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Opened 3 years ago
Last modified 3 years ago
#8807 assigned defect
Crash in msgpack_deserialize during session restore
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000184b5000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.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-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000174b2000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.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-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000164af000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6-rc2023.04.07.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-rc2023.04.07.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-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000154ac000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000144a9000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000134a6000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000124a3000 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007ff85850c680 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/serialize.py", line 70 in msgpack_deserialize
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 708 in restore
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 1004 in open
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1918 in _open_dropped_file
File "/Applications/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 240 in event
File "/Applications/ChimeraX-1.6-rc2023.04.07.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-rc2023.04.07.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-rc2023.04.07.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-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.07.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":"2023-04-09 15:42:23.00 -0400","app_version":"1.6.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","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 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"F196889A-02B4-495A-A172-DF3DACC79CBB"}
{
"uptime" : 90000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,2",
"coalitionID" : 27863,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-04-09 15:42:02.4751 -0400",
"incident" : "F196889A-02B4-495A-A172-DF3DACC79CBB",
"pid" : 55464,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-04-09 08:10:16.7172 -0400",
"procStartAbsTime" : 73763524552513,
"procExitAbsTime" : 90172529233754,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"96A8F7C9-B379-50B8-A7A6-C32844CA4E80","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6041C281-687F-C857-3DB1-B2FF0FF99DD7",
"throttleTimeout" : 2147483647,
"wakeTime" : 2044,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "45CF6B10-2536-40DA-A016-FCF5E24FB00A",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487339351\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff08000-7ffffff09000 [ 4K] r-x\/r-x SM=SHM ",
"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: 140737487339351\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff08000-7ffffff09000 [ 4K] r-x\/r-x SM=SHM ",
"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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"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
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},
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"base" : 4700889088,
"size" : 98304,
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"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/msgpack\/_cmsgpack.cpython-39-darwin.so",
"name" : "_cmsgpack.cpython-39-darwin.so"
},
{
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"base" : 4725149696,
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"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/core\/_serialize.cpython-39-darwin.so",
"name" : "_serialize.cpython-39-darwin.so"
},
{
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"base" : 4315238400,
"size" : 98304,
"uuid" : "f511de72-2757-3ff5-8524-716ba83b7953",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/sip.cpython-39-darwin.so",
"name" : "sip.cpython-39-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 4397256704,
"size" : 2834432,
"uuid" : "951581e2-ae51-392a-82d9-fdf83e162d11",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
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"size" : 4931584,
