The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202202260143 (2022-02-26 01:43:54 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x0000700023a40000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700021a3a000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700020a37000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001fa34000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.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/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001ea31000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001da2e000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001ba25000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700019999000 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000116a02600 (most recent call first):
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.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/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/nm/w9pkld9n7yl1ym16p_khb_7m0000gp/T/AppTranslocation/A3C7FB0E-870C-424A-A485-79A85AF3E897/d/ChimeraX_Daily.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":"2022-03-02 11:26:40.00 -0500","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"D6E626CB-4B94-433C-B4AF-FFAC5112C44B","name":"ChimeraX"}
{
"uptime" : 340000,
"procLaunch" : "2022-03-02 11:21:27.3681 -0500",
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,2",
"procStartAbsTime" : 341138521864524,
"coalitionID" : 25159,
"osVersion" : {
"train" : "macOS 12.2.1",
"build" : "21D62",
"releaseType" : "User"
},
"captureTime" : "2022-03-02 11:26:27.4884 -0500",
"incident" : "D6E626CB-4B94-433C-B4AF-FFAC5112C44B",
"bug_type" : "309",
"pid" : 39422,
"procExitAbsTime" : 341438269985102,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A61E97D6-E4FA-5007-933E-619BB2D81FB5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5ACA4380-F575-1634-4BEA-36B96781F47A",
"wakeTime" : 7284,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "982110D4-DA6B-42F0-B0CB-437D641886F2",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["Assertion failed: (backingScaleFactor > 0.f), function drawnFocusRingBitmapForTime, file NSAutomaticFocusRing.m, line 346."]},
"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" : [{"triggered":true,"id":1904463,"threadState":{"r13":{"value":5534044160},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":6},"rsi":{"value":6},"r8":{"value":140514656870216},"cr2":{"value":140514659075328},"rdx":{"value":0},"r10":{"value":4674561536,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":1455221859223064265},"r15":{"value":22},"rbx":{"value":4674561536,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703324692754,"matchesCrashFrame":1},"rbp":{"value":140514656868992},"rsp":{"value":140514656868952},"r12":{"value":259},"rcx":{"value":140514656868952},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":28946,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":25108,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":278980,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15917,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":531728,"symbol":"abort","symbolLocation":123,"imageIndex":2},{"imageOffset":528574,"symbol":"__assert_rtn","symbolLocation":314,"imageIndex":2},{"imageOffset":2019291,"symbol":"+[_NSAutomaticFocusRing showForView:forceRect:isAccessibilityRequest:]","symbolLocation":4826,"imageIndex":5},{"imageOffset":10667785,"symbol":"-[NSColorPanelFavoriteSwatch setSelected:]","symbolLocation":137,"imageIndex":5},{"imageOffset":1097036,"symbol":"__93-[_NSCollectionViewCore _dequeueReusableViewOfKind:withIdentifier:forIndexPath:viewCategory:]_block_invoke.808","symbolLocation":95,"imageIndex":6},{"imageOffset":317337,"symbol":"+[_NSUIAnimator performWithoutAnimation:]","symbolLocation":87,"imageIndex":6},{"imageOffset":314733,"symbol":"-[_NSCollectionViewCore _dequeueReusableViewOfKind:withIdentifier:forIndexPath:viewCategory:]","symbolLocation":1661,"imageIndex":6},{"imageOffset":312900,"symbol":"-[_NSCollectionViewCore dequeueReusableItemWithReuseIdentifier:forIndexPath:]","symbolLocation":72,"imageIndex":6},{"imageOffset":2331609,"symbol":"-[NSCollectionView makeItemWithIdentifier:forIndexPath:]","symbolLocation":88,"imageIndex":5},{"imageOffset":10671210,"symbol":"-[NSColorPanelFavoritesList collectionView:itemForRepresentedObjectAtIndexPath:]","symbolLocation":50,"imageIndex":5},{"imageOffset":2331336,"symbol":"-[_NSCollectionViewDataSourceAdapter