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Opened 21 months ago
Closed 21 months ago
#14411 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002970bb000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002960af000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002950a3000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000294097000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029308b000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029207f000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000291073000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000290067000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028f05b000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028e04f000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028d043000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001d9849000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.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-1.6.1.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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.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":"2024-01-17 22:09:53.00 +0900","app_version":"1.6.1","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"B4DD2E13-34D4-4F1B-AF05-00A1B58108A3"}
{
"uptime" : 610000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 14833,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-01-17 22:09:43.3200 +0900",
"codeSigningMonitor" : 1,
"incident" : "B4DD2E13-34D4-4F1B-AF05-00A1B58108A3",
"pid" : 35664,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-05 13:06:06.2894 +0900",
"procStartAbsTime" : 6753616386980,
"procExitAbsTime" : 14669745025278,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"71729226-441C-50DF-84AE-FCE7BE4F4FDC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3BF76BAA-6565-346B-F892-86061A0F3DCB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 42431,
"sleepWakeUUID" : "D760855A-3E14-452D-B920-691138F3DA34",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4309319656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100db0000-100db4000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":35664},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4309319656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100db0000-100db4000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6493400333},{"value":5369363480},{"value":5183327690515668744},{"value":0},{"value":6157527336},{"value":18367201322503662328},{"value":18367201330129206008},{"value":78},{"value":0},{"value":49},{"value":16},{"value":5724176384},{"value":196607},{"value":328},{"value":8095773504},{"value":0},{"value":11},{"value":7944310784,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":7944311008,"symbolLocation":224,"symbol":"_main_thread"},{"value":5636033024},{"value":1},{"value":32769},{"value":32768},{"value":7944317256,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6493215936},"cpsr":{"value":1073745920},"fp":{"value":5369363280},"sp":{"value":5369363248},"esr":{"value":1442840704,"description":" Address size 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}
],
"experiments" : [
{
"treatmentId" : "52e9806b-48cf-4718-ba06-6aaa79468566",
"experimentId" : "6553f184553f07431fda611f",
"deploymentId" : 400000004
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/ihansol/Documents/Lab_Roh/2024_internship/7xw2.pdb
7xw2.pdb title:
Cryo-em structure of human dicer-pre-miRNA In A dicing state [more info...]
Chain information for 7xw2.pdb #1
---
Chain | Description | UniProt
A | endoribonuclease dicer | DICER_HUMAN 1-1922
C | RNA (73-mer) |
Non-standard residues in 7xw2.pdb #1
---
CA — calcium ion
> open /Users/ihansol/Documents/Lab_Roh/2024_internship/emd_33489.map
Opened emd_33489.map as #2, grid size 280,280,280, pixel 0.849, shown at level
0.0531, step 2, values float32
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.1408
> volume #2 step 1
> volume #2 level 0.355
> volume #2 level 0.1499
> volume #2 level 0.1134
> show #!1 models
> transparency 50
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J762_007_volume_map.mrc
Opened cryosparc_P4_J762_007_volume_map.mrc as #3, grid size 450,450,450,
pixel 1.08, shown at level 0.00638, step 2, values float32
