![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Closed 23 months ago
#10238 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
Current thread 0x00007ff85507db40 (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":"2023-11-27 19:59:51.00 +0100","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 14.1.1 (23B81)","roots_installed":0,"name":"ChimeraX","incident_id":"1BBBD5A3-934E-4958-BE29-6B8DA4DD2E2C"}
{
"uptime" : 210000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 7791,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2023-11-27 19:59:44.5232 +0100",
"codeSigningMonitor" : 0,
"incident" : "1BBBD5A3-934E-4958-BE29-6B8DA4DD2E2C",
"pid" : 13677,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-11-24 15:59:21.2704 +0100",
"procStartAbsTime" : 8093456760410,
"procExitAbsTime" : 214554127324919,
"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":"1B621CC7-A08E-58E5-A30C-B64306F232D4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5A8EFE95-C9B8-50CB-3111-3AE68D059CBA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 27642,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "592314B4-3C69-449D-9048-A364D68F692D",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737488089064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffbf000-7ffffffc0000 [ 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"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":13677},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737488089064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffbf000-7ffffffc0000 [ 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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===== 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/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/tige-LSU-novel-different-AP-tRNA.cxs format session
opened ChimeraX session
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!11 models
> hide #7 models
> hide #4 models
> hide #13 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4,6,8,10,12,14 atoms
> select add #6
42 atoms, 45 bonds, 1 residue, 1 model selected
> show sel atoms
> select subtract #6
Nothing selected
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #4 models
> hide #10 models
> select #8/Aw:71
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style sel sphere
Changed 31 atom styles
> select #8/Aw:69
33 atoms, 35 bonds, 1 residue, 1 model selected
> select #8/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #8
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> nucleotides sel atoms
> style sel sphere
Changed 2161 atom styles
> select clear
> select #8/Aw:69
33 atoms, 35 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #12
42 atoms, 45 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/hybrid-tRNA-mitoribosome-7qi6.pdb
Summary of feedback from opening
/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
fromAsitetoPsite/hybrid-tRNA-mitoribosome-7qi6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLUAB 53
LEUAB 63 1 11
Start residue of secondary structure not found: HELIX 2 2 ASNAB 64 HISAB 69 1
6
Start residue of secondary structure not found: HELIX 3 3 ASNAB 74 PHEAB 79 1
6
Start residue of secondary structure not found: HELIX 4 4 SERAB 80 ALAAB 87 1
8
Start residue of secondary structure not found: HELIX 5 5 GLYAB 96 ARGAB 98 1
3
1011 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYSA (45 )
Cannot find LINK/SSBOND residue 5F0A (184 )
Cannot find LINK/SSBOND residue A (76 )
Cannot find LINK/SSBOND residue C (2437 )
Cannot find LINK/SSBOND residue A (2451 )
898 messages similar to the above omitted
Chain information for hybrid-tRNA-mitoribosome-7qi6.pdb #15
---
Chain | Description
Aw | No description available
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> hide sel cartoons
> nucleotides sel fill
> nucleotides sel atoms
> hide sel atoms
> show sel cartoons
> hide #8 models
> select clear
> select #15/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select #15/Aw:71
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> select subtract #15
Nothing selected
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> hide sel cartoons
> show #8 models
> select #8/Aw:69@OP1
1 atom, 1 residue, 1 model selected
> select up
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> hide H
> select clear
> show #7 models
> show #!9 models
> select add #9
1482 atoms, 1655 bonds, 1 pseudobond, 70 residues, 2 models selected
> ui tool show "Color Actions"
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> color #7 #7a81ff8e
> select clear
> color #7 #7a81ff8f
> color #15 #73fdffff
> select clear
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> color sel byhetero
> select clear
> hide #15 models
> show #15 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/figure-tige-LSU-1-tRNA-3.tif width 1201 height 757
> supersample 3
> show #!9 models
> hide #6-8,12,14-15#!9 atoms
> select add #12
42 atoms, 45 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #12 #ff40ffff