collectionView:itemForRepresentedObjectAtIndexPath:]","symbolLocation":438,"imageIndex":5},{"imageOffset":311990,"symbol":"-[_NSCollectionViewCore _createPreparedCellForItemAtIndexPath:withLayoutAttributes:applyAttributes:isFocused:notify:]","symbolLocation":100,"imageIndex":6},{"imageOffset":311884,"symbol":"-[_NSCollectionViewCore _createPreparedCellForItemAtIndexPath:withLayoutAttributes:applyAttributes:]","symbolLocation":31,"imageIndex":6},{"imageOffset":215058,"symbol":"-[_NSCollectionViewCore _updateVisibleCellsNow:]","symbolLocation":4348,"imageIndex":6},{"imageOffset":170090,"symbol":"-[_NSCollectionViewCore _layoutItems]","symbolLocation":271,"imageIndex":6},{"imageOffset":1092073,"symbol":"-[_NSCollectionViewCore _itemAtIndexPath:includePrefetchedCells:]","symbolLocation":230,"imageIndex":6},{"imageOffset":1066082,"symbol":"__74-[_NSCollectionViewCore _selectItemsAtIndexPaths:animated:notifyDelegate:]_block_invoke","symbolLocation":37,"imageIndex":6},{"imageOffset":721526,"symbol":"__NSSET_IS_CALLING_OUT_TO_A_BLOCK__","symbolLocation":7,"imageIndex":7},{"imageOffset":997614,"symbol":"-[__NSSingleObjectSetI enumerateObjectsWithOptions:usingBlock:]","symbolLocation":111,"imageIndex":7},{"imageOffset":1065967,"symbol":"-[_NSCollectionViewCore _selectItemsAtIndexPaths:animated:notifyDelegate:]","symbolLocation":402,"imageIndex":6},{"imageOffset":10177826,"symbol":"-[NSCollectionView _selectItemsAtIndexPaths:scrollPosition:notifyDelegate:]","symbolLocation":151,"imageIndex":5},{"imageOffset":10179918,"symbol":"-[NSCollectionView setSelectionIndexPaths:]","symbolLocation":232,"imageIndex":5},{"imageOffset":483107,"symbol":"__CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__","symbolLocation":12,"imageIndex":7},{"imageOffset":1127417,"symbol":"___CFXRegistrationPost_block_invoke","symbolLocation":49,"imageIndex":7},{"imageOffset":1127286,"symbol":"_CFXRegistrationPost","symbolLocation":496,"imageIndex":7},{"imageOffset":292918,"symbol":"_CFXNotificationPost","symbolLocation":733,"imageIndex":7},{"imageOffset":37310,"symbol":"-[NSNotificationCenter postNotificationName:object:userInfo:]","symbolLocation":82,"imageIndex":8},{"imageOffset":11453563,"symbol":"-[NSFavoriteColorsStore setColorEntries:]","symbolLocation":191,"imageIndex":5},{"imageOffset":11454905,"symbol":"-[NSFavoriteColorsStore updatingFromBacking:]","symbolLocation":19,"imageIndex":5},{"imageOffset":11455015,"symbol":"-[NSFavoriteColorsStore updateColorsFromBacking]","symbolLocation":99,"imageIndex":5},{"imageOffset":483107,"symbol":"__CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__","symbolLocation":12,"imageIndex":7},{"imageOffset":1127417,"symbol":"___CFXRegistrationPost_block_invoke","symbolLocation":49,"imageIndex":7},{"imageOffset":1127286,"symbol":"_CFXRegistrationPost","symbolLocation":496,"imageIndex":7},{"imageOffset":292918,"symbol":"_CFXNotificationPost","symbolLocation":733,"imageIndex":7},{"imageOffset":37310,"symbol":"-[NSNotificationCenter postNotificationName:object:userInfo:]","symbolLocation":82,"imageIndex":8},{"imageOffset":11453563,"symbol":"-[NSFavoriteColorsStore setColorEntries:]","symbolLocation":191,"imageIndex":5},{"imageOffset":11463206,"symbol":"-[NSGridFavoriteStoreTransposer writeColorsToBacking:]","symbolLocation":312,"imageIndex":5},{"imageOffset":11453517,"symbol":"-[NSFavoriteColorsStore 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"size" : 4096,
"uuid" : "9596eff5-d2be-396c-9c4e-6177235c3dae",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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"size" : 131002368,
"uuid" : "86651daf-3bff-3a6f-b313-e84d303e55eb",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
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"arch" : "x86_64",
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"size" : 8192,
"uuid" : "d6125191-ebf8-3e9e-aa83-52e897d6ea11",
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"name" : "select.cpython-39-darwin.so"
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===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202202260143 (2022-02-26)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jpark05/Desktop/220201 MIT related /DHFR Manuscript
> documents/Figure 4 Recognition fig blot/230302 chimera/5dfr and 1rg7.cxs"
Log from Wed Mar 2 10:24:24 2022UCSF ChimeraX version: 1.4.dev202202260143
(2022-02-26)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jpark05/Desktop/5dfr.pdb
5dfr.pdb title:
Crystal structure of unliganded escherichia coli dihydrofolate reductase.
