3F90FCC"", ""pid"" : 6604, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-09-08 10:38:16.2208 +0200"", ""procStartAbsTime"" : 6651131506471128, ""procExitAbsTime"" : 6993212219867330, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""779C63CD-13F5-56E9-8E6A-A12AEF46EFBB"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""BF10E68F-7EB4-A7BF-BFD0-67ED6F3CDCA0"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""deviceNotCapable""]}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""bootSessionUUID"" : ""68F55CCD-537A-4DC7-A4F2-8C8E14EDDEA3"", ""bridgeVersion"" : {""build"":""22P5072"",""train"":""9.5""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. Bytes before following region: 4486905856\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b70c000-10b710000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000000"",""rawCodes"":[1,0],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000000""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":6604}, ""vmregioninfo"" : ""0 is not in any region. Bytes before following region: 4486905856\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b70c000-10b710000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0}, ""faultingThread"" : 0, ""threads"" : 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B / DIMM 0), 16 GB, DDR4, 2667 MHz, 029E, CMSA64GX4M4A2666C18 USB Device: USB31Bus USB Device: USB Laser Mouse USB Device: T2Bus USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Display: iMac, Retina 5K (5120 x 2880), Main, MirrorOff, Online Display: ROG PG278QR, 2048 x 1152, MirrorOff, Online Model: iMac20,2, BootROM 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0), 8 processors, 8-Core Intel Core i7, 3,8 GHz, 32 GB, SMC Graphics: AMD Radeon Pro 5700, AMD Radeon Pro 5700, PCIe, 8 GB AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x7BF), wl0: Jul 26 2024 22:36:01 version 9.30.514.0.32.5.94 FWID 01-68d7ff80 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet still retrieving bundle list from toolshed > isolde shorthand Error running startup command 'isolde shorthand': Unknown command: isolde shorthand UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_it014_half2_class001.mrc Opened run_it014_half2_class001.mrc as #1, grid size 512,512,512, pixel 1.05, shown at level 0.00282, step 2, values float32 > volume #1 level 0.001956 > volume #1 level 0.00149 > volume #1 level 0.0008918 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_it024_half2_class001.mrc Opened run_it024_half2_class001.mrc as #2, grid size 512,512,512, pixel 1.05, shown at level 0.00282, step 2, values float32 > volume #2 level 0.0009973 > ui tool show ""Map Filter"" > volume bin #2 binSize 2 Opened run_it024_half2_class001.mrc binned as #3, grid size 256,256,256, pixel 2.1, shown at step 1, values float32 > volume #3 level 0.001055 > close #3 > volume bin #2 binSize 8 Opened run_it024_half2_class001.mrc binned as #3, grid size 64,64,64, pixel 8.4, shown at step 1, values float32 > volume #3 level 0.0004786 > volume #3 level 0.0002436 > volume #3 level 0.0001497 > set bgColor black > set bgColor white > set bgColor black > volume #3 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #3 style surface > volume #3 change image level -0.0004297,0 level 0.003037,0.8 level 0.0116,1 > volume #3 level 0.0004551 > close session > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class006.mrc Opened run_it030_class006.mrc as #1, grid size 512,512,512, pixel 1.05, shown at level 0.0002, step 2, values float32 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class005.mrc Opened run_it030_class005.mrc as #2, grid size 512,512,512, pixel 1.05, shown at level 0.0026, step 2, values float32 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class004.mrc Opened run_it030_class004.mrc as #3, grid size 512,512,512, pixel 1.05, shown at level 0.075, step 2, values float32 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class003.mrc Opened run_it030_class003.mrc as #4, grid size 512,512,512, pixel 1.05, shown at level 1.8, step 2, values float32 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class002.mrc