Opened 2 years ago

Closed 2 years ago

#10188 closed defect (nonchimerax)

Graphics crash, macOS 14.1.1, Intel Iris Plus Graphics 655

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304150037 (2023-04-15 00:37:23 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007ff84fb24b40 (most recent call first):
  File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
  File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
  File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
  File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
  File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.6-rc2023.04.15.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-rc2023.04.15.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-rc2023.04.15.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-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6-rc2023.04.15.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" : 130000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,2",
  "coalitionID" : 2265,
  "osVersion" : {
    "train" : "macOS 14.1.1",
    "build" : "23B81",
    "releaseType" : "User"
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  "captureTime" : "2023-11-18 21:54:10.8138 +0100",
  "codeSigningMonitor" : 0,
  "incident" : "95359877-8FE4-4627-AA9A-3C689C7C4153",
  "pid" : 33432,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-11-18 14:35:49.0946 +0100",
  "procStartAbsTime" : 112971244334222,
  "procExitAbsTime" : 139242777199613,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3C18038A-1839-5728-A3A7-57BDBB3C7A0C","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "9B98626C-34AA-4037-BF37-43F9688AEC0C",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 17198,
  "bridgeVersion" : {"build":"21P1069","train":"8.1"},
  "sleepWakeUUID" : "22AF1C2B-8420-4833-A4D3-4FB594BEC4C4",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":33432},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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  "faultingThread" : 0,
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    "uuid" : "8d45a5d3-7bfc-33a6-a3d4-cd98010fbfec",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/psutil\/_psutil_osx.abi3.so",
    "name" : "_psutil_osx.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5084532736,
    "size" : 176128,
    "uuid" : "5e4388ca-929a-385d-8f7e-4a6c443b3eab",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/pdb\/_pdbio.cpython-39-darwin.so",
    "name" : "_pdbio.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5081825280,
    "size" : 446464,
    "uuid" : "363f0a7f-8a13-3465-82ee-3a637fe01cc3",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-39-darwin.so",
    "name" : "_mmcif.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5083185152,
    "size" : 454656,
    "uuid" : "5a0f30d4-b4ba-316a-8278-78d0c72f5977",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/mmcif.cpython-39-darwin.so",
    "name" : "mmcif.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5081186304,
    "size" : 20480,
    "uuid" : "ba973aa3-7e75-3e17-ba66-60209a667b0d",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/graphics\/_graphics.cpython-39-darwin.so",
    "name" : "_graphics.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5080797184,
    "size" : 77824,
    "uuid" : "45e679b6-43af-3a5e-b39a-4521b5380f01",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/atomic\/_ribbons.cpython-39-darwin.so",
    "name" : "_ribbons.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5080952832,
    "size" : 16384,
    "uuid" : "3b220334-2123-365c-babe-beb387dab5ca",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/linalg\/lapack_lite.cpython-39-darwin.so",
    "name" : "lapack_lite.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5081612288,
    "size" : 98304,
    "uuid" : "da802e8c-8946-3174-a88d-c460d9f502f9",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/msgpack\/_cmsgpack.cpython-39-darwin.so",
    "name" : "_cmsgpack.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5081321472,
    "size" : 143360,
    "uuid" : "809e113e-a9e6-304f-8c5d-9c998d93032c",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/core\/_serialize.cpython-39-darwin.so",
    "name" : "_serialize.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5080338432,
    "size" : 212992,
    "uuid" : "0a572b0f-7271-319c-9f17-7d1821eaccd7",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/lz4\/frame\/_frame.cpython-39-darwin.so",
    "name" : "_frame.cpython-39-darwin.so"
  },

[deleted to fit within ticket limits]

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3

210 contacts  

> show (#!9#!5.1-2 & sel) target ab

> select clear

> ui tool show "Side View"

> select #9/A:146

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #5.1/B:131

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

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A #2.1/A

Alignment identifier is 2  

> ui tool show "Show Sequence Viewer"

> sequence chain #4.1/B #4.2/C #5.1/B #5.2/C

Alignment identifier is 3  

> select #4.1/B:108 #4.2/C:108 #5.1/B:108 #5.2/C:108

32 atoms, 28 bonds, 4 residues, 4 models selected  

> select #4.1/B:108-158 #4.2/C:108-158 #5.1/B:108-158 #5.2/C:108-158

1620 atoms, 1664 bonds, 204 residues, 4 models selected  
3 [ID: 3] region 4 chains [108-158] RMSD: 67.396  
  

> select #4.1/B:19-27 #4.2/C:19-27 #5.1/B:19-27 #5.2/C:19-27

280 atoms, 284 bonds, 36 residues, 4 models selected  

> select #4.1/B:27-47 #4.2/C:27-47 #5.1/B:27-47 #5.2/C:27-47

684 atoms, 684 bonds, 84 residues, 4 models selected  
3 [ID: 3] region 4 chains [27-47] RMSD: 74.213  
  

