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Opened 5 months ago
Closed 5 months ago
#17924 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5-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 0x000000029cc6b000 (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 0x000000029bc5f000 (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 0x000000029ac53000 (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 0x0000000299c47000 (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 0x0000000298c3b000 (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 0x0000000297c2f000 (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 0x0000000296c23000 (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 0x0000000295c17000 (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 0x0000000294c0b000 (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 0x0000000293bff000 (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 0x0000000292bf3000 (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 0x00000001f448e080 (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":"2025-06-06 09:41:47.00 +0800","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 13.5 (22G74)","roots_installed":0,"name":"ChimeraX","incident_id":"F57F8138-8F8C-42EA-9848-6ED7441E97AA"}
{
"uptime" : 220000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 13031,
"osVersion" : {
"train" : "macOS 13.5",
"build" : "22G74",
"releaseType" : "User"
},
"captureTime" : "2025-06-06 09:41:28.2234 +0800",
"incident" : "F57F8138-8F8C-42EA-9848-6ED7441E97AA",
"pid" : 33017,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-04 12:41:26.8946 +0800",
"procStartAbsTime" : 1824784438334,
"procExitAbsTime" : 5309750683021,
"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":"625613FD-F93A-5F3F-93B7-876932719AB7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "189119B5-EF18-835F-661A-27B4F5EE4E7F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3,
"sleepWakeUUID" : "22802192-5023-45A5-BAE4-51785AF329FF",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105554055790568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"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":33017},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105554055790568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":1102196,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6866304429},{"value":5234785304},{"value":8237878467295753440},{"value":0},{"value":6125007304},{"value":9594123514253969434},{"value":9594123513377876122},{"value":78},{"value":0},{"value":49},{"value":16},{"value":11401166848},{"value":0},{"value":328},{"value":8472179616},{"value":0},{"value":11},{"value":8393384064,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8393384288,"symbolLocation":224,"symbol":"_main_thread"},{"value":4344890160},{"value":1},{"value":32769},{"value":32768},{"value":8393390496,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6866123816},"cpsr":{"value":1073745920},"fp":{"value":5234785104},"sp":{"value":5234785072},"esr":{"value":1442840704,"description":" Address size 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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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
> open /Users/bijie/Desktop/manuscript/VHH5/model_rsf16-coot-1.pdb
Chain information for model_rsf16-coot-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> set bgColor white
> set bgColor gray
> set bgColor white
> set bgColor gray
> show cartoons
> hide cartoons
> hide atoms
> show cartoons
> select /F
858 atoms, 878 bonds, 112 residues, 1 model selected
> select /F
858 atoms, 878 bonds, 112 residues, 1 model selected
> select /E
1593 atoms, 1631 bonds, 209 residues, 1 model selected
> hide target m
> show target m
> hide sel target a
> cartoon hide sel
> select /D
1682 atoms, 1727 bonds, 223 residues, 1 model selected
> cartoon hide sel
> select /C
820 atoms, 844 bonds, 98 residues, 1 model selected
> select /B
2229 atoms, 2296 bonds, 273 residues, 1 model selected
> select sel : show sel atoms
> style sel stick
Changed 2759 atom styles
> select /C
820 atoms, 844 bonds, 98 residues, 1 model selected
> select /C
820 atoms, 844 bonds, 98 residues, 1 model selected
> select /C
820 atoms, 844 bonds, 98 residues, 1 model selected
> select /B
2229 atoms, 2296 bonds, 273 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> ui mousemode right select
> select clear
> select /A
74 atoms, 75 bonds, 9 residues, 1 model selected
> select /B
2229 atoms, 2296 bonds, 273 residues, 1 model selected
> select clear
> select /F:45
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:99
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /F:100
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:101
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select /F:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /F:97
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /F:98
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select /F:97
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /F:98
12 atoms, 12 bonds, 1 residue, 1 model selected
> open /Users/bijie/Desktop/trendsreview/ver1/2f53.pdb
2f53.pdb title:
Directed evolution of human T-cell receptor CDR2 residues by phage display
dramatically enhances affinity for cognate peptide-MHC without apparent cross-
reactivity [more info...]
