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Opened 2 years ago
Closed 2 years ago
#9974 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-10.16-x86_64-i386-64bit
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 0x000070001ca3b000 (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 0x000070001ba38000 (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 0x000070001aa35000 (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 0x0000700019a32000 (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 0x0000700018a2f000 (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 0x0000700017a2c000 (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 0x0000700016a29000 (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 0x0000700015a26000 (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 0x0000700014a23000 (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 0x0000700013a20000 (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 0x0000700012a1d000 (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 0x00007ff847f80640 (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":"2023-10-12 18:12:24.00 -0400","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","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 13.4.1 (22F82)","roots_installed":0,"name":"ChimeraX","incident_id":"30E03418-3815-4C65-AB12-E2E9172FC0DA"}
{
"uptime" : 1100000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 62616,
"osVersion" : {
"train" : "macOS 13.4.1",
"build" : "22F82",
"releaseType" : "User"
},
"captureTime" : "2023-10-12 18:10:27.5294 -0400",
"incident" : "30E03418-3815-4C65-AB12-E2E9172FC0DA",
"pid" : 31917,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-09-26 13:26:40.5347 -0400",
"procStartAbsTime" : 615090186622108,
"procExitAbsTime" : 1149886173760649,
"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":"B06F2E52-8747-5D43-A067-C981D90F2A0D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3E9CC359-36F5-C643-CB1A-D9479CD21E44",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 79,
"bridgeVersion" : {"build":"20P5060","train":"7.5"},
"sleepWakeUUID" : "E5870146-199F-4193-9E80-CF6650C32180",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486499816\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe3b000-7fffffe3c000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486499816\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe3b000-7fffffe3c000 [ 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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"sharedCache" : {
"base" : 140703200624640,
"size" : 21474836480,
"uuid" : "e15dc6ac-9320-3b97-95de-b6e917a43ec4"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 9088K 11 \nCG image 284K 28 \nColorSync 264K 30 \nCoreAnimation 204K 26 \nCoreGraphics 16K 3 \nCoreUI image data 560K 8 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.5G 868 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 140K 35 \nStack 331.3M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 292.4M 279 \n__CTF 824 1 \n__DATA 47.5M 774 \n__DATA_CONST 41.1M 396 \n__DATA_DIRTY 1802K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 202.7M 153 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 946.5M 776 \ndyld private memory 292K 4 \nmapped file 214.4M 59 \nshared memory 3004K 30 \n=========== ======= ======= \nTOTAL 3.9G 3775 \nTOTAL, minus reserved VM space 3.7G 3775 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "4a5cf050672ae1fbf75a2a0cdef146f29a5901d5",
"trialInfo" : {
"rollouts" : [
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jeongmin/Desktop/A3A_Cas9.cxs
Opened cryosparc_P4_J65_003_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 1.74, shown at level 0.306, step 1, values float32
Opened cryosparc_P4_J65_003_volume_map_sharp.mrc z flip as #2, grid size
128,128,128, pixel 1.74, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J87_004_volume_map_sharp.mrc as #4, grid size 256,256,256,
pixel 0.87, shown at level 0.0788, step 1, values float32
Opened cryosparc_P4_J87_004_volume_map_sharp.mrc z flip as #5, grid size
256,256,256, pixel 0.87, shown at level 0.06, step 1, values float32
Log from Mon May 1 13:44:56 2023 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: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jeongmin/Downloads/cryosparc_P4_J65_003_volume_map_sharp.mrc
Opened cryosparc_P4_J65_003_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 1.74, shown at level 0.228, step 1, values float32
> volume flip #1
Opened cryosparc_P4_J65_003_volume_map_sharp.mrc z flip as #2, grid size
128,128,128, pixel 1.74, shown at step 1, values float32
> open 5f9r
Summary of feedback from opening 5f9r fetched from pdb
---
notes | Fetching compressed mmCIF 5f9r from
http://files.rcsb.org/download/5f9r.cif
Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
5f9r title:
Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9
in complex with single-guided RNA and double-stranded DNA primed for target
DNA cleavage [more info...]