> select clear
> select add #6
42 atoms, 45 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #6 #ff40ffff
> select add #6
42 atoms, 45 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> color #6 #ff40ff3c
> color #6 #ff40ff2e
> select clear
> color #6 #ff40ff29
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/figure-tige-LSU-1-tRNA-1.tif width 1201 height 757
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> color #9 #228b2280
> color #9 #228b2270
> color #7 #7a81ffbc
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> select add #7
2165 atoms, 2328 bonds, 74 residues, 1 model selected
> color sel medium blue
> color #7 #7a81ffde
> ui tool show "Color Actions"
> color sel medium blue
> color #7 #0000cd8d
> color #7 #0000cd8c
> select clear
> select add #7
2165 atoms, 2328 bonds, 74 residues, 1 model selected
> color sel blue
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/figure-tige-LSU-1-tRNA-1.tif width 1201 height 757
> supersample 3 transparentBackground true
> color #6 #ff40ff5d
> color #6 #ff40ff69
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/figure-tige-LSU-1-tRNA-1.tif width 1201 height 757
> supersample 3 transparentBackground true
> select add #12
42 atoms, 45 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> color #6 #ff40ff2e
> color #6 #ff40ff26
> select clear
> select #8/Aw:71
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> select clear
> hide #!9 models
> hide #15 models
> show #15 models
> show #6-8,12,14-15 atoms
> hide #6-8,12,14-15 atoms
> show #6-8,12,14-15 atoms
> hide #6-8,12,14-15 atoms
> hide #15 models
> show #15 models
> show #6-8,12,14-15 cartoons
> hide #8 models
> select #15/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select #15/Aw:69
33 atoms, 35 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select #15/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> show #8 models
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> hide sel cartoons
> select clear
> select #8/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/Aw:69
33 atoms, 35 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select add #12
75 atoms, 80 bonds, 2 residues, 2 models selected
> show sel atoms
> select add #8
2203 atoms, 2375 bonds, 69 residues, 2 models selected
> select subtract #8
42 atoms, 45 bonds, 1 residue, 1 model selected
> select add #6
84 atoms, 90 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> select #8/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> select #8/Aw:71
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/Aw:69@H4'
1 atom, 1 residue, 1 model selected
> select up
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #15/Aw:69@O4'
1 atom, 1 residue, 1 model selected
> select up
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #8 models
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> select subtract #15
Nothing selected
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> select clear
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> show sel cartoons
> select #15/Aw:70
31 atoms, 32 bonds, 1 residue, 1 model selected
> select #15/Aw:71
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> select subtract #15
Nothing selected
> select add #15
2161 atoms, 2330 bonds, 68 residues, 1 model selected
> hide sel cartoons
> select clear
> show #8 models
> select add #12
42 atoms, 45 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel brown
> color sel purple
> color sel byhetero
> select subtract #12
Nothing selected
> select add #6
42 atoms, 45 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel purple
> select clear
> hide H
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM-
> fromAsitetoPsite/figure-tige-LSU-1-tRNA-3.tif width 1201 height 757
> supersample 3 transparentBackground true
> open "/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tigecycline-bound
> compare WT mitoribosome.cxs"
opened ChimeraX session
> ui tool show "Side View"
> show #!6 models
> hide #!6 models
Drag select of 2374 residues
> select up
43541 atoms, 46523 bonds, 3762 residues, 1 model selected
> select up
56207 atoms, 59472 bonds, 5309 residues, 1 model selected
> select up
56265 atoms, 59532 bonds, 5313 residues, 1 model selected
> select up
176233 atoms, 184658 bonds, 18240 residues, 1 model selected
> select down
56265 atoms, 59532 bonds, 5313 residues, 1 model selected
> select clear
Drag select of 4592 residues
> select up
56516 atoms, 59770 bonds, 5344 residues, 1 model selected
> select up
68446 atoms, 71964 bonds, 6804 residues, 1 model selected
> color sel yellow
> select clear
> select #1/AA:1536
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
20260 atoms, 22661 bonds, 954 residues, 1 model selected
> color sel light gray
> select clear
> lighting simple
Drag select of 4082 residues
> select up
68874 atoms, 73807 bonds, 5853 residues, 1 model selected
> select up
82452 atoms, 87737 bonds, 7495 residues, 1 model selected
> select up
