![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17049 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-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 0x00007ff84db779c0 (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":"2025-03-08 20:57:38.00 -0800","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":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.7.4 (22H420)","roots_installed":0,"name":"ChimeraX","incident_id":"E07604B4-4A16-449A-88AB-580B995EFBA8"}
{
"uptime" : 380000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 2024,
"osVersion" : {
"train" : "macOS 13.7.4",
"build" : "22H420",
"releaseType" : "User"
},
"captureTime" : "2025-03-08 20:57:32.9723 -0800",
"incident" : "E07604B4-4A16-449A-88AB-580B995EFBA8",
"pid" : 18662,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-07 21:05:53.0980 -0800",
"procStartAbsTime" : 343047890924330,
"procExitAbsTime" : 383150892382527,
"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":"153C487E-9E05-5E3A-A748-3DA2F55B5EF9","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F24801D6-C783-D0EB-FE81-23671F61C372",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 32,
"sleepWakeUUID" : "DE87079C-F171-44DB-8813-E77F839E5AF0",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486696424\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe6b000-7fffffe6c000 [ 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":18662},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486696424\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe6b000-7fffffe6c000 [ 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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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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{
"source" : "P",
"arch" : "x86_64",
"base" : 140703297675264,
"size" : 623536,
"uuid" : "35147f34-023b-37a6-80df-5753d952a289",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
}
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"sharedCache" : {
"base" : 140703297052672,
"size" : 21474836480,
"uuid" : "d23d12c3-82ca-30a7-9d43-7c7c0380823f"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "28251ae1b8d0dcdab290e0c9ba8638e00f3138d7",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64c17a9925d75a7281053d4c",
"factorPackIds" : {
"SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
},
"deploymentId" : 240000002
},
{
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"factorPackIds" : {
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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
> set bgColor white
> lighting flat
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
> close
> cd "/Users/sebols/Library/CloudStorage/GoogleDrive-sebols@uw.edu/My
> Drive/Projects/Main-LOR24/LOR24 Data/Fig 6/"
Current working directory is: /Users/sebols/Library/CloudStorage/GoogleDrive-
sebols@uw.edu/My Drive/Projects/Main-LOR24/LOR24 Data/Fig 6
> open ./1Fab_scrubbed/250226_LOR24_PreF_1Fab.pdb
Chain information for 250226_LOR24_PreF_1Fab.pdb #1
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
> open ./1Fab_scrubbed/250304_MPE8_PreF_1Fab.pdb
Chain information for 250304_MPE8_PreF_1Fab.pdb #2
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
> open ./1Fab_scrubbed/250304_LOR69_PreF_1Fab.pdb
Chain information for 250304_LOR69_PreF_1Fab.pdb #3
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
> graphics bgColor white
> graphics silhouettes true width 2.5
> lighting gentle
> delete H
> color all byhetero
> view matrix camera
> -0.78633,0.1369,-0.60241,54.349,-0.61512,-0.083145,0.78404,283.93,0.057244,0.9871,0.1496,169.63
> hide all atoms
> show all cartoons
> mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45
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 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_MPE8_PreF_1Fab.pdb, chain A (#2), sequence alignment score = 47.9
RMSD between 13 pruned atom pairs is 0.344 angstroms; (across all 13 pairs:
0.344)
Matchmaker 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_LOR69_PreF_1Fab.pdb, chain A (#3), sequence alignment score = 68.7