Chain information for 5f9r #3
---
Chain | Description | UniProt
A | RNA (116-MER) |
B | CRISPR-associated endonuclease Cas9/Csn1 | CAS9_STRP1
C | DNA (30-MER) |
D | DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') |
Non-standard residues in 5f9r #3
---
GTP — guanosine-5'-triphosphate
SO4 — sulfate ion
> ui mousemode right "translate selected models"
> select add #3
13652 atoms, 14243 bonds, 146 pseudobonds, 1530 residues, 2 models selected
> view matrix models #3,1,0,0,83.021,0,1,0,101.2,0,0,1,174.08
> select subtract #3
Nothing selected
> select add #3
13652 atoms, 14243 bonds, 146 pseudobonds, 1530 residues, 2 models selected
> view matrix models
> #3,-0.82856,-0.29632,-0.47506,-9.641,-0.54532,0.61943,0.56474,115.79,0.12692,0.72698,-0.67482,91.359
> view matrix models
> #3,-0.82856,-0.29632,-0.47506,47.527,-0.54532,0.61943,0.56474,141.63,0.12692,0.72698,-0.67482,85.91
> view matrix models
> #3,-0.92924,-0.10474,-0.35432,55.835,-0.29773,0.78016,0.55018,145.39,0.2188,0.61674,-0.75614,87.65
> view matrix models
> #3,-0.98368,-0.021961,-0.17858,73.63,-0.10124,0.88807,0.44843,157.62,0.14875,0.45919,-0.8758,73.018
> select subtract #3
Nothing selected
> fitmap #3 inMap #2
Fit molecule 5f9r (#3) to map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip
(#2) using 13652 atoms
average map value = 0.2545, steps = 140
shifted from previous position = 13.3
rotated from previous position = 26.5 degrees
atoms outside contour = 6701, contour level = 0.22835
Position of 5f9r (#3) relative to cryosparc_P4_J65_003_volume_map_sharp.mrc z
flip (#2) coordinates:
Matrix rotation and translation
-0.89649491 -0.44014457 -0.05069144 75.17382605
-0.40363710 0.76419720 0.50307030 136.66721882
-0.18268540 0.47146091 -0.86275759 61.03807044
Axis -0.22489751 0.93912335 0.25974687
Axis point 54.47513854 0.00000000 9.67472743
Rotation angle (degrees) 175.97021224
Shift along axis 127.29541780
> transparency #2.1 50
> lighting soft
> set bgColor white
> graphics silhouettes true
> lighting simple
> volume #2 level 0.1366
> volume #2 level 0.1999
> select :1048
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 7 atom styles
> view matrix models
> #3,-0.89649,-0.44014,-0.050691,84.036,-0.40364,0.7642,0.50307,108.81,-0.18269,0.47146,-0.86276,41.021
> ui mousemode right translate
[Repeated 1 time(s)]
> volume #2 level 0.2283
> volume #2 level 0.1461
> surface dust #2 size 17.4
> volume #2 level 0.03855
> volume #2 level 0.06702
> sel:1065
Unknown command: sel:1065
> select :1065
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 7 atom styles
> volume #2 level 0.1334
> volume #2 level 0.05437
> volume #1 level 0.2568
> hide #!1 models
> volume #2 level 0.1588
> volume #2 level 0.07018
[Repeated 1 time(s)]
> volume #2 level 0.1145
> volume #2 level 0.105
> volume #2 level 0.1746
> volume #2 level 0.1461
> volume #2 level 0.105
> volume #2 level 0.1271
> volume #2 level 0.1018
[Repeated 1 time(s)]
> volume #2 level 0.05437
> volume #2 level 0.124
> volume #2 level 0.09233
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #2 level -0.07533
> volume #2 level -0.03737
> volume #2 level 0.01008
> volume #2 level 0.03222
> volume #2 level 0.086
> open /Users/jeongmin/Downloads/cryosparc_P4_J87_004_volume_map_sharp.mrc