Chain information for 2f53.pdb #2
---
Chain | Description | UniProt
A | MHC class I antigen A*2 | 1A02_HUMAN 1-275
B | β-2-microglobulin | B2MG_HUMAN 1-99
C | cancer/testis antigen 1B | CTG1B_HUMAN 1-9
D | T-cell receptor, α chain | Q6PIZ8_HUMAN 20-191
E | T-cell receptor, β chain |
Non-standard residues in 2f53.pdb #2
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
> hide #1 models
> ui mousemode right zoom
> show #!2 target m
> ui mousemode right zoom
> hide #!2 atoms
> show #!2 cartoons
> hide #!2 models
> hide #2.1 models
> close #2
> open /Users/bijie/Desktop/trendsreview/ver1/2bnr.pdb
2bnr.pdb title:
Structural and kinetic basis for heightened immunogenicity of T cell vaccines
[more info...]
Chain information for 2bnr.pdb #2
---
Chain | Description | UniProt
A | hla class I histocompatibility antigen | 1A02_HUMAN 1-276
B | β-2-microglobulin | B2MG_HUMAN 1-99
C | synthetic peptide |
D | T-cell receptor α chain V region |
E | TRBC1 | TCB_HUMAN 113-242
> hide #2 cartoons
> hide #2 atoms
> show #2 cartoons
> select #1/B
2229 atoms, 2296 bonds, 273 residues, 1 model selected
> select #2/A
2412 atoms, 2322 bonds, 434 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue target c
> color sel light blue target c
> color sel light steel blue target c
> color sel powder blue target c
> color sel light steel blue target c
> select #2/B
874 atoms, 861 bonds, 137 residues, 1 model selected
> color sel light gray target c
> color sel gray target c
> color sel light gray target c
> color sel dark gray target c
> color sel light gray target c
> select #2/C
81 atoms, 76 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet target c
> color sel orchid target c
> color sel medium orchid target c
> color sel dark magenta target c
> color sel magenta target c
> color sel orange red target c
> color sel orange target c
> color sel yellow target c
> color sel light pink target c
> color sel blue violet target c
> show sel atoms
> color sel medium orchid target c
> color sel byhetero target c
> color sel orchid target c
> ui mousemode right select
> select clear
> select #2/D
1695 atoms, 1591 bonds, 341 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold target c
> color sel orange target c
> color sel dark orange target c
> color sel goldenrod target c
> color sel gold target c
> color sel sienna target c
> color sel dark sea green target c
> color sel light green target c
> color sel dark sea green target c
> select #2/E
2083 atoms, 1955 bonds, 422 residues, 1 model selected
> color sel sky blue target c
> color sel light goldenrod yellow target c
> color sel yellow target c
> color sel gold target c
> color sel yellow target c
> color sel bypolymer target c
> color sel yellow target c
> color sel #ffff00ff target c
> color sel #f9ff9dff target c
> color sel #f5ffb4ff target c
> color sel #f7ff8aff target c
> color sel #f4ff79ff target c
> color sel #ffe87aff target c
> color sel #ffe879ff target c
> color sel #fff36fff target c
> color sel #ffee80ff target c
> color sel #fff19bff target c
> color sel #ffed86ff target c
> color sel #ffec86ff target c
> color sel #ffec84ff target c
> color sel #ffeb84ff target c
> color sel #ffea84ff target c
> select clear
> select ::name="HOH"
520 atoms, 520 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/D
1557 atoms, 1591 bonds, 203 residues, 1 model selected
> color sel #dd690eff target c
> color sel #dd850dff target c
> color sel #dd860cff target c
> color sel #dd9429ff target c
> color sel #dd9e0cff target c
> color sel #dda926ff target c
> color sel #dda512ff target c
> color sel #ddb635ff target c
> color sel #ddb636ff target c
> color sel #dda818ff target c
> color sel #dea818ff target c
> color sel #e0aa19ff target c
> color sel #ecb31aff target c