> select #1.1/A:399 #2.1/A:399

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1.1/A:399-535 #2.1/A:399-535

2348 atoms, 2414 bonds, 274 residues, 2 models selected  
2 [ID: 2] region 2 chains [282-418] RMSD: 48.897  
  

> select #1.1/A:536 #2.1/A:536

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1.1/A:536-617 #2.1/A:536-617

1352 atoms, 1372 bonds, 164 residues, 2 models selected  
2 [ID: 2] region 2 chains [419-500] RMSD: 48.564  
  

> select #4.1/B:97-99 #4.2/C:97-99 #5.1/B:97-99 #5.2/C:97-99

100 atoms, 96 bonds, 12 residues, 4 models selected  

> select #4.1/B:97-110 #4.2/C:97-110 #5.1/B:97-110 #5.2/C:97-110

448 atoms, 448 bonds, 56 residues, 4 models selected  
3 [ID: 3] region 4 chains [97-110] RMSD: 66.188  
  

> select #4.1/B:146-147 #4.2/C:146-147 #5.1/B:146-147 #5.2/C:146-147

68 atoms, 64 bonds, 8 residues, 4 models selected  

> select #4.1/B:146-199 #4.2/C:146-199 #5.1/B:146-199 #5.2/C:146-199

1680 atoms, 1704 bonds, 216 residues, 4 models selected  
3 [ID: 3] region 4 chains [146-199] RMSD: 68.483  
  

> select clear

> select #4.1/B:131-132 #4.2/C:131-132 #5.1/B:131-132 #5.2/C:131-132

60 atoms, 56 bonds, 8 residues, 4 models selected  

> select #4.1/B:131 #4.2/C:131 #5.1/B:131 #5.2/C:131

36 atoms, 32 bonds, 4 residues, 4 models selected  
3 [ID: 3] region 4 chains [131] RMSD: 72.867  
  

> select #4.1/B:1-2 #4.2/C:1-2 #5.1/B:1-2 #5.2/C:1-2

56 atoms, 52 bonds, 8 residues, 4 models selected  

> select #4.1/B:1-258 #4.2/C:1-258 #5.1/B:1-258 #5.2/C:1-258

8424 atoms, 8624 bonds, 1032 residues, 4 models selected  
3 [ID: 3] region 4 chains [1-258] RMSD: 65.941  
  

> select #4.1/B:1 #4.2/C:1 #5.1/B:1 #5.2/C:1

32 atoms, 28 bonds, 4 residues, 4 models selected  

> select #4.1/B #4.2/C #5.1/B #5.2/C

8456 atoms, 8656 bonds, 1036 residues, 4 models selected  
3 [ID: 3] region 4 chains [1-357] RMSD: 65.871  
  

> select clear

> select #4.1/B:132 #4.2/C:132 #5.1/B:132 #5.2/C:132

24 atoms, 20 bonds, 4 residues, 4 models selected  

> select #4.1/B:131-132 #4.2/C:131-132 #5.1/B:131-132 #5.2/C:131-132

60 atoms, 56 bonds, 8 residues, 4 models selected  
1 [ID: 1] region 4 chains [131-132] RMSD: 72.960  
  

> select #4.1/B:131 #4.2/C:131 #5.1/B:131 #5.2/C:131

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #4.1/B:131 #4.2/C:131 #5.1/B:131 #5.2/C:131

36 atoms, 32 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [131] RMSD: 72.867  
  
Drag select of 1 residues  

> select #5.1/B:130@CA

1 atom, 1 residue, 1 model selected  

> select add #5.1/B:103@CA

2 atoms, 2 residues, 1 model selected  

> select add #5.1/B:104

13 atoms, 10 bonds, 3 residues, 2 models selected  

> select add #5.1/B:102

21 atoms, 17 bonds, 4 residues, 2 models selected  

> select add #5.1/B:105

29 atoms, 24 bonds, 5 residues, 2 models selected  

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3

210 contacts  

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3

210 contacts  

> select clear

> select add #5.1/B:130

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

> select add #5.1/B:131

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add #5.1/B:104

29 atoms, 26 bonds, 3 residues, 2 models selected  

> select add #5.1/B:102@CA

30 atoms, 27 bonds, 4 residues, 2 models selected  

> interfaces select #1.1/A & ::polymer_type>0 contacting #10/A &
> ::polymer_type>0 areaCutoff 0

1 contacting residues  

> interfaces select #1.1/A & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0

0 contacting residues  

> select #1.1/A

2485 atoms, 2539 bonds, 1 pseudobond, 296 residues, 2 models selected  

> interfaces select #4.1/B & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0