82555 atoms, 87844 bonds, 7500 residues, 1 model selected
> select up
176233 atoms, 184658 bonds, 18240 residues, 1 model selected
> select down
82555 atoms, 87844 bonds, 7500 residues, 1 model selected
> select clear
Drag select of 5455 residues
> select up
77566 atoms, 82709 bonds, 6902 residues, 1 model selected
> select up
88659 atoms, 94092 bonds, 8247 residues, 1 model selected
> select up
88762 atoms, 94199 bonds, 8252 residues, 1 model selected
> select up
176233 atoms, 184658 bonds, 18240 residues, 1 model selected
> select down
88762 atoms, 94199 bonds, 8252 residues, 1 model selected
> hide #8 models
> select clear
Drag select of 6335 residues
> select up
82357 atoms, 87599 bonds, 7498 residues, 1 model selected
> select up
93223 atoms, 98741 bonds, 8808 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel sky blue
> select clear
> select add #1
176233 atoms, 184658 bonds, 23 pseudobonds, 18240 residues, 3 models selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select clear
> select #1/A:2609
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> color sel dark gray
> select clear
> select #1/AA:822
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
20260 atoms, 22661 bonds, 954 residues, 1 model selected
> select clear
> show #8 models
> color #8 #8efa00ff
> select clear
Drag select of 3550 residues
> select clear
> select #1/A:6552@C1B
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 42 atom styles
> ui tool show "Color Actions"
> color sel brown
> color sel byhetero
> color sel coral
> color sel byhetero
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige-
> bound.pdb models #1 selectedOnly true relModel #1
> open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige-
> bound.pdb
Summary of feedback from opening
/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige-
bound.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 184
ALA D 186 1 3
Start residue of secondary structure not found: HELIX 2 2 HIS D 252 LYS D 254
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA D 260 ARG D 262
1 3
Start residue of secondary structure not found: HELIX 4 4 ASN D 263 TRP D 265
1 3
Start residue of secondary structure not found: HELIX 5 5 ASN E 57 LEU E 73 1
17
996 messages similar to the above omitted
Cannot find LINK/SSBOND residue FES (201 )
Cannot find LINK/SSBOND residue FES (201 )
> select ::name="T1C"
168 atoms, 180 bonds, 4 residues, 2 models selected
> hide sel atoms
> select add #1
176275 atoms, 184703 bonds, 23 pseudobonds, 18241 residues, 4 models selected
> select subtract #1
42 atoms, 45 bonds, 1 residue, 1 model selected
> select subtract #5
Nothing selected
> select add #5
42 atoms, 45 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> select clear
> select #1/Ax:45
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> color sel forest green
> select clear
> select #1/Ax:45
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> lighting simple
> select clear
> color #8 #ff40ffff
> select clear
> select #1/L:130
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
52 atoms, 51 bonds, 6 residues, 1 model selected
> select up
890 atoms, 905 bonds, 115 residues, 1 model selected
> color #8 #00fdffff
> color #8 #ff40ffff
> select clear
> color #1,5,8 light sea green
> undo
> select clear
> select #1/L:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
52 atoms, 51 bonds, 6 residues, 1 model selected
> select up
890 atoms, 905 bonds, 115 residues, 1 model selected
> ui tool show "Color Actions"
Drag select of 925 residues
> select up
41888 atoms, 46024 bonds, 2647 residues, 1 model selected
> select clear
> select ::name="T1C"
168 atoms, 180 bonds, 4 residues, 2 models selected
> show sel atoms
> color sel purple
> ui tool show "Color Actions"
> style sel sphere
Changed 168 atom styles
> color sel byhetero
> select clear
> select #1/L:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
890 atoms, 905 bonds, 115 residues, 1 model selected
> color sel #00fdffff
> color sel #73fdffff
> color sel #73fcd6ff
> select clear
> select #1/L:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
890 atoms, 905 bonds, 115 residues, 1 model selected
> color #1 #73fdffff
> undo
> color sel #73fdffff
> color sel #73fdffed
> color sel #73fdffc6
> color sel #73fdffbb
> color sel #73fdffba
> color sel #73fdffab
> color sel #73fdffa8
> color sel #73fdffa4
> color sel #73fdffa1
> color sel #73fdff9d
> color sel #73fdff99
> color sel #73fdff97
> color sel #73fdff96
> color sel #73fdff95
> color sel #73fdff90
> color sel #73fdff8c
> color sel #73fdff88
> color sel #73fdff85
> color sel #73fdff82
> color sel #73fdff81
> color sel #73fdff7d
> color sel #73fdff7c
> color sel #73fdff7a
> color sel #73fdff78
> color sel #73fdff76
> color sel #73fdff73
> color sel #73fdff70
> color sel #73fdff6f
> color sel #73fdff6c
> color sel #73fdff69
> color sel #73fdff66
> color sel #73fdff64
> color sel #73fdff63
> select clear
> select #1/Ax:44
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> color sel #73fdff64