RMSD between 13 pruned atom pairs is 0.315 angstroms; (across all 13 pairs:
0.315)
> delete /B,C
> color /A light gray
> color #1/H #6C96C4
> color #1/L #A5BCD6
> color #2/H #6EC25F
> color #2/L #A6D79D
> color #3/H #B25D56
> color #3/L #D69B96
> rename #1 LOR24-Fab
> rename #2 MPE8_5u68
> rename #3 LOR69-Fab
> hide #1.1 models
> hide #2.1 models
> hide #3.1 models
> select clear
> select /A:51-176,190-253,278-304,322-339,353-376,392-463,474-530
7690 atoms, 7758 bonds, 3 pseudobonds, 1010 residues, 6 models selected
> delete sel
> select #1/H:1-25,34-49,60-96,113-125/L:1-24,37-50,55-89,99-110
921 atoms, 939 bonds, 3 pseudobonds, 131 residues, 2 models selected
> select add #2/H:1-25,33-49,60-96,114-124/L:1-21,33-48,54-88,99-108
2203 atoms, 2240 bonds, 3 pseudobonds, 303 residues, 3 models selected
> select add #3/H:1-25,34-49,59-61,66-96,110-125/L:1-24,34-49,53-88,99-110
3471 atoms, 3528 bonds, 3 pseudobonds, 470 residues, 4 models selected
> delete sel
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.6
> set silhouetteDepthJump 0.4
> hide #3 models
> view matrix camera
> 0.66775,-0.45742,-0.58727,116,-0.42982,0.40719,-0.80588,152.22,0.60773,0.79056,0.075298,162.68
> select #1/A:309,310,273,277/H:105
44 atoms, 41 bonds, 5 residues, 1 model selected
> select add #2/A:309,310,273,277/H:57
88 atoms, 82 bonds, 10 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 88 atom styles
> color sel byhetero
> select clear
> hide #2 models
> save ./fig_panels/LOR24_PreF_Y105.png supersample 5 transparentBackground
> true
> hide #1 models
> show #2 models
> hide #2.1 models
> save ./fig_panels/MPE8_PreF_Y56.png supersample 5 transparentBackground true
> show #1-3 models
> hide #1.1#2.1#3.1 models
> hide all atoms
> view matrix camera
> -0.43653,-0.89632,-0.077879,127.42,-0.11969,0.14364,-0.98236,103.93,0.89168,-0.41952,-0.16998,129.46
> select #1/A:344/H:52,54,56
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #2/A:344/H:28,30,31
59 atoms, 53 bonds, 8 residues, 2 models selected
> select add #3/A:344/H:103/L:32,50
97 atoms, 89 bonds, 12 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 97 atom styles
> color sel byhetero
> select clear
> hide #2-3 models
> save ./fig_panels/LOR24_PreF_D344_GRAB-motif.png supersample 5
> transparentBackground true
> hide #1 models
> show #2 models
> hide #2.1 models
> save ./fig_panels/MPE8_PreF_D344_GRAB-motif.png supersample 5
> transparentBackground true
> hide #2 models
> show #3 models
> hide #3.1 models
> save ./fig_panels/LOR69_PreF_D344_GRAB-motif.png supersample 5
> transparentBackground true
> show #1-3 models
> hide #1.1#2.1#3.1 models
> hide all atoms
> view matrix camera
> -0.44534,-0.77614,-0.44642,113.11,-0.3885,0.61673,-0.68462,145.75,0.80667,-0.13147,-0.57619,112.91
> select add #3/A:384,385/H:52-57
54 atoms, 53 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 54 atom styles
> color sel byhetero
> select clear
> hide #1-2 models
> save ./fig_panels/LOR69_PreF_D385_GRAB-motif.png supersample 5
> transparentBackground true
> show #1-3 models
> hide #1.1#2.1#3.1 models
> hide all atoms
> view matrix camera
> 0.65911,-0.71615,-0.22958,125.92,0.46568,0.62838,-0.62312,161.16,0.5905,0.30381,0.74766,181.03
> select #1/A:310,269 : select add #2/A:310,269 : select add #3/A:310,269 : select add /A:310,269
208 atoms, 200 bonds, 25 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 208 atom styles
> color sel byhetero
> select clear
> hide #2-3 models
> save ./fig_panels/LOR24_PreF_D310_D269_GRAB-motif.png supersample 5
> transparentBackground true
> hide #1 models
> show #2 models
> hide #2.1 models
> save ./fig_panels/MPE8_PreF_D310_D269_GRAB-motif.png supersample 5
> transparentBackground true
> hide #2 models
> show #3 models
> hide #3.1 models
> save ./fig_panels/LOR69_PreF_D310_D269_GRAB-motif.png supersample 5
> transparentBackground true
> show #1-3 models
> hide #1.1#2.1#3.1 models
> hide all atoms
> view matrix camera
> -0.51698,-0.75061,0.41147,140.19,-0.80783,0.58681,0.055422,179.01,-0.28305,-0.30376,-0.90973,126.27
> select #1/A:312 : select add #2/A:312 : select add #3/A:312 : select add /A:312