> hide #!1 models
> hide #!2 models
> volume #3 level -0.02735
> volume #3 level 0.0163
> show #!2 models
> close session
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J762_007_volume_map.mrc
> format mrc
Opened cryosparc_P4_J762_007_volume_map.mrc as #1, grid size 450,450,450,
pixel 1.08, shown at level 0.00638, step 2, values float32
> volume #1 level 0.02225
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_00_00281_volume.mrc
Opened cryosparc_P4_J628_class_00_00281_volume.mrc as #2, grid size
168,168,168, pixel 2.89, shown at level 0.0338, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_01_00281_volume.mrc
Opened cryosparc_P4_J628_class_01_00281_volume.mrc as #3, grid size
168,168,168, pixel 2.89, shown at level 0.0338, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_02_00281_volume.mrc
Opened cryosparc_P4_J628_class_02_00281_volume.mrc as #4, grid size
168,168,168, pixel 2.89, shown at level 0.0371, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_03_00281_volume.mrc
Opened cryosparc_P4_J628_class_03_00281_volume.mrc as #5, grid size
168,168,168, pixel 2.89, shown at level 0.0378, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_04_00281_volume.mrc
Opened cryosparc_P4_J628_class_04_00281_volume.mrc as #6, grid size
168,168,168, pixel 2.89, shown at level 0.0349, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_05_00281_volume.mrc
Opened cryosparc_P4_J628_class_05_00281_volume.mrc as #7, grid size
168,168,168, pixel 2.89, shown at level 0.0322, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_06_00281_volume.mrc
Opened cryosparc_P4_J628_class_06_00281_volume.mrc as #8, grid size
168,168,168, pixel 2.89, shown at level 0.0315, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_07_00281_volume.mrc
Opened cryosparc_P4_J628_class_07_00281_volume.mrc as #9, grid size
168,168,168, pixel 2.89, shown at level 0.0315, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_08_00281_volume.mrc
Opened cryosparc_P4_J628_class_08_00281_volume.mrc as #10, grid size
168,168,168, pixel 2.89, shown at level 0.0319, step 1, values float32
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_09_00281_volume.mrc
Opened cryosparc_P4_J628_class_09_00281_volume.mrc as #11, grid size
168,168,168, pixel 2.89, shown at level 0.0314, step 1, values float32
> volume #11 level 0.1987
> volume #10 level 0.2681
> volume #9 level 0.2027
> volume #8 level 0.1658
> volume #7 level 0.32
> volume #6 level 0.3003
> volume #5 level 0.3925
> volume #4 level 0.5084
> volume #3 level 0.2929
> volume #2 level 0.1345
> volume #3 level 0.2032
> volume #4 level 0.08478
> volume #5 level 0.09519
> volume #6 level 0.06286
> volume #7 level 0.05658
> volume #8 level 0.06986
> volume #9 level 0.1362
> volume #10 level 0.07732
> volume #11 level 0.06489
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J637_004_volume_map.mrc
Opened cryosparc_P4_J637_004_volume_map.mrc as #12, grid size 450,450,450,
pixel 1.08, shown at level 0.00971, step 2, values float32
> volume #12 step 1
> volume #12 level 0.03285
> volume #6 level 0.0908
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628__mask_solvent.mrc
Opened cryosparc_P4_J628__mask_solvent.mrc as #13, grid size 168,168,168,
pixel 2.89, shown at level 0.369, step 1, values float32
> hide #!1-13 target m
> volume #13 level 0.1645
> ui mousemode right "map eraser"
> volume erase #13 center 247.68,320.3,258.76 radius 39.366
Opened cryosparc_P4_J628__mask_solvent.mrc copy as #15, grid size 168,168,168,
pixel 2.89, shown at step 1, values float32
> volume erase #15 center 249.07,272.84,282.79 radius 39.366
> volume erase #15 center 247.55,229.8,277.28 radius 39.366
> volume erase #15 center 244.71,198.34,276.38 radius 39.366
> volume erase #15 center 236.42,172.27,255.93 radius 39.366
> volume erase #15 center 203.93,231.34,282.94 radius 39.366
> volume erase #15 center 287.67,230.12,271.24 radius 39.366
> volume erase #15 center 288.1,254.01,273.7 radius 39.366
> volume erase #15 center 219.51,267.66,284.45 radius 39.366
> volume erase #15 center 195.34,221.92,270.84 radius 39.366
> volume erase #15 center 305.61,238.97,252.49 radius 39.366
> volume erase #15 center 301.63,280.66,247.38 radius 39.366
> volume erase #15 center 279.68,300.27,260.37 radius 39.366
