Opened 2 years ago

Closed 2 years ago

#9555 closed defect (can't reproduce)

Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0

Reported by: chimerax-bug-report@… 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-13.2.1-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.
4 alphafold predictions were open at the same time. ChimeraX was left open overnight with my laptop closed. 
Fatal Python error: Segmentation fault

Current thread 0x00000001ec338140 (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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{
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  "version" : 2,
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  "deployVersion" : 210,
  "modelCode" : "Mac14,9",
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    "build" : "22D68",
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  "captureTime" : "2023-08-09 20:51:56.8796 -0400",
  "incident" : "6D04C74E-A2CF-47C1-BB8F-75CA57E95C6C",
  "pid" : 10679,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-08-03 11:37:16.8357 -0400",
  "procStartAbsTime" : 16992116329927,
  "procExitAbsTime" : 23440526316212,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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  "crashReporterKey" : "6E77FEC5-96A4-E500-0E0D-525B1375ABBE",
  "throttleTimeout" : 2147483647,
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  "sleepWakeUUID" : "1E1F02D7-EAFD-42D3-A6AB-508205ED08F8",
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    "uuid" : "7665a44d-b6d3-323b-bb24-6ce940fbfbeb",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
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    "name" : "SkyLight"
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    "uuid" : "4d52c3a5-32e6-37a2-9d6c-23c612038354",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
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    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
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    "arch" : "arm64",
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    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
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    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
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    "uuid" : "1b766dc4-2490-3425-8726-45387675bc14",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
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    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
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],
  "sharedCache" : {
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  "size" : 3447455744,
  "uuid" : "835716ae-b363-3187-b065-cf94139bfc85"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.8G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 42.6M       34 \nCG image                          1872K       81 \nColorSync                          592K       29 \nCoreAnimation                     1616K       81 \nCoreGraphics                       240K       15 \nCoreUI image data                 5120K       56 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             1.2G      451 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         904.0M       10         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       56.6M       38 \nStack                            162.4M       38 \nVM_ALLOCATE                      204.9M      513 \nVM_ALLOCATE (reserved)           224.0M        7         reserved VM address space (unallocated)\n__AUTH                            1938K      361 \n__AUTH_CONST                      24.9M      589 \n__CTF                               756        1 \n__DATA                            20.0M      727 \n__DATA_CONST                      37.9M      737 \n__DATA_DIRTY                      1984K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       796.2M      147 \n__OBJC_CONST                      4759K      325 \n__OBJC_RO                         65.5M        1 \n__OBJC_RW                         1988K        1 \n__TEXT                           825.9M      758 \ndyld private memory                256K        1 \nmapped file                      214.5M       68 \nshared memory                     3344K       36 \n===========                     =======  ======= \nTOTAL                              4.8G     5360 \nTOTAL, minus reserved VM space     3.6G     5360 \n",
  "legacyInfo" : {
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},
  "trialInfo" : {
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      "factorPackIds" : {

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  "experiments" : [
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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/josh/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select #1

5550 atoms, 5633 bonds, 694 residues, 1 model selected  

> Rename #1 "Full CREPT homodimer w_CREPT peptide ligand"

Unknown command: Rename #1 "Full CREPT homodimer w_CREPT peptide ligand"  

> rename #1 "Full CREPT homodimer w_CREPT peptide ligand"

> log metadata #1

The model has no metadata

> log chains #1

Chain information for Full CREPT homodimer w_CREPT peptide ligand #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close

> open /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close

> ui tool show AlphaFold

> open /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

>

Incomplete command: sequence  

> alphafold predict
> MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,
> MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,
> IYPALGGKDVLSEKEKKLEEYKQKLARV directory "Full CREPT homodimer w_PRTC-GG"

Missing or invalid "sequences" argument: Sequences argument "" is not a chain
specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,IYPALGGKDVLSEKEKKLEEYKQKLARV
> directory "Full CREPT homodimer w_PRTC-GG"

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in Full CREPT homodimer w_PRTC-GG  

> open Full CREPT homodimer w_PRTC-GG/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> hide #1 models

> show #1 models

> select all

10969 atoms, 11136 bonds, 1374 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2 to #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 best_model.pdb, chain B (#1) with best_model.pdb, chain A (#2),
sequence alignment score = 1642.8  
RMSD between 130 pruned atom pairs is 0.681 angstroms; (across all 326 pairs:
24.164)  
  

> select all

10969 atoms, 11136 bonds, 1374 residues, 2 models selected  

> select none

Expected an objects specifier or a keyword  

> deselect all

Unknown command: deselect all  

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

Drag select of 46 residues  

> select add #1/C:7

390 atoms, 8 bonds, 47 residues, 2 models selected  

> select add #1/C:6

399 atoms, 16 bonds, 48 residues, 2 models selected  

> select add #2/C:28

406 atoms, 22 bonds, 49 residues, 2 models selected  

> show sel atoms

> color sel byhetero

> select clear

> hide #1 models

> show #1 models

> hide #2 models

> select :9

49 atoms, 43 bonds, 6 residues, 2 models selected  

> show #2 models

> select :16

50 atoms, 44 bonds, 6 residues, 2 models selected  

> select clear

> select #2/C:16

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide #1 models

> show #1 target m

> hide #1 target m

> ui windowfill toggle

> open /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
> format pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #2 models

Drag select of 21 residues  

> show sel atoms

> select clear

> hide #3 models

> show #3 models

> show #2 models

> show #1 models

> ui tool show Matchmaker

> hide #2 models

> hide #3 models

> hide #1 models

> show #2 models

> hide #2 models

> 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 best_model.pdb, chain A (#3) with best_model.pdb, chain A (#1),
sequence alignment score = 101.3  
RMSD between 21 pruned atom pairs is 0.404 angstroms; (across all 21 pairs:
0.404)  
  

> show #1 models

> show #2 models

> show #3 models

> hide #2 models

> ui tool show Matchmaker

Drag select of 105 atoms, 21 residues, 87 bonds  
Drag select of 31 atoms, 13 residues, 27 bonds  
Drag select of 100 atoms, 21 residues, 83 bonds  

> ui tool show Matchmaker

> matchmaker #1 & sel 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 best_model.pdb, chain A (#3) with best_model.pdb, chain C (#1),
sequence alignment score = 91.9  
RMSD between 14 pruned atom pairs is 0.821 angstroms; (across all 20 pairs:
5.852)  
  

> select clear

> hide #1 models

> show #2 models

> show #1 models

> hide #1 models

Drag select of 20 atoms, 9 residues, 15 bonds  
Drag select of 7 atoms, 2 residues, 6 bonds  
Drag select of 81 atoms, 19 residues, 70 bonds  
Drag select of 35 atoms, 11 residues, 29 bonds  
Drag select of 43 atoms, 11 residues, 36 bonds  

> select subtract #2/C:28

92 atoms, 79 bonds, 26 residues, 1 model selected  

> select add #2/C:28

99 atoms, 85 bonds, 27 residues, 1 model selected  
Drag select of 61 atoms, 19 residues, 49 bonds  

> select clear

Drag select of 45 atoms, 18 residues, 29 bonds  

> select clear

Drag select of 76 atoms, 26 residues, 65 bonds  
Drag select of 26 atoms, 7 residues, 23 bonds  

> select add #2/C:7

128 atoms, 65 bonds, 26 residues, 1 model selected  

> select add #2/C:6

132 atoms, 68 bonds, 27 residues, 1 model selected  

> select add #2/C:5

140 atoms, 75 bonds, 28 residues, 1 model selected  

> select add #2/C:2@CB

141 atoms, 75 bonds, 28 residues, 1 model selected  

> ui tool show Matchmaker

> select clear

> ui tool show Matchmaker

> matchmaker #3/A to #2/C pairing ss

Parameters  
---  
Chain pairing | ss  
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 best_model.pdb, chain C (#2) with best_model.pdb, chain A (#3),
sequence alignment score = 92.9  
RMSD between 17 pruned atom pairs is 0.844 angstroms; (across all 21 pairs:
5.913)  
  

