![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#14826 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: | 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 0x00007ff84a3ae7c0 (most recent call first):
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 290000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 594,
"osVersion" : {
"train" : "macOS 14.3.1",
"build" : "23D60",
"releaseType" : "User"
},
"captureTime" : "2024-03-26 12:34:06.6434 -0400",
"codeSigningMonitor" : 0,
"incident" : "A5CA75D3-E854-482B-AB1B-093989A7842A",
"pid" : 70941,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-03-21 15:13:10.3956 -0400",
"procStartAbsTime" : 213915793684297,
"procExitAbsTime" : 293830416714734,
"procName" : "ChimeraX",
"procPath" : "\/programs\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"AC853681-4A58-5B5D-82C4-63AC68D7F50B","thirdParty":true},
"parentProc" : "Exited process",
"parentPid" : 70940,
"coalitionName" : "com.apple.Terminal",
"crashReporterKey" : "230C5750-009B-40BA-F65F-DA55A59EC0A2",
"lowPowerMode" : 1,
"responsiblePid" : 18353,
"responsibleProc" : "Terminal",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 35,
"bridgeVersion" : {"build":"21P3049","train":"8.3"},
"sleepWakeUUID" : "6B26C274-B1F8-4C83-9F1D-3CED0470F8A3",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486663656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe63000-7fffffe64000 [ 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":70941},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486663656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe63000-7fffffe64000 [ 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/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_000.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_001.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_002.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_003.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_004.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_005.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_006.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_007.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_008.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_009.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_010.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_011.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_012.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_013.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_014.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_015.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_016.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_017.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_018.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_019.mrc
Opened J117_component_000_frame_000.mrc as #1.1, grid size 320,320,320, pixel
0.861, shown at level 0.0226, step 2, values float32
Opened J117_component_000_frame_001.mrc as #1.2, grid size 320,320,320, pixel
0.861, shown at level 0.0226, step 2, values float32
Opened J117_component_000_frame_002.mrc as #1.3, grid size 320,320,320, pixel
0.861, shown at level 0.0227, step 2, values float32
Opened J117_component_000_frame_003.mrc as #1.4, grid size 320,320,320, pixel
0.861, shown at level 0.0228, step 2, values float32
Opened J117_component_000_frame_004.mrc as #1.5, grid size 320,320,320, pixel
0.861, shown at level 0.023, step 2, values float32
Opened J117_component_000_frame_005.mrc as #1.6, grid size 320,320,320, pixel
0.861, shown at level 0.0232, step 2, values float32
Opened J117_component_000_frame_006.mrc as #1.7, grid size 320,320,320, pixel
0.861, shown at level 0.0234, step 2, values float32
Opened J117_component_000_frame_007.mrc as #1.8, grid size 320,320,320, pixel
0.861, shown at level 0.0237, step 2, values float32
Opened J117_component_000_frame_008.mrc as #1.9, grid size 320,320,320, pixel
0.861, shown at level 0.024, step 2, values float32
Opened J117_component_000_frame_009.mrc as #1.10, grid size 320,320,320, pixel
0.861, shown at level 0.0243, step 2, values float32
Opened J117_component_000_frame_010.mrc as #1.11, grid size 320,320,320, pixel
0.861, shown at level 0.0246, step 2, values float32
Opened J117_component_000_frame_011.mrc as #1.12, grid size 320,320,320, pixel
0.861, shown at level 0.0249, step 2, values float32
Opened J117_component_000_frame_012.mrc as #1.13, grid size 320,320,320, pixel
0.861, shown at level 0.0253, step 2, values float32
Opened J117_component_000_frame_013.mrc as #1.14, grid size 320,320,320, pixel
0.861, shown at level 0.0257, step 2, values float32
Opened J117_component_000_frame_014.mrc as #1.15, grid size 320,320,320, pixel
0.861, shown at level 0.0261, step 2, values float32
Opened J117_component_000_frame_015.mrc as #1.16, grid size 320,320,320, pixel
0.861, shown at level 0.0267, step 2, values float32
Opened J117_component_000_frame_016.mrc as #1.17, grid size 320,320,320, pixel
0.861, shown at level 0.0272, step 2, values float32
Opened J117_component_000_frame_017.mrc as #1.18, grid size 320,320,320, pixel
0.861, shown at level 0.0278, step 2, values float32
Opened J117_component_000_frame_018.mrc as #1.19, grid size 320,320,320, pixel