"uuid" : "5bfaef33-ce47-32bf-acb3-03cbe9e68a6f",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
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"arch" : "x86_64",
"base" : 4408713216,
"size" : 5210112,
"uuid" : "6238782e-d1aa-3245-81ef-2925bf1a4c96",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
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"arch" : "x86_64",
"base" : 4514140160,
"size" : 7094272,
"uuid" : "cf0b9ade-9377-380e-9a84-904983d7bb60",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
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"base" : 4525121536,
"size" : 638976,
"uuid" : "7175bc4c-ca2f-30b6-9734-062b84bd0ae2",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703528890368,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16814067,
"uuid" : "540cedfd-5a35-3f35-8953-dcb7c4834eb5",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.40.118"
},
{
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"arch" : "x86_64",
"base" : 140703492104192,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 10559479,
"uuid" : "a58576df-7109-3a13-a338-617f135ce8a8",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703583145984,
"CFBundleShortVersionString" : "946",
"CFBundleIdentifier" : "com.apple.AE",
"size" : 458752,
"uuid" : "c9fac6a1-1ba1-3d05-870e-1348ec90c40d",
"path" : "\/System\/Library\/Frameworks\/CoreServices.framework\/Versions\/A\/Frameworks\/AE.framework\/Versions\/A\/AE",
"name" : "AE",
"CFBundleVersion" : "946"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703637991424,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112958,
"uuid" : "7bf47984-29cb-319e-a6da-0884d158f96a",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4299825152,
"CFBundleShortVersionString" : "1.6.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.6.0.0"
},
{
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"base" : 140703473164288,
"size" : 609456,
"uuid" : "bba77709-6cad-3592-ab03-09d0f7b8610e",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4882911232,
"size" : 174571520,
"uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
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"arch" : "x86_64",
"base" : 4407635968,
"size" : 8192,
"uuid" : "1eae6074-8612-3bc6-b16b-c173a995e90c",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
"name" : "_queue.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4301733888,
"size" : 20480,
"uuid" : "2f042ce6-bef0-3ad9-97f5-2da7655122a4",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
"name" : "select.cpython-39-darwin.so"
},
{
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"base" : 140703476920320,
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"size" : 4825072,
"uuid" : "c2615780-0140-315c-a455-7e03bb22d3d6",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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},
{
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"arch" : "x86_64",
"base" : 4416835584,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703472558080,
"size" : 21474836480,
"uuid" : "57815a20-af2c-3b56-9006-23abde7962b0"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 1660K 59 \nColorSync 248K 29 \nCoreAnimation 4332K 102 \nCoreGraphics 12K 2 \nCoreImage 24K 2 \nCoreUI image data 5176K 38 \nFoundation 32K 2 \nIOKit 7940K 1 \nKernel Alloc Once 1364K 4 \nMALLOC 727.7M 837 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 164K 41 \nStack 302.3M 42 \nStack Guard 56.0M 1 \nVM_ALLOCATE 140.9M 125 \n__CTF 756 1 \n__DATA 47.3M 761 \n__DATA_CONST 41.3M 389 \n__DATA_DIRTY 1823K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 212.8M 152 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1989K 2 \n__TEXT 919.3M 763 \ndyld private memory 288K 3 \nmapped file 530.5M 78 \nshared memory 3132K 33 \n=========== ======= ======= \nTOTAL 3.1G 3721 \nTOTAL, minus reserved VM space 3.0G 3721 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
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"factorPackIds" : {
"SIRI_UNDERSTANDING_TMDC" : "62cdf6dddb3b7109d6d765cd"
},
"deploymentId" : 240000007
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000012
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/eboni/Library/CloudStorage/OneDrive-HarvardUniversity/SPRING
> 2023/CB 201/Analysis 3 Worksheet/Assignment_Files/6ZZ6D_With_ConSurf.pdb"
6ZZ6D_With_ConSurf.pdb title:
Cryo-em structure of S.cerevisiae cohesin-SCC2-DNA complex [more info...]
Chain information for 6ZZ6D_With_ConSurf.pdb #1
---
Chain | Description | UniProt
A | structural maintenance of chromosomes protein 1,structural maintenance of
chromosomes protein 1,structural maintenance of chromosomes protein 1 |
SMC1_YEAST 2-71 87-195 1044-1224
B | structural maintenance of chromosomes protein 3,structural maintenance of
chromosomes protein 3,structural maintenance of chromosomes protein 3 |
SMC3_YEAST 2-228 997-1071 1104-1222
C | sister chromatid cohesion protein 1,sister chromatid cohesion protein
1,sister chromatid cohesion protein 1 | SCC1_YEAST 67-103 502-510 519-555
D | sister chromatid cohesion protein 2 | SCC2_YEAST 1-1493
F | DNA (34-mer) |
G | DNA (34-mer) |
Non-standard residues in 6ZZ6D_With_ConSurf.pdb #1
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> set bgColor white
> hide atoms
> show atoms
> show cartoons
> hide atoms
> show: ATP atoms
Unknown command: show: ATP atoms
> style stick
Changed 16597 atom styles
> show :ATP atoms
> hide #1/C:102_503 cartoons
> hide #1/B:228_998 cartoons
> color #1/A crimson
> color #1/B royal blue
> color #1/A: 82-99 blue
> color #1/F #8A2BE2
> ui tool show "Show Sequence Viewer"
> select #1/C:502-510
71 atoms, 71 bonds, 9 residues, 1 model selected
> open Q12158 fromDatabase uniprot
Summary of feedback from opening Q12158 fetched from uniprot
---
notes | Fetching Q12158 UniProt info from
https://www.uniprot.org/uniprot/Q12158.xml
Alignment identifier is Q12158
Associated 6ZZ6D_With_ConSurf.pdb chain C to Q12158 with 0 mismatches
Opened UniProt Q12158
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:541-544,551-554
60 atoms, 58 bonds, 8 residues, 1 model selected
> select /C:69-103,503-510,520-538
486 atoms, 488 bonds, 62 residues, 1 model selected
> select /C:541-544,551-554
60 atoms, 58 bonds, 8 residues, 1 model selected
> open P47037 fromDatabase uniprot
Summary of feedback from opening P47037 fetched from uniprot
---
notes | Fetching P47037 UniProt info from
https://www.uniprot.org/uniprot/P47037.xml
Alignment identifier is P47037
Opened UniProt P47037
> show :ATP atoms
> show :ATP atoms style stick
Expected ',' or a keyword
> show :ATP atoms, style stick
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> show :ATP atoms, style 'stick'
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> show :ATP atoms style 'stick'
Expected ',' or a keyword
> show :ATP atoms, 'stick'
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> hide sel cartoons
> show :ATP atoms
> style stick
Changed 16597 atom styles
> show sel atoms
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> show sel atoms
> select :ATP color sel yellow
Expected a keyword
> select :ATP 'color sel yellow'
Expected a keyword
> select :ATP 'color sel yellow'
Expected a keyword
> select :ATP
62 atoms, 66 bonds, 2 residues, 1 model selected
> color sel yellow
> open emdb:11585
Summary of feedback from opening 11585 fetched from emdb
---
note | Fetching compressed map 11585 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11585/map/emd_11585.map.gz
Opened emdb 11585 as #2, grid size 320,320,320, pixel 1.07, shown at level
0.00515, step 2, values float32
> hide sel atoms
> show sel cartoons
> hide sel atoms
> ui tool show "Volume Viewer"
> volume #2 step 1
> show #1 target m
> hide #!1 models
> show #!1 models
> volume #2 level -0.00139
> volume #2 level 0.005149
> volume #2 level 0.04298
> volume #2 level 0.05232
> volume #2 level 0.06259
> ui tool show "Volume Viewer"
> open emdb:11585
Opened emdb 11585 as #3, grid size 320,320,320, pixel 1.07, shown at level
0.00515, step 2, values float32
> hide #!3 models
> select add #2
62 atoms, 66 bonds, 2 residues, 3 models selected
> select subtract #2
62 atoms, 66 bonds, 2 residues, 1 model selected
> select add #2
62 atoms, 66 bonds, 2 residues, 3 models selected
> volume #2 level 0.05139
> select subtract #2
62 atoms, 66 bonds, 2 residues, 1 model selected
> select add #2
62 atoms, 66 bonds, 2 residues, 3 models selected
> volume #2 level 0.09529
> select subtract #2
62 atoms, 66 bonds, 2 residues, 1 model selected
> select add #2
62 atoms, 66 bonds, 2 residues, 3 models selected
> open P47037 fromDatabase uniprot
Summary of feedback from opening P47037 fetched from uniprot
---
note | Alignment identifier is P47037
Opened UniProt P47037
> volume #2 level 0.07942