> color sel #f8bd1bff target c
> color sel #ffc21cff target c
> color sel #ffc11cff target c
> color sel #fec11cff target c
> color sel #fdc01cff target c
> color sel #fcbf1cff target c
> color sel #fbbe1cff target c
> color sel #fabe1cff target c
> color sel #fabd1cff target c
> color sel #f9bd1bff target c
> color sel #f8bd1bff target c
> color sel #f8bc1bff target c
> color sel #f7bc1bff target c
> color sel #f6bb1bff target c
> color sel #f5ba1bff target c
> color sel #f4ba1bff target c
> color sel #f4b91bff target c
> color sel #f2b81bff target c
> color sel #f0b61aff target c
> color sel #efb61aff target c
> color sel #efb51aff target c
> color sel #eeb51aff target c
> color sel #eeb41aff target c
> color sel #edb41aff target c
> color sel #edb430ff target c
> color sel #eda51fff target c
> select clear
> open /Users/bijie/Desktop/trendsreview/ver1/3hae.pdb
3hae.pdb title:
Rational development of high-affinity T-cell receptor-like antibodies [more
info...]
Chain information for 3hae.pdb #3
---
Chain | Description | UniProt
A D J P | MHC class I antigen A*2 | 1A02_HUMAN 1-276
B E K Q | β-2-microglobulin FORM π 5.3 | B2MG_HUMAN 1-99
C F M R | nyeso-1 peptide |
G L N S | antibody light chain |
H I O T | antibody heavy chain |
> hide #2 models
> hide #3 cartoons
> show #3 atoms
> hide #3 atoms
> show #3 cartoons
> show #2 models
> hide #2 models
> select #3/D
2253 atoms, 2321 bonds, 276 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/J
2253 atoms, 2321 bonds, 276 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/P
2253 atoms, 2321 bonds, 276 residues, 1 model selected
> select #3/A
2253 atoms, 2321 bonds, 276 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/H
1609 atoms, 1648 bonds, 220 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/I
1609 atoms, 1648 bonds, 220 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/T
1609 atoms, 1648 bonds, 220 residues, 1 model selected
> select #3/O
1609 atoms, 1648 bonds, 220 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/G
1595 atoms, 1640 bonds, 211 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/L
1595 atoms, 1640 bonds, 211 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/N
1595 atoms, 1640 bonds, 211 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/C
75 atoms, 76 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/F
75 atoms, 76 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/M
75 atoms, 76 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/B
836 atoms, 860 bonds, 100 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/E
836 atoms, 860 bonds, 100 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/K
836 atoms, 860 bonds, 100 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2 models
> hide #2 models
> ui tool show Matchmaker
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2bnr.pdb, chain A (#2) with 3hae.pdb, chain P (#3), sequence
alignment score = 1467.8
RMSD between 273 pruned atom pairs is 0.770 angstroms; (across all 276 pairs:
0.810)
> show #2 models
> hide #3 models
> select #2/B
837 atoms, 861 bonds, 100 residues, 1 model selected
> cartoon sel
> ui tool show "Color Actions"
> show #3 models
> hide #2 models
> select #3/P
2253 atoms, 2321 bonds, 276 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dodger blue target c
> color sel #b0c4deff target c
> select #3/Q
836 atoms, 860 bonds, 100 residues, 1 model selected
> color sel dark gray target c
> show #2 models
> select #3/R
75 atoms, 76 bonds, 9 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid target c
> show sel atoms
> hide sel cartoons
> color sel orchid target ac
> select #2/C
75 atoms, 76 bonds, 9 residues, 1 model selected
> color sel orchid target ac
> hide sel cartoons
> select clear
> select #2/C