> color sel #73fdff66
> color sel #73fdff6c
> color sel #73fdff70
> color sel #73fdff80
> color sel #73fdff88
> color sel #73fdff8d
> color sel #73fdff95
> color sel #73fdff9a
> color sel #73fdff9d
> color sel #73fdff9f
> color sel #73fdffa2
> color sel #73fdffa5
> color sel #73fdffab
> color sel #73fdffb0
> color sel #73fdffb5
> color sel #73fdffb8
> color sel #73fdffbd
> color sel #73fdffc3
> color sel #73fdffca
> color sel #73fdffce
> color sel #73fdffcf
> color sel #73fdffd0
> color sel #73fdffd1
> color sel #73fdffd7
> color sel #73fdffdc
> color sel #73fdffdf
> color sel #73fdffe4
> color sel #73fdffe6
> color sel #73fdffe7
> color sel #73fdffe8
> select clear
> select #1/Ax:45
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> color sel forest green
> select clear
> select #1/Ax:45
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> color sel #73fdffe9
> color sel #73fdffef
> color sel #73fdfff6
> color sel #73fdfffa
> color sel #73fdfffb
> color sel #73fdfff0
> color sel #73fdffe1
> color sel #73fdffd1
> color sel #73fdffd0
> color sel #73fdffd1
> color sel #00f900ff
> select clear
> select #1/Ax:45
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> ui tool show "Color Actions"
> select clear
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/RRF.cxs
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall-
> RRFbound.tif width 1201 height 757 supersample 3 transparentBackground true
> select #1/AA:1557
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
20260 atoms, 22661 bonds, 954 residues, 1 model selected
> select up
20302 atoms, 22706 bonds, 955 residues, 1 model selected
> select up
176233 atoms, 184658 bonds, 18240 residues, 1 model selected
> select down
20302 atoms, 22706 bonds, 955 residues, 1 model selected
> hide sel
> select #1/Ax:67
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1482 atoms, 1655 bonds, 70 residues, 1 model selected
> hide sel
> hide cartoons target a
> undo
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/P-tRNA.pdb
> models #1 selectedOnly true relModel #1
> delete sel
> select #1/A:6553@C6
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:6552@C42
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> color sel #00f900ff
> color sel #00f900dc
> color sel #00f900c1
> color sel #00f900ae
> color sel #00f900b0
> color sel #00f900ae
> color sel #00f9008d
> color sel #00f90066
> color sel #942192ff
> color sel byhetero
> color sel #942192ff
> color sel #942192f3
> color sel #942192d1
> color sel #942192c8
> color sel #942192be
> color sel #942192b4
> color sel #942192ae
> color sel #942192a8
> color sel #942192a0
> color sel #94219296
> color sel #94219280
> color sel #94219270
> color sel #9421926c
> color sel #94219265
> color sel #9421925e
> color sel #94219257
> color sel #94219253
> color sel #9421924d
> color sel #9421924c
> color sel #9421924a
> color sel #94219242
> color sel #9421923f
> color sel #9421923c
> color sel #9421923b
> color sel #9421923c
> color sel #94219247
> color sel #9421924f
> color sel #94219251
> select #1/M:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:6552@C42
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige-
> bound.pdb
Summary of feedback from opening
/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige-
bound.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 184
ALA D 186 1 3
Start residue of secondary structure not found: HELIX 2 2 HIS D 252 LYS D 254
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA D 260 ARG D 262
1 3
Start residue of secondary structure not found: HELIX 4 4 ASN D 263 TRP D 265
1 3
Start residue of secondary structure not found: HELIX 5 5 ASN E 57 LEU E 73 1
17
996 messages similar to the above omitted
Cannot find LINK/SSBOND residue FES (201 )
Cannot find LINK/SSBOND residue FES (201 )
> transparency sel 60 target a
> select clear
> select #1/AJ:78
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
69 atoms, 68 bonds, 8 residues, 1 model selected
> select up
839 atoms, 855 bonds, 108 residues, 1 model selected
> transparency sel 80 target a
> select #1/A:6552@C42
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> transparency sel 80 target a
> color sel light gray
> style sel sphere
Changed 42 atom styles
> style sel stick
Changed 42 atom styles
> style sel stick
Changed 42 atom styles
> select #5/A:6552@C42
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> style sel stick
Changed 42 atom styles
> style sel sphere
Changed 42 atom styles
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide sel atoms
> show sel atoms
> color sel light gray
> transparency sel 80 target a
> select clear
> color #9 #942192ff
> select add #9
42 atoms, 45 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/A:2625
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> select clear
> select #1/A:2625
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> transparency sel 80 target a
> select clear
> select #1/A:2626