> volume erase #15 center 258.62,315.49,259.64 radius 39.366
> volume erase #15 center 246.98,313.49,258.11 radius 39.366
> volume erase #15 center 217.18,190.29,265.24 radius 39.366
> volume erase #15 center 200.42,193.68,261.27 radius 39.366
> volume erase #15 center 265.5,184.92,266.15 radius 39.366
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #15
2 models selected
> view matrix models #15,1,0,0,-3.496,0,1,0,54.992,0,0,1,-127.27
> ui mousemode right "map eraser"
> volume erase #15 center 228.15,254.76,186.75 radius 39.366
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,-41.409,0,1,0,-35.442,0,0,1,-30.179
> view matrix models #15,1,0,0,-32.266,0,1,0,-78.28,0,0,1,-6.6445
> volume #15 level 1
> view matrix models #15,1,0,0,-42.821,0,1,0,-121.44,0,0,1,-27.723
> save
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask.mrc
> models #15
> volume #15 gaussian 10
Expected a keyword
> molmap #15 10
No atoms specified
> volume #15 level 1
> view matrix models #15,1,0,0,-33.65,0,1,0,-68.387,0,0,1,-11.048
> view matrix models #15,1,0,0,-20.912,0,1,0,-60.78,0,0,1,-9.8763
> view matrix models #15,1,0,0,-13.717,0,1,0,-60.179,0,0,1,-4.9026
> view matrix models #15,1,0,0,-9.9415,0,1,0,-53.629,0,0,1,2.5346
> view matrix models #15,1,0,0,-10.972,0,1,0,-50.663,0,0,1,-1.5542
> gaussian #15 10
Unknown command: gaussian #15 10
> toolshed show
> ui mousemode right "contour level"
> ui mousemode right "map eraser"
> ui mousemode right "translate selected models"
> volume #15 level 1
> view matrix models #15,1,0,0,-10.943,0,1,0,-50.86,0,0,1,-1.9568
> ui tool show "Hide Dust"
> surface dust #15 size 17.36
> ui tool show "Map Coordinates"
> ui tool show "Map Statistics"
> measure mapstats sel
Map Hsp90_side_mask.mrc #15, minimum 0, maximum 1, mean 0.003797, SD 0.05919,
RMS 0.05931
> ui tool show "Measure Volume and Area"
> ui tool show "Measure and Color Blobs"
> ui tool show "Segment Map"
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
> ui tool show "Show Volume Menu"
> volume gaussian #15 sDev 10
Opened Hsp90_side_mask.mrc gaussian as #16, grid size 168,168,168, pixel 2.89,
shown at step 1, values float32
> volume #16 level 0.8772
> measure blob #!16.1 triangleNumber 1610 color #0000ccff outline true
Surface Hsp90_side_mask.mrc gaussian #16.1 blob:
volume = 1.2811e+05
area = 12868
size = 73.274 59.14 50.995
> ui mousemode right "pick blobs"
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,-10.73,0,1,0,-50.037,0,0,1,-2.1026
> view matrix models #15,1,0,0,-4.6413,0,1,0,-23.883,0,0,1,-20.686
> ui mousemode right "pick blobs"
> ui mousemode right "map eraser"
> ui mousemode right "pick blobs"
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,28.989,0,1,0,-53.863,0,0,1,-33.833
> hide #!16 models
> show #!16 models
> select add #16
5 models selected
> select subtract #15
3 models selected
> view matrix models #16,1,0,0,17.505,0,1,0,-76.371,0,0,1,-13.216
> view matrix models #16,1,0,0,13.211,0,1,0,-40.586,0,0,1,10.077
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.32653,-0.50733,-0.79749,615.5,-0.025284,-0.83875,0.54393,306.31,-0.94485,0.19777,0.26105,336.53
> view matrix models
> #16,-0.84434,-0.47578,-0.24641,620.33,0.0088869,-0.47227,0.88141,140.24,-0.53573,0.74202,0.40299,76.738
> view matrix models
> #16,-0.7913,-0.55068,-0.26569,629.9,0.035228,-0.47489,0.87934,135.01,-0.61041,0.68647,0.39518,109.78
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,633.93,0.069313,-0.46188,0.88423,122.68,-0.6679,0.6369,0.38504,137.71
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,634.33,0.069313,-0.46188,0.88423,122.11,-0.6679,0.6369,0.38504,144.08
> volume #16 level 0.807
No map chosen to save
> save
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask_0.807.mrc
> models #16
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask_0.807.mrc
Opened Hsp90_side_mask_0.807.mrc as #17, grid size 168,168,168, pixel 2.89,
shown at level 0.0306, step 1, values float32
> volume #17 level 0.844
> volume #16 style image
> volume #16 style surface
> save
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask_0.807.mrc
> models #16
> close #17
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,629.61,0.069313,-0.46188,0.88423,164.74,-0.6679,0.6369,0.38504,150.17