135 atoms, 132 bonds, 15 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 135 atom styles
> color sel byhetero
> select clear
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> view matrix camera
> -0.43653,-0.89632,-0.077879,127.42,-0.11969,0.14364,-0.98236,103.93,0.89168,-0.41952,-0.16998,129.46
> show #1-3 models
> hide #1.1#2.1#3.1 models
> hide all atoms
> view matrix camera
> -0.43653,-0.89632,-0.077879,127.42,-0.11969,0.14364,-0.98236,103.93,0.89168,-0.41952,-0.16998,129.46
> select #1/A:344/H:52,54,56
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #2/A:344/H:28,30,31
59 atoms, 53 bonds, 8 residues, 2 models selected
> select add #3/A:344/H:103/L:32,50
97 atoms, 89 bonds, 12 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 97 atom styles
> color sel byhetero
> select clear
> lighting gentle depthCue true depthCueStart 0.5 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.3 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.1 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.6
> view matrix
view matrix camera
-0.44078,-0.8764,0.19401,140.07,-0.73656,0.47669,0.47982,191.09,-0.513,0.068591,-0.85564,117.79
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.081274,0.084418,-0.99311,411.75,0.9527,0.29932,-0.052523,248.84,0.29283,-0.95041,-0.10475,381.92,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.58114,0.81357,-0.019388,121.15,-0.81181,-0.5779,0.083647,333.53,0.056848,0.06435,0.99631,-1.4823,#3.1,1,0,0,0,0,1,0,0,0,0,1,0
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.6
> set silhouetteDepthJump 0.4
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.5
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.8
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.4
> lighting gentle depthCue true depthCueStart 0.6 depthCueEnd 0.4
> lighting gentle depthCue true depthCueStart 0.6 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.1 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.01 depthCueEnd 0.6
> lighting gentle depthCue true depthCueStart 0.4 depthCueEnd 0.6
> view /A:344 clip true pad 0.4
> view /A:344 clip true pad 0.2
> view /A:344 clip true pad 0.1
> view /A:344 clip true pad 0.05
> view /A:344 clip true pad 0.1
> view /A:344 clip true pad 0.01
> view /A:344 clip true pad 0.05
> view /A:344 clip true pad 0.001
> view /A:344 clip true pad 0.01
> view /A:344 clip true pad 0.05
> ui tool show "Side View"
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> view
> show #!2 models
> show #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:383-384
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/A:383-391
74 atoms, 76 bonds, 9 residues, 1 model selected
> select #1/A:377
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:377
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:465-473
67 atoms, 68 bonds, 9 residues, 1 model selected
> select #1/A:352
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:352
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:254-263,268-276,377-382
190 atoms, 187 bonds, 25 residues, 1 model selected
> close
> cd "/Users/sebols/Library/CloudStorage/GoogleDrive-sebols@uw.edu/My
> Drive/Projects/Main-LOR24/LOR24 Data/Fig 6/"
Current working directory is: /Users/sebols/Library/CloudStorage/GoogleDrive-
sebols@uw.edu/My Drive/Projects/Main-LOR24/LOR24 Data/Fig 6
> open ./1Fab_scrubbed/250226_LOR24_PreF_1Fab.pdb
Chain information for 250226_LOR24_PreF_1Fab.pdb #1
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
> open ./1Fab_scrubbed/250304_MPE8_PreF_1Fab.pdb
Chain information for 250304_MPE8_PreF_1Fab.pdb #2
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
> open ./1Fab_scrubbed/250304_LOR69_PreF_1Fab.pdb
Chain information for 250304_LOR69_PreF_1Fab.pdb #3
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
> graphics bgColor white
> graphics silhouettes true width 2.5
> lighting gentle
> delete H
> color all byhetero
> view matrix camera
> -0.78633,0.1369,-0.60241,54.349,-0.61512,-0.083145,0.78404,283.93,0.057244,0.9871,0.1496,169.63
> hide all atoms
> show all cartoons
> mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45