Opened cryosparc_P4_J87_004_volume_map_sharp.mrc as #4, grid size 256,256,256,
pixel 0.87, shown at level 0.0788, step 1, values float32
> hide #!2 models
> volume flip #4
Opened cryosparc_P4_J87_004_volume_map_sharp.mrc z flip as #5, grid size
256,256,256, pixel 0.87, shown at step 1, values float32
> hide #!3 models
> volume #5 level 0.05529
> volume #5 level 0.0905
> show #!3 models
> ui mousemode right "translate selected atoms"
> undo
> select add #3
13652 atoms, 14243 bonds, 146 pseudobonds, 1530 residues, 2 models selected
> lighting simple
> fitmap #3 inMap #5
Fit molecule 5f9r (#3) to map cryosparc_P4_J87_004_volume_map_sharp.mrc z flip
(#5) using 13652 atoms
average map value = 0.09574, steps = 164
shifted from previous position = 4.98
rotated from previous position = 16.7 degrees
atoms outside contour = 7777, contour level = 0.090496
Position of 5f9r (#3) relative to cryosparc_P4_J87_004_volume_map_sharp.mrc z
flip (#5) coordinates:
Matrix rotation and translation
-0.98429173 -0.16938333 -0.04979038 72.55794778
-0.17288153 0.86752810 0.46637642 138.85420298
-0.03580183 0.46765829 -0.88318398 64.46642418
Axis 0.08855022 -0.96631423 -0.24165197
Axis point 42.58520987 0.00000000 15.03080350
Rotation angle (degrees) 179.58528399
Shift along axis -143.33020794
> select subtract #3
Nothing selected
> show #!2 models
> hide #!2 models
> volume #5 level 0.05998
> color #5 #99ffffff models
> surface dust #5 size 8.7
> transparency #5.1 50
> volume #5 level 0.03885
> volume #5 level 0.02242
> volume #5 level 0.07406
> volume #5 level 0.04824
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> show #!2 models
> hide #!3 models
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.98909,0.13297,-0.063354,217.89,-0.14623,-0.83499,0.53048,164.38,0.017637,0.53396,0.84532,-46.764
> fitmap #2 inMap #5
Fit map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip in map
cryosparc_P4_J87_004_volume_map_sharp.mrc z flip using 54341 points
correlation = 0.885, correlation about mean = 0.7625, overlap = 1342
steps = 148, shift = 6.26, angle = 12.6 degrees
Position of cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) relative to
cryosparc_P4_J87_004_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
-0.99935737 -0.03549261 -0.00501284 227.02537480
0.02404855 -0.76758983 0.64049007 123.43320020
-0.02658046 0.63995792 0.76795010 -42.17253956
Axis -0.00840296 0.34056344 0.94018399
Axis point 112.28605897 71.26671330 0.00000000
Rotation angle (degrees) 178.18544722
Shift along axis 0.47920364
> volume #2 level 0.1381
> volume #5 level 0.05998
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right translate
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> volume #1 level 0.3057
> hide #!1 models
> volume #2 level 0.2098
> show #!5 models
> volume #5 level 0.07641
> hide #!2 models
> show #!2 models
> show #!3 models
> open 6VPC
Summary of feedback from opening 6VPC fetched from pdb
---
notes | Fetching compressed mmCIF 6vpc from
http://files.rcsb.org/download/6vpc.cif
Fetching CCD 8AZ from http://ligand-expo.rcsb.org/reports/8/8AZ/8AZ.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
6vpc title:
Structure of the SpCas9 DNA adenine base editor - ABE8e [more info...]