> volume #16 change image level -2.29e-16,0 level 0.03057,0.8 level 0.9991,1
> volume #16 level 0.7996
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,628.25,0.069313,-0.46188,0.88423,98.537,-0.6679,0.6369,0.38504,134.8
> volume gaussian #11 sDev 10
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #17, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #17 level 0.007198
> volume gaussian #17 sDev 20
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #18, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #18 level 0.004995
> volume gaussian #18 sDev 20
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #19, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #19 level 0.004625
> volume gaussian #19 sDev 20
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #20, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #20 level 0.004777
> volume gaussian #20 sDev 20
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #21, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #21 level 0.002647
> volume gaussian #21 sDev 20
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #22, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #22 level 0.001976
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> volume #22 level 0.002122
> volume gaussian #22 sDev 20
Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #23, grid size
168,168,168, pixel 2.89, shown at step 1, values float32
> volume #23 level 0.001856
No map chosen to save
> save
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/J628_mask_0.00186.mrc
> models #23
> save /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Mask_making.cxs
> open
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J826_class_00_final_volume.mrc
Opened cryosparc_P4_J826_class_00_final_volume.mrc as #24, grid size
192,192,192, pixel 2.53, shown at level 0.0456, step 1, values float32
> hide #14 models
> ui mousemode right "translate selected models"
> volume #24 level 0.1245
> close #22
> close #20
> close #21
> close #19
> close #18
> close #17
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,615.77,0.069313,-0.46188,0.88423,102.42,-0.6679,0.6369,0.38504,181.5
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,613.81,0.069313,-0.46188,0.88423,100.68,-0.6679,0.6369,0.38504,173.94
> view matrix models
> #16,-0.74101,-0.61727,-0.26434,613.96,0.069313,-0.46188,0.88423,101.83,-0.6679,0.6369,0.38504,172.53
> volume #24 level 0.1087
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.33169,0.15469,-0.93062,461.39,-0.45283,-0.8915,0.013213,507.66,-0.8276,0.42579,0.36575,266.32
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.33169,0.15469,-0.93062,469.01,-0.45283,-0.8915,0.013213,510.72,-0.8276,0.42579,0.36575,265.42
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.17387,0.30096,-0.93765,396.86,-0.48568,-0.85451,-0.18421,549.34,-0.85667,0.42337,0.29474,287.29
> view matrix models
> #16,-0.13114,0.30798,-0.94231,385.87,-0.8357,-0.54567,-0.062046,532.66,-0.5333,0.77935,0.32894,115.87
> view matrix models
> #16,-0.16063,0.25482,-0.95356,408.21,-0.82899,-0.55918,-0.0097837,523.82,-0.5357,0.78891,0.30106,119.72
> view matrix models
> #16,-0.23167,0.14386,-0.9621,454.11,-0.80783,-0.57946,0.10788,499.99,-0.54198,0.8022,0.25046,128.18
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.23167,0.14386,-0.9621,454.36,-0.80783,-0.57946,0.10788,497.04,-0.54198,0.8022,0.25046,129.71
> save
> /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/J827_side_mask_0.8.mrc
> models #16
> save /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Mask_making.cxs
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
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
Model Number: Z15J004J4KH/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 26 days, 18 hours, 58 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
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
LG FULL HD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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: 2.2.5
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: 1.6.1
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
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 21 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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