![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 21 months ago
#14570 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-14.3-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 0x00000001dcfbdc40 (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" : 48000,
"procRole" : "Background",
"version" : 2,
"userID" : 219546281,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 3338,
"osVersion" : {
"train" : "macOS 14.3",
"build" : "23D56",
"releaseType" : "User"
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"captureTime" : "2024-02-12 11:15:32.9093 +0100",
"codeSigningMonitor" : 1,
"incident" : "DF0E34B0-1EA6-45EF-9931-B69D0CF52BCA",
"pid" : 17297,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-02-08 13:16:06.5949 +0100",
"procStartAbsTime" : 701807918101,
"procExitAbsTime" : 1173580746221,
"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":"7F83E32A-BFE9-56F4-88EA-43A0EF0A1FC9","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D55DAE4A-6BD8-4020-76A5-4D6E6D0B0139",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 2790,
"sleepWakeUUID" : "3F99DEAE-0A11-42C9-81B0-ABD140095B66",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 68719476712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- 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":17297},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 68719476712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)",
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/flogeg/Downloads/6apb.cif format mmcif
6apb.cif title:
Crystal Structure of Non-Neutralizing Infant Antibody ADI-14359 in Complex
with Postfusion RSV F Glycoprotein [more info...]
Chain information for 6apb.cif #1
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F0 | Q84850_HRSV 1-146,
A0A1P8J9V4_HRSV 147-513
H | IgG H chain |
L | ADI-14359 Fab Light Chain |
Non-standard residues in 6apb.cif #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> close
> open /Users/flogeg/Downloads/5wb0.cif
5wb0.cif title:
Crystal structure of human metapneumovirus fusion glycoprotein stabilized in
the prefusion state [more info...]
Chain information for 5wb0.cif #1
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | Q1A2Z0_9MONO 1-489
Non-standard residues in 5wb0.cif #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SO4 — sulfate ion
5wb0.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> sym #1 assembly 1
Made 3 copies for 5wb0.cif assembly 1
> select #1
3602 atoms, 3525 bonds, 1 pseudobond, 588 residues, 2 models selected
> hide #!2.1-3 atoms
> sym #2.1
5wb0.cif mmCIF Assemblies
---
> log metadata #2.1
No models had metadata
> log chains #2.1
Chain information for 5wb0.cif #2.1
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | Q1A2Z0_9MONO 1-489
> view #2.1 clip false
> show #!2.1 target m
> sym #1
5wb0.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly| 3 copies of chains A,B,F
> log metadata #1
Metadata for 5wb0.cif #1
---
Title | Crystal structure of human metapneumovirus fusion glycoprotein
stabilized in the prefusion state
Citation | Battles, M.B., Mas, V., Olmedillas, E., Cano, O., Vazquez, M.,
Rodriguez, L., Melero, J.A., McLellan, J.S. (2017). Structure and
immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein.
Nat Commun, 8, 1528-1528. PMID: 29142300. DOI: 10.1038/s41467-017-01708-9
Non-standard residues | BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose;
mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SO4 — sulfate ion
Gene source | Human metapneumovirus
Experimental method | X-ray diffraction
Resolution | 2.600Å
> log chains #1
Chain information for 5wb0.cif #1
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | Q1A2Z0_9MONO 1-489
> sequence chain #1/F
Alignment identifier is 1/F
> show #!2 target m
> open /Users/flogeg/Downloads/4jhw.cif
4jhw.cif title:
Crystal Structure of Respiratory Syncytial Virus Fusion Glycoprotein
Stabilized in the Prefusion Conformation by Human Antibody D25 [more info...]