Chain information for 6vpc #6
---
Chain | Description | UniProt
A | Cas9 (SpCas9) single-guide RNA (sgRNA) |
B | CRISPR-associated endonuclease Cas9 | A0A4U7H5M9_STRPY
C | DNA target strand (TS) |
D | DNA non-target strand (NTS) |
E F | t-RNA adenine deaminase A v8e (TadA-8e) |
Non-standard residues in 6vpc #6
---
8AZ — 8-aza-nebularine-5'-monophosphate
MG — magnesium ion
ZN — zinc ion
> hide #!2 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> ui mousemode right "translate selected atoms"
[Repeated 1 time(s)]
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!5 models
> select add #6
16309 atoms, 16926 bonds, 157 pseudobonds, 1792 residues, 4 models selected
> ui mousemode right "translate selected atoms"
> hide #!5 models
> select subtract #6
Nothing selected
> volume flip #6
[Repeated 1 time(s)]
> show #!5 models
> hide #!6 models
> show #!3 models
> lighting simple
> view
> volume #2 level 0.1707
> volume #2 level 0.1349
> volume #5 level 0.09519
> volume #5 level 0.121
> volume #5 level 0.03651
> volume #5 level 0.04824
> volume #5 level 0.05998
> hide #!5 models
> show #!3 cartoons
[Repeated 2 time(s)]
> style #!3 sphere
Changed 13652 atom styles
> style #!3 sphere
Changed 13652 atom styles
> style #!3 sphere
Changed 13652 atom styles
> style #!3 stick
Changed 13652 atom styles
> show #!3 surfaces
[Repeated 1 time(s)]
> style #!3 sphere
Changed 13652 atom styles
> style #!3 sphere
Changed 13652 atom styles
> show #!3 surfaces
> show #!3 cartoons
> show #!3 atoms
> undo
[Repeated 2 time(s)]
> show #!3 atoms
[Repeated 1 time(s)]
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> style #!3 stick
Changed 13652 atom styles
> style #!3 stick
Changed 13652 atom styles
> show #!3 surfaces
> style #!3 stick
Changed 13652 atom styles
> show #!3 surfaces
> nucleotides #!3 atoms
> style nucleic & #!3 stick
Changed 3491 atom styles
> rainbow #!3
[Repeated 1 time(s)]
> view #3 clip false
> show #!3 cartoons
[Repeated 1 time(s)]
> show #!3 target m
> style #!3 sphere
Changed 13652 atom styles
> hide #!3 target m
> view #3 clip false
> show #!3 models
> hide #!3 models
> show #!3 models
> select :1063
13 atoms, 11 bonds, 2 residues, 2 models selected
> style sel & #!3 sphere
Changed 8 atom styles
> style sel & #!3 sphere
Changed 8 atom styles
> open 5f9r
5f9r title:
Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9
in complex with single-guided RNA and double-stranded DNA primed for target
DNA cleavage [more info...]
Chain information for 5f9r #7
---
Chain | Description | UniProt
A | RNA (116-MER) |
B | CRISPR-associated endonuclease Cas9/Csn1 | CAS9_STRP1
C | DNA (30-MER) |
D | DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') |
Non-standard residues in 5f9r #7
---
GTP — guanosine-5'-triphosphate
SO4 — sulfate ion
> style sel & #!3 sphere
Changed 8 atom styles
> style sel & #!3 stick
Changed 8 atom styles
> select add #3
13657 atoms, 14247 bonds, 146 pseudobonds, 1531 residues, 4 models selected
> select subtract #3
5 atoms, 4 bonds, 1 residue, 5 models selected
> style #!3,7 stick
Changed 27304 atom styles
> style #!3,7 sphere
Changed 27304 atom styles
> style #!3,7 ball
Changed 27304 atom styles
> nucleotides #!3,7 atoms
> style nucleic & #!3,7 stick
Changed 6982 atom styles
> select :1048
20 atoms, 17 bonds, 3 residues, 3 models selected
> hide #!7 models
> hide #!3 models
> show #!3 models
> show sel & #!3 atoms
[Repeated 2 time(s)]
> style sel & #!3 sphere
Changed 7 atom styles
> style sel & #!3 sphere
Changed 7 atom styles
> style sel & #!3 sphere
Changed 7 atom styles
> hide #!2 models
> hide sel & #!3 surfaces
[Repeated 6 time(s)]
> select add #3