0 contacting residues  

> interfaces select #4.1/B & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0

0 contacting residues  

> interfaces select #4.1/B & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0

0 contacting residues  
Drag select of 2 residues  

> select add #5.1/B:131

22 atoms, 8 bonds, 3 residues, 2 models selected  

> select subtract #5.1/B:41

17 atoms, 8 bonds, 2 residues, 2 models selected  

> select subtract #5.1/B:42

9 atoms, 8 bonds, 1 residue, 2 models selected  

> label (#!5.1 & sel) attribute name

> label (#!5.1 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"

> select add #9/A:145

16 atoms, 14 bonds, 2 residues, 3 models selected  

> select subtract #9/A:145

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select add #9/A:146

20 atoms, 18 bonds, 2 residues, 3 models selected  

> select add #5.1/B:130

29 atoms, 26 bonds, 3 residues, 4 models selected  

> select add #5.1/B:104

40 atoms, 36 bonds, 4 residues, 4 models selected  

> select add #5.1/B:103

46 atoms, 41 bonds, 5 residues, 4 models selected  

> select add #5.1/B:102

54 atoms, 48 bonds, 6 residues, 4 models selected  

> select add #9/A:101

65 atoms, 59 bonds, 7 residues, 4 models selected  

> select add #9/A:109

72 atoms, 65 bonds, 8 residues, 4 models selected  

> select add #9/A:107

81 atoms, 73 bonds, 9 residues, 4 models selected  

> select add #9/A:148@CA

82 atoms, 73 bonds, 10 residues, 4 models selected  

> select subtract #9/A:148

81 atoms, 73 bonds, 9 residues, 4 models selected  

> label (#!9#!5.1 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"

> select clear

> ui tool show "Side View"

> select #9/A:139

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #9/A:140

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #9/A:141

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #9/A:201

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5.1/B:43

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:139

5 atoms, 4 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3

210 contacts  

> contacts intraModel false intraMol false ignoreHiddenModels true
> makePseudobonds false dashes 3

210 contacts  

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
> radius 0.055

210 contacts  

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
> radius 0.055

210 contacts  

> contacts saveFile "/Users/gabrielumajioka/Desktop/project T7SS /T7SS
> structure related/contact" intraModel false intraMol false
> ignoreHiddenModels true dashes 3 radius 0.055

210 contacts  

> cartoon hide (#!9 & sel)

> select

19848 atoms, 20290 bonds, 212 pseudobonds, 2426 residues, 24 models selected  

> cartoon hide (#!9#!4.1-2#!5.1-2 & sel)

> select clear

Drag select of 37 atoms, 35 bonds  

> hide (#!9 & sel) target a

Drag select of 1 atoms  
Drag select of 26 atoms, 25 bonds  

> hide (#!9 & sel) target a

Drag select of 1 atoms  

> hide (#!9 & sel) target a

> select clear

Drag select of 57 atoms, 56 bonds  

> hide (#!9 & sel) target a

Drag select of 296 atoms, 298 bonds  

> hide (#!5.2 & sel) target a

Drag select of 23 atoms, 21 bonds  

> hide (#!5.2 & sel) target a

Drag select of 17 atoms, 15 bonds  
Drag select of 29 atoms, 25 bonds  
Drag select of 4 atoms, 6 bonds  
Drag select of 24 atoms, 26 bonds  
Drag select of 1 atoms  
Drag select of 3 atoms, 2 bonds  
Drag select of 9 atoms, 7 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 10 atoms, 8 bonds  
Drag select of 7 atoms, 7 bonds  
Drag select of 8 atoms, 9 bonds  

> hide (#!9#!5.1-2 & sel) target a

Drag select of 5 atoms  

> hide (#!9#!5.1-2 & sel) target a

Drag select of 44 atoms, 43 bonds  

> hide (#!9#!5.1-2 & sel) target a

Drag select of 18 atoms, 17 bonds  
Drag select of 10 atoms, 11 bonds  
Drag select of 17 atoms, 17 bonds  

