id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10371 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.6-arm64-arm-64bit ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000289067000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028805b000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028704f000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000286043000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000285037000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028402b000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028301f000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000282013000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000281007000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000017f37f000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000017e373000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000017d367000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000017c35b000 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000100654580 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 157 in asArray File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 2786 in set_matrix File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 775 in set_projection_matrix File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 683 in _use_shader File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 759 in _opengl_shader File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 656 in shader File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 806 in _draw_geometry File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 775 in draw_self File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 768 in draw File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1555 in _draw_multiple File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1542 in draw_opaque File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1567 in draw_depth File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 243 in _draw_scene File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 177 in draw File ""/Applications/ChimeraX-1.6-rc2023.04.25.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 ""/Applications/ChimeraX-1.6-rc2023.04.25.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 ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6-rc2023.04.25.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"":""2023-12-19 09:38:22.00 -0500"",""app_version"":""1.6.0"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.6.6 (21G646)"",""incident_id"":""0A206118-5075-4222-B995-A6A153CF6AA3"",""name"":""ChimeraX""} { ""uptime"" : 72000, ""procLaunch"" : ""2023-12-18 10:00:56.1144 -0500"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""procStartAbsTime"" : 910880122, ""coalitionID"" : 579, ""osVersion"" : { ""train"" : ""macOS 12.6.6"", ""build"" : ""21G646"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-12-19 09:38:20.6329 -0500"", ""incident"" : ""0A206118-5075-4222-B995-A6A153CF6AA3"", ""bug_type"" : ""309"", ""pid"" : 540, ""procExitAbsTime"" : 1745632591315, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6-rc2023.04.25.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""B715C52B-CD1A-59AA-BC0E-0C4D2AA0A98F"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""AF362FD7-4E0E-DE40-A018-2F197AB07583"", ""wakeTime"" : 1409, ""sleepWakeUUID"" : ""4B134B50-D64F-4183-AA2D-9F6BB136C618"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 105553518919511\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 105553518919511\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""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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image 560K 29 \nColorSync 560K 28 \nCoreAnimation 384K 21 \nCoreGraphics 48K 3 \nCoreUI image data 3728K 24 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 545.8M 176 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 1.0G 10 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 47 \nStack 368.6M 47 \nVM_ALLOCATE 207.4M 364 \nVM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated)\n__AUTH 2621K 311 \n__AUTH_CONST 20.6M 510 \n__CTF 756 1 \n__DATA 23.6M 653 \n__DATA_CONST 28.0M 662 \n__DATA_DIRTY 1804K 216 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 606.6M 151 \n__OBJC_CONST 3667K 282 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 738.2M 680 \n__UNICODE 592K 1 \ndyld private memory 1024K 1 \nmapped file 503.1M 75 \nshared memory 3360K 27 \n=========== ======= ======= \nTOTAL 4.7G 4359 \nTOTAL, minus reserved VM space 3.1G 4359 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""61301e3a61217b3110231469"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""652886aa2c02f032beae8316"" }, ""deploymentId"" : 240000028 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_28/best_model.pdb > format pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > hide cartoons > show cartoons > hide atoms > show atoms > hide atoms > show atoms > hide atoms > set bgColor white > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > help help:user/preferences.html#startup > color /a blue > color /a navy blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color /a light blue > color /a teal > select clear > select /A 179 atoms, 179 bonds, 21 residues, 1 model selected > color sel light sea green > color sel cornflower blue > ui tool show ""Color Actions"" > color sel medium blue > color sel cornflower blue > color sel dim gray > color sel dark gray > color sel black > color sel cornflower blue > color sel slate gray > color sel cadet blue > color sel steel blue > select clear > select /a 179 atoms, 179 bonds, 21 residues, 1 model selected > color sel light steel blue > color sel midnight blue > color sel medium purple > color sel medium orchid > color sel orchid > color sel gold > color sel saddle brown > color sel medium turquoise > color sel light sea green > color sel cornflower blue > color sel dark slate blue > color sel slate blue > color sel medium slate blue > color sel blue > color sel steel blue > select clear > select /A:2-20 163 atoms, 163 bonds, 19 residues, 1 model selected > select /A:2-20 163 atoms, 163 bonds, 19 residues, 1 model selected > select /A:2-21 170 atoms, 170 bonds, 20 residues, 1 model selected > select /A:2-21 170 atoms, 170 bonds, 20 residues, 1 model selected > select /A:2-21 170 atoms, 170 bonds, 20 residues, 1 model selected > select /A:21 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:21 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:2-21 170 atoms, 170 bonds, 20 residues, 1 model selected > select clear > select /A:1 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /A:7 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /A:9 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /A:10 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /A:15 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:17 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /A:15 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > close > open ""/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT domain.cxs"" > format session opened ChimeraX session > close > open ""/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT domain.cxs"" > format session opened ChimeraX session > close > open ""/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT Dimer with > PEPTACgg.cxs"" format session opened ChimeraX session > open ""/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT with > PRTCggg-2.cxs"" format session opened ChimeraX session > close > open ""/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT Dimer with > PEPTACgg.cxs"" format session opened ChimeraX session > lighting soft > lighting full > lighting simple > lighting soft Drag select of 26 residues > hide sel cartoons Drag select of 22 residues Drag select of 26 residues > hide sel atoms > hide sel cartoons Drag select of 22 residues > select clear > select /C:7 4 atoms, 3 bonds, 1 residue, 1 model selected Drag select of 7 residues > hide sel cartoons > select /c 227 atoms, 229 bonds, 28 residues, 1 model selected > ui tool show ""Color Actions"" > color sel slate gray > color sel steel blue > select clear > select /C:8 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /C:14 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /C:16 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > select /C:17 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /C:16 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:22 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /C:24 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.6.6 (21G646) Kernel Version: Darwin 21.6.0 Time since boot: 23:38 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Thunderbolt Display: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202304252053 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX