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Opened 2 years ago
Closed 2 years ago
#10039 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 0x00007ff858962700 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-10-21 21:01:54.00 +0200","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.6 (22G120)","roots_installed":0,"name":"ChimeraX","incident_id":"D22DEF93-8E23-4B1F-B2BF-BB2DF0059522"}
{
"uptime" : 24000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 1346,
"osVersion" : {
"train" : "macOS 13.6",
"build" : "22G120",
"releaseType" : "User"
},
"captureTime" : "2023-10-21 21:01:34.4621 +0200",
"incident" : "D22DEF93-8E23-4B1F-B2BF-BB2DF0059522",
"pid" : 2445,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-21 14:04:12.7753 +0200",
"procStartAbsTime" : 2259648454170,
"procExitAbsTime" : 24408481382761,
"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":"8A3E5B6F-CB07-58CB-B464-8BF5066EF728","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E42A0C0F-3F75-6953-8AA3-C5AE878B565C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 17424,
"sleepWakeUUID" : "7BE25886-BEE4-485A-A564-374A747B7B8D",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486565352\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe4b000-7fffffe4c000 [ 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":2445},
"ktriageinfo" : "VM - (arg = 0x0) Waiting on busy page was interrupted\nVM - (arg = 0x0) Waiting on busy page was interrupted\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486565352\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe4b000-7fffffe4c000 [ 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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"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=1.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 7200K 12 \nCG image 480K 34 \nColorSync 264K 30 \nCoreAnimation 188K 23 \nCoreGraphics 16K 3 \nCoreUI image data 4536K 34 \nFoundation 32K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.3G 1150 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 88K 22 \nStack 146.7M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 215.7M 189 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 49.4M 827 \n__DATA_CONST 41.1M 395 \n__DATA_DIRTY 1802K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 209.0M 202 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 1.0G 825 \ndyld private memory 292K 4 \nmapped file 214.4M 59 \nshared memory 3000K 31 \n=========== ======= ======= \nTOTAL 3.5G 4124 \nTOTAL, minus reserved VM space 3.3G 4124 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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"logWritingSignature" : "1f8df15f76495ddc69b3389a5a0a6e0c71b9b2d3",
"trialInfo" : {
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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/max.graf/Downloads/pdbfiles/PDB/TREX2-UAP56_on_P203-J138-coot-9.pdb
Summary of feedback from opening
/Users/max.graf/Downloads/pdbfiles/PDB/TREX2-UAP56_on_P203-J138-coot-9.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA1 7 VAL A
107 PHE A 110 0
Start residue of secondary structure not found: SHEET 2 AA1 7 ILE A 130 GLY A
133 1
Start residue of secondary structure not found: SHEET 3 AA1 7 VAL A 78 MET A
81 1
Start residue of secondary structure not found: SHEET 4 AA1 7 HIS A 154 ASP A
158 1
Start residue of secondary structure not found: SHEET 5 AA1 7 GLN A 185 SER A
190 1
9 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 AA3 7 VAL B 107 PHE B
110 0
Start residue of secondary structure not found: SHEET 2 AA3 7 ILE B 130 GLY B
133 1
Start residue of secondary structure not found: SHEET 3 AA3 7 VAL B 78 MET B
81 1
Start residue of secondary structure not found: SHEET 4 AA3 7 HIS B 154 ASP B
158 1
Start residue of secondary structure not found: SHEET 5 AA3 7 GLN B 185 SER B
190 1
Start residue of secondary structure not found: SHEET 6 AA3 7 VAL B 47 GLN B
50 1
8 messages similar to the above omitted
Chain information for TREX2-UAP56_on_P203-J138-coot-9.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
> open /Users/max.graf/Downloads/pdbfiles/PDB/TREX2_P203_J189-coot-3.pdb
Summary of feedback from opening
/Users/max.graf/Downloads/pdbfiles/PDB/TREX2_P203_J189-coot-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 59 59 PHE H
47 PHE H 50 1 4
Start residue of secondary structure not found: HELIX 60 60 PRO H 54 ASP H 62
1 9
Start residue of secondary structure not found: HELIX 61 61 GLU H 70 GLN H 78
1 9
Start residue of secondary structure not found: HELIX 62 62 ALA H 79 LEU H 81
1 3
Start residue of secondary structure not found: HELIX 63 63 LYS H 95 GLN H 106
1 12
15 messages similar to the above omitted
Cannot find LINK/SSBOND residue GLY (92 )
Cannot find LINK/SSBOND residue LYS (95 )
Cannot find LINK/SSBOND residue THR (96 )
Chain information for TREX2_P203_J189-coot-3.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/max.graf/Downloads/pdbfiles/PDB/HsUAP56_5suq_conf.pdb
Summary of feedback from opening
/Users/max.graf/Downloads/pdbfiles/PDB/HsUAP56_5suq_conf.pdb
---
warning | Ignored bad PDB record found on line 1
Chain information for HsUAP56_5suq_conf.pdb #3
---
Chain | Description
H | No description available
Y | No description available
> open
> /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J138_004_volume_map_sharp.mrc
Opened cryosparc_P203_J138_004_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 0.878, shown at level 0.0592, step 1, values float32
> open
> /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J189_map_sharp_onGrid_J138.mrc
Opened cryosparc_P203_J189_map_sharp_onGrid_J138.mrc as #5, grid size
256,256,256, pixel 0.878, shown at level 0.0513, step 1, values float32
> open
> /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J138_004_volume_map.mrc
Opened cryosparc_P203_J138_004_volume_map.mrc as #6, grid size 256,256,256,
pixel 0.878, shown at level 0.0429, step 1, values float32
> open
> /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J183_001_volume_map.mrc
Opened cryosparc_P203_J183_001_volume_map.mrc as #7, grid size 256,256,256,
pixel 0.878, shown at level 0.0513, step 1, values float32
> open
> /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J192_map_J183_lowpass_10.mrc
Opened cryosparc_P203_J192_map_J183_lowpass_10.mrc as #8, grid size
256,256,256, pixel 0.878, shown at level 0.0528, step 1, values float32
> open
> /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J192_map_J183_lowpass_10_RecA2-only.mrc
Opened cryosparc_P203_J192_map_J183_lowpass_10_RecA2-only.mrc as #9, grid size
256,256,256, pixel 0.878, shown at level 9.62e-06, step 1, values float32
> hide
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2.2 sides 24 thickness 1.2
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs
> lighting shadows false
> lighting soft intensity 0.4 fillIntensity 0.5 ambientIntensity 1
> camera ortho
> graphics silhouettes true
> windowsize 800 800
> size #1-10 pseudobondRadius 0.5
Changed 10 pseudobond radii
> select #1-10 minimumLength 1
10 pseudobonds, 2 models selected
> hide sel
> set bgColor white
> color #1/H plum target abcspf
> color #1,2/B #334195 target abcspf
> color #1,2/A #92D2FD target abcspf
> color #1,2/C dodger blue target abcspf
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.918,0.4868,0.86346,-0.13218,93.226,0.8725,-0.47336,0.1211,130.91
> windowsize 600 600
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #3 models
> show #3 models
> hide #!8 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.8 sides 12 divisions 20
> select add #3
3052 atoms, 3106 bonds, 10 pseudobonds, 377 residues, 3 models selected
> show #!2 models
> hide #!1 models
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.918,0.4868,0.86346,-0.13218,93.226,0.8725,-0.47336,0.1211,130.91
> view matrix
view matrix camera
0.041991,-0.17428,-0.9838,-48.051,0.4868,0.86346,-0.13218,90.538,0.8725,-0.47336,0.1211,135.02
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,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.051,0.4868,0.86346,-0.13218,90.538,0.8725,-0.47336,0.1211,135.02
> show #!1 models
> hide #!1 models
> zoom 0.9
> show #!1 models
> hide #!2 models
> zoom 1.05
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.051,0.4868,0.86346,-0.13218,90.538,0.8725,-0.47336,0.1211,135.02
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view matrix
view matrix camera
0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
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,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
> hide #3 models
> save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2.png pixelSize
> 0.1 supersample 4 transparentBackground true
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> select subtract #3
10 pseudobonds, 2 models selected
> show #!1 models
> hide #!2 models
> save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56reca2.png
> pixelSize 0.1 supersample 4 transparentBackground true
> show #1/B,C target s
> show #1/A target s
> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal
Summary of feedback from opening
/Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal
---
notes | Alignment identifier is clustalo_alignment_9971470_PCID2.clustal
Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain B to
sp|Q5JVF3|PCID2_HUMAN with 0 mismatches
Associated TREX2_P203_J189-coot-3.pdb chain B to sp|Q5JVF3|PCID2_HUMAN with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo_alignment_9971470_PCID2.clustal
Opened 8 sequences from clustalo_alignment_9971470_PCID2.clustal
> color byattribute seq_conservation palette blue:red:yellow
17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to
2.59
> color byattribute seq_conservation
17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to
2.59
> hide #1/C target acs
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
> turn y 15
> undo
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
> open /Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal
Summary of feedback from opening
/Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal
---
notes | Alignment identifier is clustalo_alignment_4391299_GANP.clustal
Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain A to H.sapiens with 0
mismatches
Associated TREX2_P203_J189-coot-3.pdb chain A to H.sapiens with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo_alignment_4391299_GANP.clustal
Opened 8 sequences from clustalo_alignment_4391299_GANP.clustal
> select up
10 pseudobonds, 2 models selected
> color byattribute seq_conservation
17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to
2.85
> select clear
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
> turn y 30
> show #1/H:10-15 target a y 30
Expected a keyword
> show #1/H:10-15 target a
> color byhetero
> undo
> color #1/H byhetero
> size stickRadius 0.3
Changed 17856 bond radii
> size stickRadius 0.4
Changed 17856 bond radii
> size stickRadius 0.3
Changed 17856 bond radii
> turn y -30
> transparency #1/A 80 target s
> transparency #1/A 80 target cs
> transparency #1/A 80 target acs
> transparency #1/A 90 target acs
> transparency #1/A 0 target acs
> hide #1/A,B target s
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
> color #1,2/B #334195 target abcspf
> color #1,2/A #92D2FD target abcspf
> color #1,2/C dodger blue target abcspf
> view matrix camera
> 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68
> zoom 1.25
> turn y 30
> show #1/B:374,376,388 target a
> color byhetero
> turn y -30
> turn y 25
> show #1/A:891 target a
> show #1/A:895 target a
> hide #1/A:891 target a
> zoom 1.25
> turn y5
Expected an axis vector or a keyword
> turn y 5
> turn y -5
> undo
> view matrix
view matrix camera
-0.21504,-0.20983,-0.9538,-39.646,0.44046,0.85084,-0.28648,44.383,0.87163,-0.48171,-0.09054,114.94
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,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix camera
> -0.21504,-0.20983,-0.9538,-39.646,0.44046,0.85084,-0.28648,44.383,0.87163,-0.48171,-0.09054,114.94
> ui tool show "Side View"
> save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56reca2.png
> pixelSize 0.1 supersample 4 transparentBackground true
> save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56ntd.png
> pixelSize 0.1 supersample 4 transparentBackground true
> view matrix camera
> 0.75602,0.035073,-0.6536,-20.296,-0.14069,-0.96651,-0.2146,29.646,-0.63925,0.2542,-0.72577,-47.817
> view matrix camera
> 0.929,-0.040789,-0.36783,-1.2168,-0.094083,-0.98728,-0.12815,35.885,-0.35793,0.15366,-0.92102,-62.294
> view matrix camera
> -0.21504,-0.20983,-0.9538,-39.646,0.44046,0.85084,-0.28648,44.383,0.87163,-0.48171,-0.09054,114.94
> save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56ntd.png
> pixelSize 0.1 supersample 4 transparentBackground true
> save /Volumes/Plaschka/max.graf/Master_thesis/png/fig8a_trex2-uap56ntd.png
> pixelSize 0.1 supersample 4 transparentBackground true
> show #1/A,B target s
> open /Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal
Summary of feedback from opening
/Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal
---
notes | Alignment identifier is clustalo_alignment_4391299_GANP.clustal
Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain A to H.sapiens with 0
mismatches
Associated TREX2_P203_J189-coot-3.pdb chain A to H.sapiens with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo_alignment_4391299_GANP.clustal
Opened 8 sequences from clustalo_alignment_4391299_GANP.clustal
> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal
Summary of feedback from opening
/Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal
---
notes | Alignment identifier is clustalo_alignment_9971470_PCID2.clustal
Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain B to
sp|Q5JVF3|PCID2_HUMAN with 0 mismatches
Associated TREX2_P203_J189-coot-3.pdb chain B to sp|Q5JVF3|PCID2_HUMAN with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo_alignment_9971470_PCID2.clustal
Opened 8 sequences from clustalo_alignment_9971470_PCID2.clustal
> color byattribute seq_conservation
17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to
2.85
> save
> /Volumes/Plaschka/max.graf/Master_thesis/png/fig8a_trex2-uap56ntd_conservation.png
> pixelSize 0.1 supersample 4 transparentBackground true
> hide #1/A target c
> transparency #1/A 90
> hide #1/A target ac
> transparency #1/A 95
> save
> /Volumes/Plaschka/max.graf/Master_thesis/png/fig8a_trex2-uap56ntd_conservation.png
> pixelSize 0.1 supersample 4 transparentBackground true
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-20.6.4
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: 8 GB
System Firmware Version: 515.0.0.0.0
OS Loader Version: 577.140.2~15
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.6 (22G120)
Kernel Version: Darwin 22.6.0
Time since boot: 20 hours, 51 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:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2723QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 6C0HGH3
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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