Opened run_it030_class002.mrc as #5, grid size 512,512,512, pixel 1.05, shown at level 0.0663, step 2, values float32 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class001.mrc Opened run_it030_class001.mrc as #6, grid size 512,512,512, pixel 1.05, shown at level 0.00456, step 2, values float32 > tile 5 models tiled > volume #6 level 0.001683 > volume #6 level 0.0007488 > volume #2 level 0.0008627 > volume #6 level 0.0005333 > volume #6 level 0.00021 > volume #6 level 0.0004974 > volume #2 level 0.0004776 > hide #!2 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > ~tile > volume #2 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #2 style surface region 0,0,0,511,511,511 step 1 > hide #!6 models > show #!6 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > volume #6 level 0.001539 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > volume #6 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #6 style surface region 0,0,0,511,511,511 step 1 > volume #6 change image level -0.0005871,0 level 0.004556,0.8 level 0.0157,1 > volume #6 level 0.001359 > volume #6 level 0.0008889 > volume #6 level 0.0006361 > volume #6 level 0.0007444 > volume #6 level 0.001431 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_class001.mrc Opened run_class001.mrc as #7, grid size 512,512,512, pixel 1.05, shown at level 0.00278, step 2, values float32 > ~tile > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > volume #7 level 0.000704 > volume #7 level 0.0003846 > volume #6 level 0.001178 > volume #6 level 0.0008889 > volume #6 level 0.0004194 > shape sphere radius 5 > select add #8 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,292.66,0,1,0,74.965,0,0,1,318.35 > view matrix models #8,1,0,0,249.06,0,1,0,227.64,0,0,1,426.39 > view matrix models #8,1,0,0,296.94,0,1,0,260.04,0,0,1,418.89 > view matrix models #8,1,0,0,308.83,0,1,0,259.28,0,0,1,399.22 > volume #6 level 0.0007444 > view matrix models #8,1,0,0,340.95,0,1,0,246.69,0,0,1,397.34 > view matrix models #8,1,0,0,340.28,0,1,0,247.29,0,0,1,392.2 > select subtract #8 Nothing selected > show #!7 models > hide #!7 models > volume onesmask #8 Opened mask masked as #9, grid size 101,101,101, pixel 0.1, shown at step 1, values int8 > hide #8 models > vop resample #9 ongrid #7 Opened mask masked resampled as #10, grid size 512,512,512, pixel 1.05, shown at step 1, values int8 > save /Users/jabrilg/Desktop/j64_recent_sphere.mrc models #10 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map.mrc Opened j64_recent_map.mrc as #11, grid size 512,512,512, pixel 1.05, shown at level 0.00279, step 2, values float32 > volume #11 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #11 style surface region 0,0,0,511,511,511 step 1 > hide #!6 models > volume #11 change image level -0.0005418,0 level 0.002786,0.8 level > 0.03411,1 > close session > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_class001.mrc Opened run_class001.mrc as #1, grid size 512,512,512, pixel 1.05, shown at level 0.00278, step 2, values float32 > volume #1 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #1 style surface region 0,0,0,511,511,511 step 1 > shape sphere radius 2 > select add #2 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,326.26,0,1,0,36.382,0,0,1,160.15 > volume #1 change image level -0.0006178,0 level 0.002778,0.8 level 0.03544,1 > volume #1 level 0.001282 > view matrix models #2,1,0,0,380.91,0,1,0,187.68,0,0,1,122.21 > view matrix models #2,1,0,0,360.27,0,1,0,225.12,0,0,1,196.55 > view matrix models #2,1,0,0,366.36,0,1,0,226.03,0,0,1,197.98 > view matrix models #2,1,0,0,366.94,0,1,0,254.74,0,0,1,180.11 > view matrix models #2,1,0,0,375.3,0,1,0,251.96,0,0,1,175.52 > volume onesmask #2 Opened mask masked as #3, grid size 101,101,101, pixel 0.04, shown at step 1, values int8 > vop resample #3 ongrid #1 Opened mask masked resampled as #4, grid size 512,512,512, pixel 1.05, shown at step 1, values int8 > save /Users/jabrilg/Desktop/j64_recent_sphere2.mrc models #4 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map.mrc Opened j64_recent_map.mrc as #5, grid size 512,512,512, pixel 1.05, shown at level 0.00279, step 