Ligand-induced conformational changes and cooperativity In binding [more
info...]
Chain information for 5dfr.pdb #1
---
Chain | Description | UniProt
A | dihydrofolate reductase | DYR_ECOLI
Non-standard residues in 5dfr.pdb #1
---
CL — chloride ion
> fetch 1rg7
Unknown command: fetch 1rg7
> open "/Users/jpark05/Desktop/1rg7 (1).pdb"
1rg7 (1).pdb title:
Dihydrofolate reductase complexed with methotrexate [more info...]
Chain information for 1rg7 (1).pdb #2
---
Chain | Description | UniProt
A | DHFR | DYR_ECOLI
Non-standard residues in 1rg7 (1).pdb #2
---
MTX — methotrexate
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> close #2
> open /Users/jpark05/Desktop/1rg7_edit.pdb
Summary of feedback from opening /Users/jpark05/Desktop/1rg7_edit.pdb
---
error | Non-ASCII character on line 3 of PDB file
warnings | Ignored bad PDB record found on line 1
}q
Ignored bad PDB record found on line 2
(]q(K?X?
PDB file contains non-ASCII character or control character
> open /Users/jpark05/Desktop/1rg7.pdb
1rg7.pdb title:
Dihydrofolate reductase complexed with methotrexate [more info...]
Chain information for 1rg7.pdb #2
---
Chain | Description | UniProt
A | DHFR | DYR_ECOLI
Non-standard residues in 1rg7.pdb #2
---
MTX — methotrexate
> $ solvent
Unknown command: $ solvent
> $ delete solvent
Unknown command: $ delete solvent
> hide solvent
> hide side chain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2 atoms
> show #2 atoms
> hide #2 atoms
> show mtx
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2 surfaces
[Repeated 1 time(s)]
> show #2 surfaces
> hide #!2 surfaces
> ui tool show "Color Actions"
Alignment identifier is 1/A
Alignment identifier is 2/A
> color #2 #3d72afff
> lighting flat
> set bgColor white
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
> hide #!2 atoms
[Repeated 1 time(s)]
> show #!2 atoms
> hide #!2 atoms
> select ligand
33 atoms, 35 bonds, 1 residue, 1 model selected
> show ligand
> color sel byhetero
> color sel byelement
> select #2/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:21-42
177 atoms, 182 bonds, 22 residues, 1 model selected
> color (#!2 & sel) orange
> color (#!2 & sel) orange red
> select #2/A:2-5,39-43,58-62,73-75,91-95,107-115,133-135,151-158
347 atoms, 348 bonds, 42 residues, 1 model selected
> select #2/A:43
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:43-56
110 atoms, 114 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> select #2/A:93-95
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #2/A:93-117
199 atoms, 203 bonds, 25 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indigo
> color sel dark violet
> color sel dark orchid
> clear select
Unknown command: clear select
> select clear
> save "/Users/jpark05/Desktop/220302 1rg7 with mtx peptide blot.cxs"
> show #!1 models
> hide #!2 models
> ui tool show "Color Actions"
> color #1 #3d72afff
> select #2/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:21-42
177 atoms, 182 bonds, 22 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange red
> color #1 orange red
> undo
> select #2/A:25-35,44-50,78-85,97-106
298 atoms, 304 bonds, 36 residues, 1 model selected
> select #2/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:21-42
177 atoms, 182 bonds, 22 residues, 1 model selected
> color #1 orange red
> undo
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:21-42
185 atoms, 192 bonds, 22 residues, 1 model selected
> color sel orange red
> select #1/A:43
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:43-56
110 atoms, 114 bonds, 14 residues, 1 model selected
> color sel forest green
> select #1/A:1-8,39-43,58-63,73-75,91-95,108-116,132-141,150-159
462 atoms, 466 bonds, 56 residues, 1 model selected
> select #1/A:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:93-117
199 atoms, 203 bonds, 25 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orchid
> select clear
> show #!2 models
> align 1fg7, 5dfr
Missing or invalid "atoms" argument: invalid atoms specifier
> align 1rg7, 5dfr
Missing or invalid "atoms" argument: invalid atoms specifier
> align 1rg7 to 5dfr
Missing or invalid "atoms" argument: invalid atoms specifier
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> matchmaker 5dfr to 1rg7, bring 5dfr
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> ui tool show Toolbar
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1rg7.pdb, chain A (#2) with 5dfr.pdb, chain A (#1), sequence