13665 atoms, 14254 bonds, 146 pseudobonds, 1532 residues, 5 models selected
> select subtract #3
13 atoms, 11 bonds, 2 residues, 6 models selected
> select add #3
13665 atoms, 14254 bonds, 146 pseudobonds, 1532 residues, 4 models selected
> hide sel & #!3 surfaces
[Repeated 1 time(s)]
> hide sel & #!3 atoms
> show #!2 models
> select subtract #3
13 atoms, 11 bonds, 2 residues, 6 models selected
> hide #!3 models
> show #!6 models
> hide sel & #!6 atoms
> select add #6
16316 atoms, 16932 bonds, 157 pseudobonds, 1793 residues, 5 models selected
> select add #7
29961 atoms, 31169 bonds, 303 pseudobonds, 3322 residues, 6 models selected
> select subtract #7
16309 atoms, 16926 bonds, 157 pseudobonds, 1792 residues, 4 models selected
> select subtract #6
Nothing selected
> select add #6
16309 atoms, 16926 bonds, 157 pseudobonds, 1792 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> fitmap #6 inMap #2
Fit molecule 6vpc (#6) to map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip
(#2) using 16309 atoms
average map value = 0.09211, steps = 144
shifted from previous position = 12.2
rotated from previous position = 5.57 degrees
atoms outside contour = 11604, contour level = 0.13485
Position of 6vpc (#6) relative to cryosparc_P4_J65_003_volume_map_sharp.mrc z
flip (#2) coordinates:
Matrix rotation and translation
-0.99780088 0.00375893 0.06617603 221.43948330
0.03833365 -0.78176037 0.62239959 129.04354049
0.05407335 0.62356763 0.77989709 -60.16807777
Axis 0.03186975 0.33021967 0.94336593
Axis point 111.09796843 76.12908193 0.00000000
Rotation angle (degrees) 178.94998492
Shift along axis -7.09057903
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.15601,0.52519,0.83656,-40.238,0.96317,0.26866,0.010959,-37.785,-0.21899,0.80747,-0.54776,125.53
> view matrix models
> #6,0.41847,-0.87223,0.25319,133.94,0.033701,-0.26367,-0.96402,264.39,0.90761,0.41195,-0.080941,-23.145
> view matrix models
> #6,-0.85794,-0.3921,0.33197,218.68,-0.019499,-0.62084,-0.78369,279.42,0.51339,-0.67883,0.525,70.677
> view matrix models
> #6,-0.85794,-0.3921,0.33197,235.82,-0.019499,-0.62084,-0.78369,277.37,0.51339,-0.67883,0.525,65.184
> view matrix models
> #6,-0.95854,-0.2833,0.030828,262.48,0.14341,-0.57305,-0.80688,257.13,0.24625,-0.769,0.58991,106.19
> fitmap #6 inMap #2
Fit molecule 6vpc (#6) to map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip
(#2) using 16309 atoms
average map value = 0.2222, steps = 128
shifted from previous position = 10.2
rotated from previous position = 18.9 degrees
atoms outside contour = 6064, contour level = 0.13485
Position of 6vpc (#6) relative to cryosparc_P4_J65_003_volume_map_sharp.mrc z
flip (#2) coordinates:
Matrix rotation and translation
0.99458213 0.01889308 0.10222251 -22.63766958
-0.09874880 -0.13554974 0.98583718 27.10701277
0.03248173 -0.99059039 -0.13294968 237.70773492
Axis -0.99761454 0.03520211 -0.05938050
Axis point 0.00000000 117.19763526 107.83568756
Rotation angle (degrees) 97.87189415
Shift along axis 9.42268886
> ui mousemode right translate
[Repeated 2 time(s)]
> select subtract #6
Nothing selected
> hide #!6 models
> show #!3 models
> show #!3 atoms
> hide #!3 atoms
> select :1048
20 atoms, 17 bonds, 3 residues, 3 models selected
> show sel & #!3 atoms
> select :1063
21 atoms, 18 bonds, 3 residues, 3 models selected
> show sel & #!3 atoms
> select :1063
21 atoms, 18 bonds, 3 residues, 3 models selected
> show sel & #!3 atoms
[Repeated 1 time(s)]
> style sel & #!3 sphere
Changed 8 atom styles
> show #!6 models
> hide #!6 models
> volume #2 level 0.07949
> volume #2 level 0.2032
> save /Users/jeongmin/Desktop/A3A_Cas9.cxs
——— End of log from Mon May 1 13:44:56 2023 ———
opened ChimeraX session