0.861, shown at level 0.0284, step 2, values float32
Opened J117_component_000_frame_019.mrc as #1.20, grid size 320,320,320, pixel
0.861, shown at level 0.029, step 2, values float32
> vseries play #1 loop true
No volume series specified
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/*.mrc
> vseries true
Opened map series J117_component_000_frame_000.mrc as #2, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0226, step 2, values float32
> close #1
> vseries play #2 loop true
> stop
> vseries stop
Missing or invalid "series" argument: empty atom specifier
> vseries stop #2
> volume #2.7 step 1
> volume #2.7 level 0.06643
> volume #2.7 level 0.07131
> volume #2.7 level 0.07023
> vseries play #2 loop true
> movie record
> movie encode /Users/bravine/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/bravine/Desktop/movie.mp4
> movie record
> movie encode /Users/bravine/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/bravine/Desktop/movie.mp4
> movie record
> movie encode /Users/bravine/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> vseries stop #2 loop true
Expected fewer arguments
> vseries stop #2
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_001/*.mrc
> vseries true
Opened map series J117_component_001_frame_000.mrc as #1, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0251, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_002/*.mrc
> vseries true
Opened map series J117_component_002_frame_000.mrc as #3, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0247, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_003/*.mrc
> vseries true
Opened map series J117_component_003_frame_000.mrc as #4, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0279, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_004/*.mrc
> vseries true
Opened map series J117_component_004_frame_000.mrc as #5, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0243, step 2, values float32
> volume #1.20 color #ff4e54
> volume #1.20 color #ff6d6c
> volume #1.20 color #85ffa1
> volume #1.20 color #99ff9a
> volume #1.20 level 0.07
> volume #4.20 level 0.07
> volume #5.20 level 0.07
> volume #1.20 step 1
> volume #3.20 step 1
> volume #4.20 step 1
> volume #5.20 step 1
> volume #3.20 level 0.07
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select down
Nothing selected
> vseries play #1 loop true
> vseries stop #
Missing or invalid "series" argument: invalid map series specifier
> vseries stop #1
> vseries play #1 loop false
> vseries play #2 loop false
> show #!2 models
> hide #!1 models
> vseries play #2 loop false
> hide #!2 models
> show #!3 models
> vseries play #3 loop false
> show #!1 models
> hide #!3 models
> vseries play #1 loop false
> show #!2 models
> hide #!1 models
> vseries play #2 loop false
> show #!4 models
> hide #!2 models
> vseries play #4 loop false
> hide #!4 models
> show #!5 models
> vseries play #5 loop false
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!5 models
> vseries play #5 loop false
> vseries play #2 loop false
> close #1-5
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J103_NMIDPIWImask.mrc
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J108_PAZmask.mrc
Opened cryosparc_P339_J103_NMIDPIWImask.mrc as #1.1, grid size 320,320,320,
pixel 0.861, shown at level 1, step 2, values float32
Opened cryosparc_P339_J108_PAZmask.mrc as #1.2, grid size 320,320,320, pixel
0.861, shown at level 0.798, step 2, values float32
> volume #1.1 step 1
> volume #1.2 step 1
> volume #1.2 level 0.9749
> close #1
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J103_NMIDPIWImask.mrc
Opened cryosparc_P339_J103_NMIDPIWImask.mrc as #1, grid size 320,320,320,
pixel 0.861, shown at level 1, step 2, values float32
> volume #1 level 0.9749
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J108_PAZmask.mrc
Opened cryosparc_P339_J108_PAZmask.mrc as #2, grid size 320,320,320, pixel
0.861, shown at level 0.798, step 2, values float32
> volume #2 step 1
> volume #1 step 1
> volume #2 level 0.9809
> ui mousemode right "mark plane"
> volume #1 color #b2b2b24c
> volume #1 color #b2b2b24d
> volume #2 color #ffffb271
> volume #2 color #ffffb270
> volume #2 color #ffffb25e
> ui mousemode right "mark plane"
> ui mousemode right "mark point"
> marker #3 position 136.6,142.6,139.3 color yellow radius 1
> marker #3 position 123.9,140.2,124.7 color yellow radius 1
> ui mousemode right "delete markers"
> marker delete #3:2
> ui mousemode right "move markers"
> marker change #3:1 position 133.6,142.1,136.1
> marker change #3:1 position 118.6,152.2,123.5
> marker change
Missing or invalid "someMarkers" argument: empty atom specifier
> marker change coordinateSystem #1
Missing or invalid "someMarkers" argument: invalid atoms specifier
> marker change #3 coordinateSystem #1
> getcrd #3
Atom /M:1@M 118.582 152.189 123.484
> marker change #3 coordinateSystem #2
> getcrd #3
Atom /M:1@M 118.582 152.189 123.484
> close #1
> close #3
> close #2
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_000/*.mrc
> vseries true
Opened map series J118_component_000_frame_000.mrc as #1, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0278, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_001/*.mrc
> vseries true
Opened map series J118_component_001_frame_000.mrc as #2, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0252, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_002/*.mrc
> vseries true
Opened map series J118_component_002_frame_000.mrc as #3, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.026, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_003/*.mrc
> vseries true
Opened map series J118_component_003_frame_000.mrc as #4, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0255, step 2, values float32
> open
> /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_004/*.mrc
> vseries true
Opened map series J118_component_004_frame_000.mrc as #5, 20 images, grid size
320,320,320, pixel 0.861, shown at level 0.0254, step 2, values float32
> color #2 #76bf80ff models
> volume #1.1 step 1
> volume #2.1 step 1
> volume #3.1 step 1
> volume #4.1 step 1
> volume #5.1 step 1
> volume #1.1 level 0.03509
> volume #2.1 level 0.035
> volume #3.1 level 0.035
> volume #5.1 level 0.035
> vseries play #1 loop false
> vseries play #2 loop false
> hide #!1 models
> vseries play #2 loop false
> vseries play #3 loop false
> hide #!2 models
> vseries play #3 loop false
> hide #!3 models
> vseries play #4 loop false
> hide #!4 models
> vseries play #5 loop false
> hide #!5 models
> show #!1 models
> vseries play #1 loop false
> ui tool show Rotamers
Window position QRect(2415,251 600x300) outside any known screen, using
primary screen
No residues selected
> close #1-5
> open /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO-
> clade/4f3t-hAgo2.cif /Users/bravine/Documents/JTLab/WAGOs/structural-
> overlays/AGO-clade/4kre-hAgo1.cif
> /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO-clade/4krf-
> hAgo1.cif /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO-
> clade/5js2-hAgo2.cif /Users/bravine/Documents/JTLab/WAGOs/structural-
> overlays/AGO-clade/5vm9-hAgo3.cif
> /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO-
> clade/5w6v-hAgo1.cif /Users/bravine/Documents/JTLab/WAGOs/structural-
> overlays/AGO-clade/6oon-hAgo4.cif
4f3t-hAgo2.cif title:
Human Argonaute-2 - miR-20a complex [more info...]
Chain information for 4f3t-hAgo2.cif #1
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
R | RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*G*CP*AP*GP*G)-3')
|
Non-standard residues in 4f3t-hAgo2.cif #1
---
IPH — phenol
4kre-hAgo1.cif title:
Structure of Human Argonaute-1 bound to endogenous Sf9 RNA [more info...]
Chain information for 4kre-hAgo1.cif #2
---
Chain | Description | UniProt
A | Protein argonaute-1 | AGO1_HUMAN 1-857
R | RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*A*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
|
4krf-hAgo1.cif title:
Structure of Human Argonaute-1 let-7 complex [more info...]
Chain information for 4krf-hAgo1.cif #3
---
Chain | Description | UniProt
A | Protein argonaute-1 | AGO1_HUMAN 1-857
R | RNA
(5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')
|
5js2-hAgo2.cif title:
Human Argonaute-2 Bound to a Modified siRNA [more info...]
Chain information for 5js2-hAgo2.cif #4
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN 1-859
B | modified siRNA |
Non-standard residues in 5js2-hAgo2.cif #4
---
6NW — 2'-O-methyl-5'-O-thiophosphonoadenosine
6OO — 2'-O-methyl-5'-O-thiophosphonocytidine
6OP — 1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-
hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione
F2T — 2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine
IPH — phenol
MG — magnesium ion
PO4 — phosphate ion
UFT — 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
5vm9-hAgo3.cif title:
Human Argonaute3 bound to guide RNA [more info...]
Chain information for 5vm9-hAgo3.cif #5
---
Chain | Description | UniProt
A C | Protein argonaute-3 | AGO3_HUMAN 1-860
B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') |
D | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') |
5vm9-hAgo3.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
5w6v-hAgo1.cif title:
The Structure of human Argonaute-1 in complex with the hook motif of human
GW182 [more info...]
Chain information for 5w6v-hAgo1.cif #6
---
Chain | Description | UniProt
A | Protein argonaute-1 | AGO1_HUMAN 1-857
B | Trinucleotide repeat-containing gene 6A protein | TNR6A_HUMAN 820-841
R | RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*AP*A)-3') |
6oon-hAgo4.cif title:
Human Argonaute4 bound to guide RNA [more info...]
Chain information for 6oon-hAgo4.cif #7
---
Chain | Description | UniProt
A | Protein argonaute-4 | AGO4_HUMAN 1-861
B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') |
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 INTEL-22.1.29
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.80.5.0.1 (iBridge: 21.16.3049.0.0,0)
OS Loader Version: 580~1337
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 13 days, 15 hours, 42 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Thunderbolt Display:
Display Type: LCD
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: C02PX25NF2GC
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
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 , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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