> show #1 models

> hide #1 models

> ui tool show Matchmaker

> matchmaker #1 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 best_model.pdb, chain A (#2) with best_model.pdb, chain B (#1),
sequence alignment score = 1642.8  
RMSD between 130 pruned atom pairs is 0.681 angstroms; (across all 326 pairs:
24.164)  
  

> show #1 models

> hide #2 models

> hide #1 models

> show #2 models

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display3  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display3  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display3  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display3  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

> hide #2 models

> show #2 models

> hide #2 models

> show #1 models

> hide #3 models

> select #1/C:14

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

2 hydrogen bonds found  

> undo

> select #1/C:14

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ~hbonds

> select clear

> hbonds sel reveal true

Atom specifier selects no atoms  

> hbonds sel reveal true

Atom specifier selects no atoms  
Drag select of 55 atoms, 88 residues, 45 bonds  

> hbonds sel reveal true

286 hydrogen bonds found  

> select clear

Drag select of 252 atoms, 268 residues, 210 bonds, 109 pseudobonds  

> ~hbonds

> select clear

> hide #1 models

> show #2 models

> show #1 models

> hide #2 models

> select #1/C:14

12 atoms, 12 bonds, 1 residue, 1 model selected  

> rainbow sel

> undo

> select clear

> color #1 bychain

> select #1/C:14

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #1

5550 atoms, 5633 bonds, 694 residues, 1 model selected  

> select C

6981 atoms, 5551 bonds, 1395 residues, 3 models selected  

> select clear

> select C

6981 atoms, 5551 bonds, 1395 residues, 3 models selected  

> select clear

> select :C

Nothing selected  

> select \C

Expected an objects specifier or a keyword  

> select /C

406 atoms, 408 bonds, 49 residues, 2 models selected  

> color sel & #1 byhetero

> select clear

> select #1/C:14

12 atoms, 12 bonds, 1 residue, 1 model selected  

> lighting flat

> undo

> lighting full

> lighting simple

> select clear

> ui tool show "Side View"

Drag select of 209 atoms, 147 residues, 174 bonds  

> select all

11148 atoms, 11315 bonds, 1395 residues, 3 models selected  

> hide sel & #1 atoms

> select /c

406 atoms, 408 bonds, 49 residues, 2 models selected  

> show sel & #1 atoms

> select clear

> open "/Users/josh/Desktop/Full CREPT homodimer w_PRTC-GG/query.fasta"

Failed opening file /Users/josh/Desktop/Full CREPT homodimer w_PRTC-
GG/query.fasta:  
Sequence '3' differs in length from preceding sequences, and it is therefore
impossible to open these sequences as an alignment. If you want to open the
sequences individually, specify 'false' as the value of the 'alignment'
keyword in the 'open' command.  

> alphafold predict
> MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,MSSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKATEEKKSLKRTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,KDVLSEKEKKLEEYKQKLARV
> directory "CREPT homodimer w_PRTC binding domain"

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in CREPT homodimer w_PRTC binding domain  

> open CREPT homodimer w_PRTC binding domain/best_model.pdb

Chain information for best_model.pdb #4  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> hide #1 models

Drag select of 21 residues  

> show sel atoms

> color sel byhetero

> select clear

Unsupported scale factor (0.000000) detected on Display0  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display0  

Unsupported scale factor (0.000000) detected on Display2  

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  

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  

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  

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  

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  

Unsupported scale factor (0.000000) detected on Display0  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display0  

Unsupported scale factor (0.000000) detected on Display2  

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 Metal - 83
OpenGL renderer: Apple M2 Pro
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: Mac14,9
      Model Number: FPHH3LL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 42 days, 22 hours, 9 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        XG270HU:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 144.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2417H:
          Resolution: 1080 x 1920
          UI Looks like: 1080 x 1920 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: 90


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 pett, 2 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to pett
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 pett, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

Symptoms described match what we expect. User was running AlphaFold predictions, so this crash was unfortunate.

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