alignment score = 771
RMSD between 148 pruned atom pairs is 0.813 angstroms; (across all 154 pairs:
1.146)
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "/Users/jpark05/Desktop/220302 1rg7 mtx peptide blot colors.png" width
> 899 height 572 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "/Users/jpark05/Desktop/5dfr and 1rg7.cxs"
——— End of log from Wed Mar 2 10:24:24 2022 ———
opened ChimeraX session
> select :19-47
464 atoms, 482 bonds, 56 residues, 2 models selected
> color (#!2 & sel) orange red
> select :43-56
220 atoms, 228 bonds, 28 residues, 2 models selected
> color (#!2 & sel) forest green
> select :93-117
398 atoms, 406 bonds, 50 residues, 2 models selected
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> select clear
> save "/Users/jpark05/Desktop/220201 MIT related /DHFR Manuscript
> documents/Figure 4 Recognition fig blot/230302 chimera/220302 1rg7 colors
> final.png" width 1092 height 581 supersample 3
> hide #!1 target m
> show #!1 target m
> hide #!2 target m
> save "/Users/jpark05/Desktop/220201 MIT related /DHFR Manuscript
> documents/Figure 4 Recognition fig blot/230302 chimera/220302 5dfr colors
> final.png" width 1092 height 581 supersample 3
> hide #!2 target m
> hide #!1 target m
> show #!2 target m
> save "/Users/jpark05/Desktop/220201 MIT related /DHFR Manuscript
> documents/Figure 4 Recognition fig blot/230302 chimera/220302 5dfr 1rg7
> final.cxs"
> select :43-56
220 atoms, 228 bonds, 28 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #4882cbff
> select :93-117
398 atoms, 406 bonds, 50 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #4882cbff
> select clear
> undo
> select :43-56
220 atoms, 228 bonds, 28 residues, 2 models selected
> color (#!2 & sel) #4c85ccff
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4.dev202202260143 (2022-02-26)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jpark05/Desktop/220201 MIT related /Manuscript documents/Figure
> 4 Recognition fig blot/230302 chimera/5dfr and 1rg7.cxs" format session
No such file/path: /Users/jpark05/Desktop/220201 MIT related /Manuscript
documents/Figure 4 Recognition fig blot/230302 chimera/5dfr and 1rg7.cxs
> open "/Users/jpark05/Desktop/220201 MIT related /Manuscript documents/Figure
> 4 Recognition fig blot/230302 chimera/5dfr and 1rg7.cxs" format session
No such file/path: /Users/jpark05/Desktop/220201 MIT related /Manuscript
documents/Figure 4 Recognition fig blot/230302 chimera/5dfr and 1rg7.cxs
OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.
Locale: UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 3.1 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: 447.80.3.0.0
OS Loader Version: 540.80.2~11
SMC Version (system): 2.44f6
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 7 days 15:01
Graphics/Displays:
Intel Iris Plus Graphics 650:
Chipset Model: Intel Iris Plus Graphics 650
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5927
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: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.5.2
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
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: 1.36.2
ChimeraX-AtomicLibrary: 6.0.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
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: 1.5.1
ChimeraX-CommandLine: 1.2.1
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202202260143
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-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: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.2
ChimeraX-ModelPanel: 1.3.2
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: 1.8
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.7.7
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.29.1
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.26
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.2
kiwisolver: 1.3.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.0
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.0
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.28
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
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: 5.2.2
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.8
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Looks like a native Mac color swatch issue that we've seen before, NSColorPanelFavoriteSwatch in stack trace.