75 atoms, 76 bonds, 9 residues, 1 model selected
> color sel byhetero target ac
> select #3/R
75 atoms, 76 bonds, 9 residues, 1 model selected
> color sel byhetero target ac
> hide #2 models
> show #2 models
> select clear
> hide #2 models
> select #3/T
1609 atoms, 1648 bonds, 220 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark sea green target ac
> color sel dark olive green target ac
> color sel olive drab target ac
> color sel sea green target ac
> color sel medium sea green target ac
> color sel forest green target ac
> color sel lime green target ac
> color sel spring green target ac
> color sel chartreuse target ac
> color sel yellow green target ac
> color sel dark olive green target ac
> color sel dark sea green target ac
> color sel dark olive green target ac
> select #3/S
1595 atoms, 1640 bonds, 211 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark sea green target ac
> show #2 models
> hide #2 models
> select clear
> save /Users/bijie/Desktop/trendsreview/ver1/1.cxs
> open /Users/bijie/Desktop/trendsreview/ver1/9dl1.pdb
9dl1.pdb title:
Crystal structure of hla-A*02:01/ny-eso-1 (sllmwitqv) and A target specific
tracer-I [more info...]
Chain information for 9dl1.pdb #4
---
Chain | Description | UniProt
A D | tracer-I |
B F | MHC class I antigen, A-2 α chain |
C G | β-2-microglobulin | B2MG_HUMAN 1-99
E H | cancer/testis antigen 1 | CTG1B_HUMAN 1-8
Non-standard residues in 9dl1.pdb #4
---
SO4 — sulfate ion
> hide #3 models
> hide #!4 atoms
> show #!4 cartoons
> select #4/A
1068 atoms, 1033 bonds, 1 pseudobond, 175 residues, 2 models selected
> select #4/D
1136 atoms, 1086 bonds, 197 residues, 1 model selected
> cartoon hide sel
> select clear
> select #4/E#4/H
164 atoms, 154 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid target ac
> show sel atoms
> hide sel cartoons
> color sel byhetero target ac
> select ::name="HOH"
522 atoms, 522 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/A#4/D
2075 atoms, 2119 bonds, 1 pseudobond, 243 residues, 2 models selected
> select #4/B#4/F
4502 atoms, 4634 bonds, 552 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #b0c4deff target ac
> select #2/B#4/C#4/G
2485 atoms, 2557 bonds, 297 residues, 2 models selected
> color sel dark gray target ac
> select clear
> ui tool show Matchmaker
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9dl1.pdb, chain B (#4) with 2bnr.pdb, chain A (#2), sequence
alignment score = 1482.7
RMSD between 271 pruned atom pairs is 0.466 angstroms; (across all 275 pairs:
0.563)
> show #3 models
> show #2 models
> hide #2 models
> hide #3 models
> hide #!4 models
> show #2 models
> show #3 models
> ui tool show Matchmaker
> matchmaker #2 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3hae.pdb, chain P (#3) with 2bnr.pdb, chain A (#2), sequence
alignment score = 1467.8
RMSD between 273 pruned atom pairs is 0.770 angstroms; (across all 276 pairs:
0.810)
> show #!4 models
> ui tool show Matchmaker
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9dl1.pdb, chain B (#4) with 2bnr.pdb, chain A (#2), sequence
alignment score = 1482.7
RMSD between 271 pruned atom pairs is 0.466 angstroms; (across all 275 pairs:
0.563)
> hide #!4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> ui tool show Matchmaker
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2bnr.pdb, chain A (#2) with 3hae.pdb, chain P (#3), sequence
alignment score = 1467.8
RMSD between 273 pruned atom pairs is 0.770 angstroms; (across all 276 pairs:
0.810)
> ui tool show Matchmaker
> matchmaker #!4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2bnr.pdb, chain A (#2) with 9dl1.pdb, chain B (#4), sequence
alignment score = 1482.7
RMSD between 271 pruned atom pairs is 0.466 angstroms; (across all 275 pairs:
0.563)
> show #!4 models