> save /Users/jeongmin/Desktop/image1.png supersample 3
> save /Users/jeongmin/Desktop/image2.png supersample 3
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> open /Users/jeongmin/Downloads/cryosparc_P4_J118_class_01_final_volume.mrc
Opened cryosparc_P4_J118_class_01_final_volume.mrc as #8, grid size
128,128,128, pixel 1.66, shown at level 1.29, step 1, values float32
> hide #!5 models
> volume #2 level 0.1446
> volume #2 level 0.1186
> hide #!2 models
> volume #2 level 0.1316
> volume flip #8
Opened cryosparc_P4_J118_class_01_final_volume.mrc z flip as #9, grid size
128,128,128, pixel 1.66, shown at step 1, values float32
> volume #2 level 0.1609
> volume #2 level 0.1804
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!2 models
> show #!8 models
> volume #8 level 1.596
> volume #8 level 1.388
> volume #9 level 1.405
> hide #!8 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> hide #!2 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> show #!5 models
> hide #!4 models
> volume #5 level 0.0459
> save /Users/jeongmin/Desktop/image3.png supersample 3
> volume #5 level 0.05763
> open "/Users/jeongmin/Downloads/5keg (1).pdb"
5keg (1).pdb title:
Crystal structure of APOBEC3A In complex with A single-stranded DNA [more
info...]
Chain information for 5keg (1).pdb #10
---
Chain | Description | UniProt
A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199
B | DNA (5'-D(*TP*TP*CP*TP*T)-3') |
Non-standard residues in 5keg (1).pdb #10
---
CA — calcium ion
CL — chloride ion
ZN — zinc ion
> open "/Users/jeongmin/Downloads/5keg (1).pdb"
5keg (1).pdb title:
Crystal structure of APOBEC3A In complex with A single-stranded DNA [more
info...]
Chain information for 5keg (1).pdb #11
---
Chain | Description | UniProt
A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199
B | DNA (5'-D(*TP*TP*CP*TP*T)-3') |
Non-standard residues in 5keg (1).pdb #11
---
CA — calcium ion
CL — chloride ion
ZN — zinc ion
> open "/Users/jeongmin/Downloads/5keg (1).pdb"
5keg (1).pdb title:
Crystal structure of APOBEC3A In complex with A single-stranded DNA [more
info...]
Chain information for 5keg (1).pdb #12
---
Chain | Description | UniProt
A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199
B | DNA (5'-D(*TP*TP*CP*TP*T)-3') |
Non-standard residues in 5keg (1).pdb #12
---
CA — calcium ion
CL — chloride ion
ZN — zinc ion
> open "/Users/jeongmin/Downloads/5keg (2).pdb"
5keg (2).pdb title:
Crystal structure of APOBEC3A In complex with A single-stranded DNA [more
info...]
Chain information for 5keg (2).pdb #13
---
Chain | Description | UniProt
A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199
B | DNA (5'-D(*TP*TP*CP*TP*T)-3') |
Non-standard residues in 5keg (2).pdb #13
---
CA — calcium ion
CL — chloride ion
ZN — zinc ion
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
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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
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)
OpenGL version: 4.1 INTEL-20.6.1
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
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: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0)
OS Loader Version: 577~170
Software:
System Software Overview:
System Version: macOS 13.4.1 (22F82)
Kernel Version: Darwin 22.5.0
Time since boot: 33 days, 4 hours, 42 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
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: 1.5.9.1
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 , 2 years 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 , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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