Chain information for 4jhw.cif #3
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_HRSVA 26-136 137-513
H | D25 antigen-binding fragment heavy chain |
L | D25 light chain |
4jhw.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> select up
3602 atoms, 3525 bonds, 1 pseudobond, 588 residues, 2 models selected
> select up
10380 atoms, 10439 bonds, 1 pseudobond, 1474 residues, 4 models selected
> select up
10380 atoms, 10439 bonds, 1 pseudobond, 1474 residues, 4 models selected
> sym #3 assembly 1
Made 3 copies for 4jhw.cif assembly 1
> select #4:F,H
Nothing selected
> select #4:F
Nothing selected
> select #4 /F
10428 atoms, 10596 bonds, 3 pseudobonds, 1347 residues, 6 models selected
> select #4 /l,H
9906 atoms, 10146 bonds, 1311 residues, 3 models selected
> hide sel cartoons
> matchmaker #2 to #4
Specify a single 'to' model only
> matchmaker #2 to #4.1
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 4jhw.cif, chain F (#4.1) with 5wb0.cif, chain F (#2.1), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
Matchmaker 4jhw.cif, chain F (#4.1) with 5wb0.cif, chain F (#2.2), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
Matchmaker 4jhw.cif, chain F (#4.1) with 5wb0.cif, chain F (#2.3), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
> ui mousemode right rotate
> matchmaker #2.1-2.3 to #4
Specify a single 'to' model only
> matchmaker #2 to #4.2
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 4jhw.cif, chain F (#4.2) with 5wb0.cif, chain F (#2.1), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
Matchmaker 4jhw.cif, chain F (#4.2) with 5wb0.cif, chain F (#2.2), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
Matchmaker 4jhw.cif, chain F (#4.2) with 5wb0.cif, chain F (#2.3), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
> matchmaker #1 to #4
Specify a single 'to' model only
> matchmaker #1 to #3
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 4jhw.cif, chain F (#3) with 5wb0.cif, chain F (#1), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
> show #!1 models
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> show #!2 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select add #4
20334 atoms, 20742 bonds, 3 pseudobonds, 2658 residues, 7 models selected
> select subtract #4
Nothing selected
> hide #!2 models
> show #!3 models
> hide #!4 models
> select #3 /H, L
3302 atoms, 3382 bonds, 437 residues, 1 model selected
> hide sel cartoons
> close #2
> close #4
> hide sel atoms
> select #1
3602 atoms, 3525 bonds, 1 pseudobond, 588 residues, 2 models selected
> hide sel atoms
> select #3
6778 atoms, 6914 bonds, 1 pseudobond, 886 residues, 2 models selected
> hide sel atoms
> sym #1 assembly 1
Made 3 copies for 5wb0.cif assembly 1
> sym #13assembly 1
Missing or invalid "structures" argument: invalid atomic structures specifier
> sym #3 assembly 1
Made 3 copies for 4jhw.cif assembly 1
> select #4 /
Expected a keyword
> select #4 /L,H
9906 atoms, 10146 bonds, 1311 residues, 3 models selected
> hide sel atoms
> hide sel surfaces
> matchmaker #2.1 to #4.1
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 4jhw.cif, chain F (#4.1) with 5wb0.cif, chain F (#2.1), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
> matchmaker #2.2 to #4.2
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 4jhw.cif, chain F (#4.2) with 5wb0.cif, chain F (#2.2), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
> matchmaker #2.3 to #4.3
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 4jhw.cif, chain F (#4.3) with 5wb0.cif, chain F (#2.3), sequence
alignment score = 1209.1
RMSD between 336 pruned atom pairs is 1.060 angstroms; (across all 432 pairs:
2.140)
> ui mousemode right "move picked models"
> view matrix models
> #2.3,-0.88605,-0.37356,0.27453,27.386,-0.37808,0.23961,-0.89422,159.48,0.26826,-0.89612,-0.35355,3.1743
> undo
> select #3
6778 atoms, 6914 bonds, 1 pseudobond, 886 residues, 2 models selected
> select #4
20334 atoms, 20742 bonds, 3 pseudobonds, 2658 residues, 7 models selected
> hide sel atoms
> select #2
10806 atoms, 10575 bonds, 3 pseudobonds, 1764 residues, 7 models selected
> hide sel atoms
> ~select
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> select #2
10806 atoms, 10575 bonds, 3 pseudobonds, 1764 residues, 7 models selected
> color sel #4DB5BC
> select #4
20334 atoms, 20742 bonds, 3 pseudobonds, 2658 residues, 7 models selected
> color sel #B84145
> ¨s
Unknown command: ¨s
> ~select
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/flogeg/Desktop/movie1.mp4
Movie saved to /Users/flogeg/Desktop/movie1.mp4
> view orient
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save /Users/flogeg/Desktop/RSV-MPV-overlay.tif width 1344 height 903
> supersample 3 transparentBackground true
> save /Users/flogeg/Desktop/RSV-MPV-overlay.cxs
> open /Users/flogeg/Desktop/RSV-MPV-overlay.cxs format session
opened ChimeraX session
> color #2.1 #a1a1a1ff
> open /Users/flogeg/Desktop/PreF.cxs
opened ChimeraX session
> select
> #1/F:30-33,38-48,51-60,176-181,185-194,243-244,286-289,296-305,309-318,321-322,333-336,340-344,349-352,358-361,364-367,373-375,395-398,404-407,411-415,422-426,430-434,439-443,449-452,455-458,466-469
1030 atoms, 1031 bonds, 133 residues, 1 model selected
> ~select /2:26-44
1030 atoms, 1031 bonds, 133 residues, 2 models selected
> ~select #2:26-44
1030 atoms, 1031 bonds, 133 residues, 2 models selected
> select #2:26-44
1374 atoms, 1407 bonds, 171 residues, 3 models selected
> color sel #4DB5BC
> select #2:313-318
162 atoms, 168 bonds, 18 residues, 3 models selected
> color sel #4DB5BC
> select
> #1/F:73-95,148-159,162-172,195-210,216-240,253-262,267-284,376-385,473-478,491-513
1235 atoms, 1236 bonds, 154 residues, 1 model selected
> select #2:313-318
162 atoms, 168 bonds, 18 residues, 3 models selected
> select #2:380-394
369 atoms, 378 bonds, 45 residues, 3 models selected
> select #2:313-318
162 atoms, 168 bonds, 18 residues, 3 models selected
> select #2:380-394
369 atoms, 378 bonds, 45 residues, 3 models selected
> color sel #4DB5BC
> select up
10428 atoms, 10596 bonds, 1347 residues, 6 models selected
> select #2:45-54
735 atoms, 750 bonds, 93 residues, 3 models selected
> color sel #FF876F
> select #2:301-312
276 atoms, 282 bonds, 36 residues, 3 models selected
> color sel #FF876F
> select #2:337-353
405 atoms, 420 bonds, 51 residues, 3 models selected
> color sel #FF876F
> select #2:359-378
468 atoms, 471 bonds, 60 residues, 3 models selected
> color sel #FF876F
> select #2:55-62
546 atoms, 552 bonds, 72 residues, 3 models selected
> color sel #870052
> select #2:146-194
3252 atoms, 3297 bonds, 441 residues, 3 models selected
> color sel #870052
> select #2:267-300
828 atoms, 831 bonds, 102 residues, 3 models selected
> select #2:287-300
330 atoms, 330 bonds, 42 residues, 3 models selected
> color sel #870052
> select up
483 atoms, 489 bonds, 60 residues, 6 models selected
> select up
10428 atoms, 10596 bonds, 1347 residues, 6 models selected
> select up
20334 atoms, 20742 bonds, 2658 residues, 6 models selected
> select #2:55-62
546 atoms, 552 bonds, 72 residues, 3 models selected
> select #2:63-97
2517 atoms, 2544 bonds, 324 residues, 3 models selected
> select #2:63-97
2517 atoms, 2544 bonds, 324 residues, 3 models selected
> color sel #F59A00
> select up
3246 atoms, 3300 bonds, 417 residues, 12 models selected
> select #2:195-244
2052 atoms, 2073 bonds, 258 residues, 3 models selected
> select up
2178 atoms, 2205 bonds, 273 residues, 12 models selected
> color sel #F59A00
> select
> #1/F:30-33,38-48,51-60,176-181,185-194,243-244,286-289,296-305,309-318,321-322,333-336,340-344,349-352,358-361,364-367,373-375,395-398,404-407,411-415,422-426,430-434,439-443,449-452,455-458,466-469
1030 atoms, 1031 bonds, 133 residues, 1 model selected
> select #2:245-286
1005 atoms, 1014 bonds, 126 residues, 3 models selected
> color sel #54B986
> color sel #094334
> select #2:402-472
1578 atoms, 1596 bonds, 213 residues, 3 models selected
> color sel #002C34
> color sel marine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel navy blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel blue
> color sel #002C34
> color sel #051650
> select #2:245-286
1005 atoms, 1014 bonds, 126 residues, 3 models selected
> color sel #154406
> select #2:319-336, 395-401, 473-513
1554 atoms, 1575 bonds, 198 residues, 3 models selected
> color sel #4F0433
> view matrix models #2.3,0,1,0,-101.29,0,0,1,150.37,1,0,0,10.066
> undo
> select #2:245-286
1005 atoms, 1014 bonds, 126 residues, 3 models selected
> Color sel #FFC66D
Unknown command: Color sel #FFC66D
> color sel #FFC66D
> select #2:402-472
1578 atoms, 1596 bonds, 213 residues, 3 models selected
> color sel #154406
> select #2:319-336, 395-401, 473-513
1554 atoms, 1575 bonds, 198 residues, 3 models selected
> color sel #4DB5BC
> select #2:26-44, 313-318, 380-394
1905 atoms, 1953 bonds, 234 residues, 3 models selected
> select #2:26-44, 313-318, 380-394
1905 atoms, 1953 bonds, 234 residues, 3 models selected
> color sel #B84145
> select #2:45-54, 301-312, 337-353, 359-378
1884 atoms, 1923 bonds, 240 residues, 3 models selected
> color sel #FF876F
> view matrix models #2.2,0,0,1,-26.888,1,0,0,107.51,0,1,0,-142.82
> undo
> select #2:63-97, 195-244
4569 atoms, 4620 bonds, 582 residues, 3 models selected
> color sel #4F0433
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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 Metal - 88
OpenGL renderer: Apple M2
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: Mac14,7
Model Number: Z16S000NZKS/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D56)
Kernel Version: Darwin 23.3.0
Time since boot: 6 days, 20 hours, 44 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: No
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 , 21 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 , 21 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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