> ui windowfill toggle
> undo
> select clear
> hide #3 models
> set bgColor white
> set bgColor #ffffff00
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting soft
> show #3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #3 models
> hide #2 models
> show #3 models
> hide #3 models
> show #3 models
> show #2 models
> hide #3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #2 models
> show #2 models
> hide #!4 models
> show #!4 models
> hide #2 models
> hide #!4 models
> show #2 models
> show #3 models
> hide #2 models
> show #2 models
> hide #3 models
> save "/Users/bijie/Desktop/trendsreview/ver1/figure 2.cxs"
No map chosen to save
> save /Users/bijie/Desktop/trendsreview/ver1/2bnr.tif width 703 height 586
> supersample 3
> show #3 models
> hide #2 models
> save /Users/bijie/Desktop/trendsreview/ver1/3hae.tif width 703 height 586
> supersample 3
> show #!4 models
> hide #3 models
> save /Users/bijie/Desktop/trendsreview/ver1/9dl1.tif width 703 height 586
> supersample 3
> show #3 models
> hide #3 models
> save /Users/bijie/Desktop/trendsreview/ver1/9dl1.png width 703 height 586
> supersample 3
> show #3 models
> hide #!4 models
> save /Users/bijie/Desktop/trendsreview/ver1/3hae.png width 703 height 586
> supersample 3
> show #2 models
> hide #3 models
> save /Users/bijie/Desktop/trendsreview/ver1/2bnr.png width 703 height 586
> supersample 3
> save /Users/bijie/Desktop/trendsreview/ver1/2bnr.png width 703 height 586
> supersample 3 transparentBackground true
> show #3 models
> hide #2 models
> save /Users/bijie/Desktop/trendsreview/ver1/3hae.png width 703 height 586
> supersample 3
> save /Users/bijie/Desktop/trendsreview/ver1/3hae.png width 703 height 586
> supersample 3 transparentBackground true
> show #!4 models
> hide #3 models
> save /Users/bijie/Desktop/trendsreview/ver1/9dl1.png width 703 height 586
> supersample 3 transparentBackground true
> show #3 models
> hide #!4 models
> hide #3 models
> show #2 models
> select #2/D
1557 atoms, 1591 bonds, 203 residues, 1 model selected
> select sel : select #2/E
1902 atoms, 1955 bonds, 241 residues, 1 model selected
> cartoon hide sel
> select #2/A
2254 atoms, 2322 bonds, 276 residues, 1 model selected
> show sel surfaces
> select clear
> select #2/D
1557 atoms, 1591 bonds, 203 residues, 1 model selected
> select sel : select sel : color (#!2 & sel) orange
> select #2/C
75 atoms, 76 bonds, 9 residues, 1 model selected
> show sel surfaces
> transparency (#!2 & sel) 70
> ui tool show "Color Actions"
> color sel orchid target ac
> color sel byhetero target ac
> color sel dark violet target s
> color sel orchid target s
> transparency (#!2 & sel) 80
> transparency (#!2 & sel) 40
> transparency (#!2 & sel) 50
> transparency (#!2 & sel) 60
> ui tool show "Show Sequence Viewer"
> sequence chain #2/D
Alignment identifier is 2/D
> select #2/D:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/D
1557 atoms, 1591 bonds, 203 residues, 1 model selected
> select #2/D:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/D:52-204
1169 atoms, 1194 bonds, 153 residues, 1 model selected
> select #2/D:154-204
399 atoms, 408 bonds, 51 residues, 1 model selected
> select #2/D
1557 atoms, 1591 bonds, 203 residues, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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 - 83.1
OpenGL renderer: Apple M1
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: MacBookPro17,1
Model Number: Z11F000BPCH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 6 days, 18 hours, 19 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
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 , 5 months ago
| 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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