2, values float32 > volume #5 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #5 style surface region 0,0,0,511,511,511 step 1 > show #!1 models > select subtract #2 Nothing selected > color #5 #ffb3ff8a models > color #5 #ffb3ff74 models > hide #!5 models > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map2.mrc Opened j64_recent_map2.mrc as #6, grid size 512,512,512, pixel 1.05, shown at level 0.00279, step 2, values float32 > hide #!6 models > show #!6 models > hide #!1 models > show #!1 models > volume #6 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #6 style surface region 0,0,0,511,511,511 step 1 > hide #!1 models > volume #6 change image level -0.000458,0 level 0.002789,0.8 level 0.03283,1 > volume #6 level 0.0013 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map_corrected.mrc Opened j64_recent_map_corrected.mrc as #7, grid size 512,512,512, pixel 1.05, shown at level 0.000631, step 2, values float32 > close #7 > show #!5 models > hide #!5 models > show #!1 models > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map2.mrc Opened j64_recent_map2.mrc as #7, grid size 512,512,512, pixel 1.05, shown at level 0.00279, step 2, values float32 > hide #!6 models > show #!6 models > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map_2p1px_box256.mrc Opened j64_recent_map_2p1px_box256.mrc as #8, grid size 256,256,256, pixel 2.1, shown at level 0.00279, step 1, values float32 > hide #!6 models > hide #!4 models > hide #!7 models > hide #!8 models > show #!8 models > hide #!1 models > show #!1 models > volume #8 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #8 style surface > hide #!1 models > show #!1 models > hide #!1 models > volume #8 style image colorMode auto8 imageMode ""full region"" > volume #8 level -0.0004495,0 level 0.002787,0.8 level 0.03422,1 > volume #8 level -0.004304,0.04615 level 0.002787,0.8 level 0.03422,1 > volume #8 style surface > ui tool show ""Map Coordinates"" > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job067/run_class001.mrc Opened run_class001.mrc as #9, grid size 256,256,256, pixel 2.1, shown at level 0.0246, step 1, values float32 > volume #9 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #9 style surface > volume #9 change image level -0.0008415,0 level 0.02455,0.8 level 0.1633,1 > volume #9 level 0.006645 > volume #9 level 0.001376 > volume #9 level 0.002781 > close session > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job067/run_class001.mrc Opened run_class001.mrc as #1, grid size 256,256,256, pixel 2.1, shown at level 0.0246, step 1, values float32 > volume #1 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #1 style surface > volume #1 change image level -0.0008415,0 level 0.02455,0.8 level 0.1633,1 > volume #1 level 0.006136 > volume #1 level 0.02661 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job068/run_it003_half2_class001.mrc Opened run_it003_half2_class001.mrc as #2, grid size 256,256,256, pixel 2.1, shown at level 0.0261, step 1, values float32 > volume #2 level 0.005503 > volume #2 level 0.001999 > volume #2 level 0.002954 > volume #2 level 0.0106 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet still retrieving bundle list from toolshed > isolde shorthand Error running startup command 'isolde shorthand': Unknown command: isolde shorthand UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-7.0.3 OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,2 Processor Name: 8-Core Intel Core i7 Processor Speed: 3,8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0) OS Loader Version: 583~1350 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 80 days, 22 hours, 34 minutes Graphics/Displays: AMD Radeon Pro 5700: Chipset Model: AMD Radeon Pro 5700 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x731b Revision ID: 0x0040 ROM Revision: 113-D1820Q-231 VBIOS Version: 113-D182A2XG-013 Option ROM Version: 113-D182A2XG-013 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal ROG PG278QR: Resolution: 2048 x 1152 UI Looks like: 2048 x 1152 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: #ASOT2TO5phXd Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX