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Opened 2 years ago
Closed 2 years ago
#9929 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-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000204752080 (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
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{
"uptime" : 700000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 54893,
"osVersion" : {
"train" : "macOS 13.5.2",
"build" : "22G91",
"releaseType" : "User"
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"captureTime" : "2023-10-08 19:02:09.1256 +0800",
"incident" : "969F5B08-D651-4C6D-8AB7-6D1406E7DADF",
"pid" : 96214,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-08 14:12:20.5889 +0800",
"procStartAbsTime" : 16610033288624,
"procExitAbsTime" : 17027273714385,
"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"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8026ABDA-C978-978E-4C7F-184163BBA1EE",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 31102,
"sleepWakeUUID" : "B05D9C81-0BD8-44F2-A365-FDAECFCEE803",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105554055790568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":96214},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105554055790568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
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"uuid" : "6d458354-3c39-3f35-a3bb-d01a78817b4a",
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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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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/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used/selected_prediction.pdb
Chain information for selected_prediction.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> set bgColor white
> select /A:1-743
11476 atoms, 11600 bonds, 743 residues, 1 model selected
> color sel light sea green
> select /B:1-159
2561 atoms, 2589 bonds, 159 residues, 1 model selected
> ui mousemode right zoom
> color sel purple
> color sel magenta
> select /B:1-159
2561 atoms, 2589 bonds, 159 residues, 1 model selected
> select /B:1-159
2561 atoms, 2589 bonds, 159 residues, 1 model selected
Alignment identifier is 1/B
> select /B
2561 atoms, 2589 bonds, 159 residues, 1 model selected
Drag select of 3 residues
> select /B:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> select /A
11476 atoms, 11600 bonds, 743 residues, 1 model selected
Alignment identifier is 1/A
> select /A
11476 atoms, 11600 bonds, 743 residues, 1 model selected
> select /A:136
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:136
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:132
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:132
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select /A:136
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> select /A:132
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> select /A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel red
> select /A:132
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> hide sel cartoons
> show sel atoms
> show sel cartoons
> select /A:132
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select /A:136
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select
> /A:26-35,68-71,88-93,102-114,123-132,138-146,149-158,216-232,251-280,282-284,287-289,537-545,551-560,562-567,643-682,686-698,702-715
3427 atoms, 3434 bonds, 207 residues, 1 model selected
> select /A:142-143
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /A:142-143
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /A:143
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:143
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> select /B
2561 atoms, 2589 bonds, 159 residues, 1 model selected
Alignment identifier is 1/B
> select /B:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> select /C
2672 atoms, 2713 bonds, 169 residues, 1 model selected
Alignment identifier is 1/C
> select /C:135
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:135
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> save
> /Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used/BAP1-ASXL1-E2-reded.cxs
> open
> "/Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/job151_map_and_model-002
> interaction analysis.cxs"
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008,
step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> hide #!1 models
> open
> /Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used/BAP1-ASXL1-E2-reded.cxs
opened ChimeraX session
> open
> "/Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/job151_map_and_model-002
> interaction analysis.cxs" format session
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008,
step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> hide #!1 models
Mismatch between Cocoa '\x0' and Carbon 'd' for virtual key 2 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'D' for virtual key 2 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'd' for virtual key 2 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'D' for virtual key 2 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2202' for virtual key 2 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ce' for virtual key 2 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2202' for virtual key 2 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ce' for virtual key 2 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> delete 1ubq
Missing or invalid "atoms" argument: invalid atoms specifier
> delete A
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #10/A
> delete I
> delete /I
> delete /J
> delete /A G
Expected a keyword
> delete /A /G
> delete /B /H /C /D
> delete /E/F
> open /A
'/A' has no suffix
> open #10/A
'#10/A' has no suffix
> open 1ubq
Summary of feedback from opening 1ubq fetched from pdb
---
note | Fetching compressed mmCIF 1ubq from
http://files.rcsb.org/download/1ubq.cif
1ubq title:
Structure of ubiquitin refined At 1.8 angstroms resolution [more info...]
Chain information for 1ubq #4
---
Chain | Description | UniProt
A | UBIQUITIN | UBIQ_HUMAN 1-76
> delete 1ubq
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #4/A
> open
> /Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used/BAP1-ASXL1-E2-reded.cxs
opened ChimeraX session
> open
> "/Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/job151_map_and_model-002
> interaction analysis.cxs"
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008,
step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> open
> /Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used/BAP1-ASXL1-E2-reded.cxs
opened ChimeraX session
> cd
> /Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used
Current working directory is:
/Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open job151
'job151' has no suffix
> open job151.cxs
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008,
step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> hide #!1 models
> open BAP1-ASXL1-E2-reded.cxs
opened ChimeraX session
> open job151.cxs
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008,
step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> open
> /Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/AlphaFold/BAP1-ASXL1-E2-used/selected_prediction.pdb
Chain information for selected_prediction.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!1 models
> delete /J/I
> delete #2/A/e/f/g
> delete #2/C/D/H
> delete #2/B
> ui tool show Matchmaker
> matchmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8h1t, chain L (#2) with selected_prediction.pdb, chain A (#4),
sequence alignment score = 2965.4
RMSD between 221 pruned atom pairs is 1.178 angstroms; (across all 301 pairs:
5.104)
> select #4/B
2561 atoms, 2589 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #4/A
11476 atoms, 11600 bonds, 743 residues, 1 model selected
> color sel orange
> select #4/C
2672 atoms, 2713 bonds, 169 residues, 1 model selected
> color sel light gray
> hide #10/A
> hide #!10 models
> select #4/B
2561 atoms, 2589 bonds, 159 residues, 1 model selected
Alignment identifier is 4/B
> select #4/B:1-159
2561 atoms, 2589 bonds, 159 residues, 1 model selected
> select #4/B:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/B:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> select #2/K
520 atoms, 523 bonds, 73 residues, 1 model selected
> select #2/N
903 atoms, 922 bonds, 109 residues, 1 model selected
Alignment identifier is 2/N
> select #2/N:351
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/N:351
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> show sel cartoons
> show sel atoms
> select #4/C
2672 atoms, 2713 bonds, 169 residues, 1 model selected
Alignment identifier is 4/C
> select #4/C:135
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/C:135
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> open /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB_for_fig1.cxs
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level
-0.0121, step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> open /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB_for_fig1.cxs
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level
-0.0121, step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> open /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB_for_fig1.cxs
> format session
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level
-0.0121, step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> open /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB+Ub_for_Fig1.cxs
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level
-0.0121, step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> select #10/A
660 atoms, 608 bonds, 134 residues, 1 model selected
> color (#!10 & sel) yellow
> select #2/L
2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected
> color (#!2 & sel) dark gray
> select #2/N
903 atoms, 922 bonds, 109 residues, 1 model selected
> color (#!2 & sel) blue
> color (#!2 & sel) cornflower blue
> color (#!2 & sel) medium blue
> hide #!10 models
> open /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB+Ub_for_Fig1.cxs
Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level
-0.0121, step 2, values float32
Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at
level 0.008, step 1, values float32
Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown
at level 0.00982, step 1, values float32
opened ChimeraX session
> select #2/L
2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected
> color (#!2 & sel) dark gray
> select #2/N
903 atoms, 922 bonds, 109 residues, 1 model selected
> ui tool show "Color Actions"
> color sel coral
> color sel gold
> color sel yellow
> color sel gold
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel sandy brown
> color sel deep sky blue
> color sel cyan
> select #10/A
660 atoms, 608 bonds, 134 residues, 1 model selected
> color sel yellow
> color sel orange
> color sel gold
> color sel light goldenrod yellow
> color sel old lace
> color sel gold
> color sel orange
> color sel gold
> color sel yellow
> color sel gold
> select #2/N
903 atoms, 922 bonds, 109 residues, 1 model selected
> color sel sienna
> color sel coral
> color sel gold
> color sel dark orange
> color sel goldenrod
> color sel sandy brown
> color sel cyan
> color sel deep sky blue
> color sel sea green
> color sel medium sea green
> color sel forest green
> color sel lime green
> color sel spring green
> color sel lawn green
> color sel chartreuse
> color sel green
> color sel lime
> color sel olive
> color sel dark salmon
> color sel salmon
> color sel light salmon
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel tomato
> color sel brown
> color sel chocolate
> color sel saddle brown
> color sel coral
> color sel indian red
> color sel medium turquoise
> color sel turquoise
> color sel dodger blue
> select #2/L
2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected
> color sel light gray
> color sel gray
> color sel dark gray
> color sel dim gray
> color sel light gray
> color sel gray
> color sel light gray
> color sel dark gray
Drag select of 8h1t_L SES surface, 860 of 339594 triangles, 2 atoms, 3 bonds
Drag select of 1ubq_A SES surface, 284 of 74954 triangles
Drag select of 8h1t_L SES surface, 7126 of 339594 triangles, 1ubq_A SES
surface, 1934 of 74954 triangles, 28 atoms, 28 bonds, 1 residues
> select clear
Drag select of 8h1t_L SES surface, 40 of 339594 triangles, 8h1t_N SES surface,
1604 of 143458 triangles, 10 atoms, 1 residues, 8 bonds
> show sel atoms
> show sel cartoons
> show sel surfaces
> color (#!2 & sel) red
> undo
Alignment identifier is 2/N
> select #2/N:351-352
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/N:351-352
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/N:351
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/N:351
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
Drag select of 8h1t_L SES surface, 10 of 339594 triangles
> select clear
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> ~hbonds
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> save /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB_for_fig1.tif
> width 1148 height 903 supersample 4 transparentBackground true
> show #!10 models
> save /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/PR-DUB-Ub_for_fig1.tif
> width 1148 height 903 supersample 4 transparentBackground true
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
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
> open /Users/zhangtianyi/T/LiuLab/课题/ASXL/drawing/Fig1/Ub.pdb
Ub.pdb title:
Structure of ubiquitin refined At 1.8 angstroms resolution [more info...]
Chain information for Ub.pdb #1
---
Chain | Description | UniProt
A | ubiquitin | UBIQ_HUMAN 1-76
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD92CH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 35分钟58秒钟
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 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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Hi Tianyi,
--Eric