> volume #2 level 0.07701
> volume #2 level 0.07846
> volume #2 color #ff40ff
> close #3
> surface dust #2
> volume #2 level 0.07425
> volume #2 level 0.05651
> undo
> volume #2 level 0.0785
> volume #2 level 0.06823
> volume #2 level 0.0388
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:37-49,57-65,125-136,150-228,998-1060,1127-1146,1161-1176,1213-1222
1771 atoms, 1776 bonds, 222 residues, 1 model selected
> volume #2 level 0.04938
> volume #2 level 0.08448
> hide #!2 models
> select
> /B:5-9,17-20,27-31,76-81,104-109,114-117,145-146,1067-1070,1106-1109,1150-1154,1180-1184,1196-1202,1207-1212
524 atoms, 520 bonds, 63 residues, 1 model selected
> select /B:37-49,57-65,125-136,150-228,998-1060,1127-1146,1161-1176,1213-1222
1771 atoms, 1776 bonds, 222 residues, 1 model selected
> show #!2 models
> volume #2 level 0.09121
> volume #2 level 0.1061
> volume #2 level 0.0941
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select
> /D:222-236,251-262,279-291,305-322,338-352,356-373,387-406,409-424,444-456,459-466,475-506,510-524,531-548,555-579,598-616,618-634,648-662,679-688,691-709,712-730,736-749,751-765,768-778,783-801,803-817,822-845,850-866,870-883,892-917,928-942,949-962,967-981,987-1001,1006-1022,1027-1049,1060-1075,1092-1104,1110-1147,1151-1175,1204-1221,1224-1242,1245-1258,1261-1302,1312-1320,1325-1341,1356-1368,1373-1398,1414-1434,1449-1454,1467-1473
6908 atoms, 6979 bonds, 875 residues, 1 model selected
> volume #2 level 0.08803
> volume #2 level 0.07635
> volume #2 level 0.07822
> volume #2 level 0.09176
> volume #2 level 0.08289
> volume #2 level 0.08102
> volume #2 level 0.08523
> volume #2 level 0.02498
> volume #2 level 0.06421
> volume #2 level 0.05487
> volume #2 level 0.03338
> volume #2 level 0.06141
> volume #2 level 0.03899
> volume #2 level 0.04599
> volume #2 level 0.08523
> volume #2 level 0.08056
> volume #2 level 0.07168
> volume #2 level 0.0558
> volume #2 level 0.04506
> volume #2 level 0.04926
> color zone #2 near #1 distance 4.5
> hide #!2 models
> color #1/A crimson
> color #1/B royal blue
> color #1/C green
> color #1/D #FFD700
> color #1/F grey
> color #1/G dark gray
> volume #2 color #942192
> volume #2 level 0.06701
> volume #2 level 0.08663
> volume #2 level 0.02451
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> show sel atoms
> hide sel atoms
> hide #!2 models
> show #!2 models
> hide #!1 models
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> show #!1 models
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> select add #2
6908 atoms, 6979 bonds, 875 residues, 3 models selected
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> volume #2 level 0.02825
> color zone #2 near #2 distance 4.5
color zone: No atoms specified.
> color #2/A crimson
> color #2/B royal blue
> select subtract #2
6908 atoms, 6979 bonds, 875 residues, 1 model selected
> select add #1
16597 atoms, 16989 bonds, 32 pseudobonds, 1988 residues, 3 models selected
> select subtract #1
Nothing selected
> color #2/B royal blue
> hide #!2 models
> show #!2 models
> select #3
Nothing selected
> color sel blue
> hide #!2 models
> save PDB.png transparentBackground true
> open "/Users/eboni/Library/CloudStorage/OneDrive-HarvardUniversity/SPRING
> 2023/CB 201/Analysis 3 Worksheet/Assignment_Files/integrative_model.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.
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: 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: 499.40.2.0.0
OS Loader Version: 564.40.4~66
SMC Version (system): 2.44f6
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 3 days, 2 hours, 53 minutes
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 Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
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: 1.6rc202304072249
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
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: 1.10.2
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: 6.2.0
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: 3.2.0
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
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: 6.2
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
Change History (1)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in msgpack_deserialize during session restore |
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Looks like it was doing garbage collection