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 509326 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide sel atoms
> select clear
> select #1/AA:1495
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
20260 atoms, 22661 bonds, 954 residues, 1 model selected
> hide sel atoms
> select #1/A:2580
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> hide sel cartoons
> select #1/H:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
43 atoms, 43 bonds, 4 residues, 1 model selected
> select up
1661 atoms, 1698 bonds, 202 residues, 1 model selected
> select up
174751 atoms, 183003 bonds, 18170 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 36 atoms, 34 bonds, 11 shapes
> select up
85 atoms, 93 bonds, 6 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 7 atoms, 7 bonds, 2 shapes
> select up
43 atoms, 47 bonds, 2 residues, 1 model selected
> select up
680 atoms, 761 bonds, 32 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 12 atoms, 7 bonds, 6 shapes
> hide sel atoms
Drag select of 3 atoms
> hide sel atoms
> select add #1
174751 atoms, 183003 bonds, 22 pseudobonds, 18170 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
174751 atoms, 183003 bonds, 22 pseudobonds, 18170 residues, 3 models selected
> show sel cartoons
> select clear
> select #1/N:149
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 6 residues, 1 model selected
> select up
1786 atoms, 1833 bonds, 222 residues, 1 model selected
> select clear
> select #5/A:6552@C42
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> transparency sel 50 target a
> color sel gray
> select clear
> select #1/A:2579
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> select up
33112 atoms, 37043 bonds, 1558 residues, 1 model selected
> select down
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> color sel light gray
> select clear
> select #1/A:2610
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33028 atoms, 36953 bonds, 1556 residues, 1 model selected
> color sel light gray
> lighting simple
> lighting soft
> select clear
> lighting simple
> lighting soft
> lighting simple
> select clear
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/RRF-2.tif
> width 1201 height 757 supersample 3 transparentBackground true
> select clear
> select ::name="T1C"
210 atoms, 225 bonds, 5 residues, 3 models selected
> show sel atoms
> select clear
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall-
> RRFbound.tif width 1201 height 757 supersample 3 transparentBackground true
> lighting full
> lighting simple
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting simple
> lighting soft
> lighting flat
> lighting simple
> lighting soft
> select #1/s:78
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
75 atoms, 74 bonds, 9 residues, 1 model selected
> select up
709 atoms, 731 bonds, 87 residues, 1 model selected
> color sel light sea green
> select clear
> select #1/s:356
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
60 atoms, 60 bonds, 8 residues, 1 model selected
> select up
2446 atoms, 2508 bonds, 299 residues, 1 model selected
> color sel light sea green
> select clear
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall-
> RRFbound.tif width 1201 height 757 supersample 3 transparentBackground true
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting flat
> select protein
970185 atoms, 983997 bonds, 60 pseudobonds, 73817 residues, 11 models selected
> select subtract #8
968684 atoms, 982487 bonds, 60 pseudobonds, 73624 residues, 10 models selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select clear
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall-
> RRFbound-2.tif width 1201 height 757 supersample 3 transparentBackground
> true
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting soft
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall-
> RRFbound-2.tif width 1201 height 757 supersample 3 transparentBackground
> true
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall-
> RRFbound-3.tif width 1201 height 757 supersample 3 transparentBackground
> true
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/RRF.cxs
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
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 ATI-5.1.35
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies 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: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 3 days, 22 hours, 42 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
B277U:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 70.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: TDBEE003853B
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 2.4a
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-Clipper: 0.21.0
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-ISOLDE: 1.6.0
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 , 23 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 , 23 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Duc,
--Eric