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 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_MPE8_PreF_1Fab.pdb, chain A (#2), sequence alignment score = 47.9
RMSD between 13 pruned atom pairs is 0.344 angstroms; (across all 13 pairs:
0.344)
Matchmaker 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_LOR69_PreF_1Fab.pdb, chain A (#3), sequence alignment score = 68.7
RMSD between 13 pruned atom pairs is 0.315 angstroms; (across all 13 pairs:
0.315)
> hide #!2 models
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C
Alignment identifier is 1
> select #1/A-C:364
33 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A-C:364
33 atoms, 30 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 33 atom styles
> color sel byhetero
> select
> #1/A-C:74-98,149-158,161-172,195-206,217-240,254-263,268-276,278-283,355-357,369-371,377-382,474-477,492-518
3363 atoms, 3342 bonds, 453 residues, 1 model selected
> select #1/A-C:497
15 atoms, 12 bonds, 3 residues, 1 model selected
> select #1/A-C:497
15 atoms, 12 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> color sel byhetero
> select #1/A-C:479
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A-C:479
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select #1/A-C:479,497,378
54 atoms, 45 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 54 atom styles
> color sel byhetero
> color sel orange
> select #1/A-C:42,45,50,272,276,305,307,310,312,344,346,347,363,364
312 atoms, 279 bonds, 42 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 312 atom styles
> color sel medium blue
> style sel sphere
Changed 312 atom styles
> select #1/A-C:377,378,380,385,390
96 atoms, 84 bonds, 15 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 96 atom styles
> color sel red
> select #1/A-C:479,497
39 atoms, 33 bonds, 6 residues, 1 model selected
> style sel sphere
Changed 39 atom styles
> select #1/A-C:50,305,307,346,347
84 atoms, 72 bonds, 15 residues, 1 model selected
> color sel forest green
> mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45
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 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_MPE8_PreF_1Fab.pdb, chain A (#2), sequence alignment score = 47.9
RMSD between 13 pruned atom pairs is 0.344 angstroms; (across all 13 pairs:
0.344)
Matchmaker 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with
250304_LOR69_PreF_1Fab.pdb, chain A (#3), sequence alignment score = 68.7
RMSD between 13 pruned atom pairs is 0.315 angstroms; (across all 13 pairs:
0.315)
> delete /C
> color /A light gray
> color #1/H #6C96C4
> color #1/L #A5BCD6
> color #2/H #6EC25F
> color #2/L #A6D79D
> color #3/H #B25D56
> color #3/L #D69B96
> rename #1 LOR24-Fab
> rename #2 MPE8_5u68
> rename #3 LOR69-Fab
> hide #1.1 models
> hide #2.1 models
> hide #3.1 models
> select clear
> select /A:51-176,190-253,278-304,322-339,353-360,365-376,392-463,474-530
7589 atoms, 7654 bonds, 3 pseudobonds, 998 residues, 6 models selected
> select add /B:1-420,436-447,459-530
17372 atoms, 17568 bonds, 6 pseudobonds, 2282 residues, 6 models selected
> delete sel
> show #!3 models
> hide #!1 models
> select #3/H:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/H:59
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show #!2 models
> select add #3
2866 atoms, 2922 bonds, 8 pseudobonds, 371 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> select #2/H:33
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/L
Alignment identifier is 2/L
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
> set bgColor white
> lighting flat
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 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.4 (22H420)
Kernel Version: Darwin 22.6.0
Time since boot: 1 hour, 9 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
27E2N1100:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: UK02410065555
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 0,00
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 , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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