> hide (#!9#!5.1-2 & sel) target a

Drag select of 1 atoms, 2 bonds, 11 pseudobonds  

> select #5.1/B:43@N

1 atom, 1 residue, 1 model selected  

> select clear

> show #!9#!4.1-2#!5.1-2 cartoons

> hide #!9#!4.1-2#!5.1-2 cartoons

Drag select of 4 atoms, 6 bonds  

> select clear

> select #5.1/B:47@CD1

1 atom, 1 residue, 1 model selected  

> select add #5.1/B:47@CG2

1 atom, 1 bond, 1 residue, 1 model selected  

> hide (#!5.1 & sel) target ab

Drag select of 6 atoms, 2 bonds  

> hide (#!5.1 & sel) target a

Drag select of 8 atoms, 7 bonds  

> hide (#!5.1 & sel) target a

Drag select of 7 atoms, 6 bonds  

> hide (#!5.1 & sel) target a

Drag select of 4 atoms, 3 bonds  

> hide (#!9 & sel) target a

> hide sel cartoons

> show sel cartoons

> select

19848 atoms, 20290 bonds, 212 pseudobonds, 2426 residues, 24 models selected  

> show sel & #!9#!4.1-2#!5.1-2 cartoons

> hide sel & #!9#!4.1-2#!5.1-2 cartoons

> select clear

> select #9/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> show sel cartoons

> select #4.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select #5.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> show sel cartoons

> select #5.2/C

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> show sel cartoons

> select #4.2/C

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select #9/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> select #5.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> show sel atoms

> select #10/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> select #2.2/D

637 atoms, 651 bonds, 79 residues, 1 model selected  

> select #10/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> select #9/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> show sel atoms

> select #4.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select #5.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select #4.2/C

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select #5.2/C

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> show sel atoms

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
> radius 0.055

210 contacts  

> interfaces select #9/A & ::polymer_type>0 contacting #4.1/B &
> ::polymer_type>0 areaCutoff 0

0 contacting residues  

> interfaces select #10/A & ::polymer_type>0 contacting #4.1/B &
> ::polymer_type>0 areaCutoff 0

10 contacting residues  

> hide #!9#!4.1-2#!5.1-2 cartoons

Drag select of 526 atoms, 535 bonds  

> hide (#!5.2 & sel) target a

Drag select of 335 atoms, 307 bonds, 4 pseudobonds  

> hide (#!9#!5.2 & sel) target a

Drag select of 1241 atoms, 1266 bonds  

> hide (#!9#!5.2 & sel) target a

Drag select of 2503 atoms, 2553 bonds  

> hide (#!9#!5.1-2 & sel) target a

> select clear

Drag select of 365 atoms, 355 bonds  

> hide (#!5.1 & sel) target a

Drag select of 441 atoms, 431 bonds, 17 pseudobonds  
Drag select of 479 atoms, 460 bonds, 23 pseudobonds  
Drag select of 459 atoms, 443 bonds, 19 pseudobonds  
Drag select of 270 atoms, 264 bonds, 2 pseudobonds  

> select clear

Drag select of 305 atoms, 295 bonds  

> select subtract #5.2/C:46@CB

304 atoms, 293 bonds, 50 residues, 4 models selected  

> select subtract #5.2/C:46@CG

303 atoms, 292 bonds, 50 residues, 5 models selected  

> select subtract #5.2/C:46@OD1

302 atoms, 292 bonds, 50 residues, 5 models selected  

> select clear

Drag select of 175 atoms, 170 bonds  

> hide (#!5.2 & sel) target a

Drag select of 50 atoms, 37 bonds  

> hide (#!5.2 & sel) target a

Drag select of 32 atoms, 26 bonds  

> hide (#!5.1-2 & sel) target a

Drag select of 65 atoms, 59 bonds  

> hide (#!5.1-2 & sel) target a

Drag select of 11 atoms, 11 bonds  
Drag select of 27 atoms, 23 bonds  

> select clear

Drag select of 21 atoms, 18 bonds  
Drag select of 7 atoms, 6 bonds  

> hide (#!5.1 & sel) target a

Drag select of 87 atoms, 85 bonds  
Drag select of 33 atoms, 29 bonds  
Drag select of 31 atoms, 33 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 37 atoms, 31 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 26 atoms, 26 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 16 atoms, 14 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 27 atoms, 25 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 25 atoms, 24 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 10 atoms, 6 bonds  

> hide (#!9#!5.1 & sel) target a

Drag select of 2 atoms  

> hide (#!9#!5.1 & sel) target a

> select helix

8282 atoms, 8370 bonds, 986 residues, 12 models selected  

> select clear

> show #!9#!4.1-2#!5.1-2 cartoons

> select #5.1/B:188

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5.2/C:104

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (#!5.2 & sel) target ab

> label (#!5.2 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"

> select clear

> select #9/A:182

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

> select add #9/A:185

17 atoms, 15 bonds, 2 residues, 2 models selected  

> select add #9/A:204

24 atoms, 22 bonds, 3 residues, 2 models selected  

> label (#!9 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select clear

> select #5.2/C:46

8 atoms, 7 bonds, 1 residue, 1 model selected  

> label (#!5.2 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"

> select #5.2/C:43

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show (#!5.2 & sel) target ab

> select #9/A:200

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

> select #9/A:199

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:199

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:199

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:199

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:199

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> color sel byhetero

> select clear

> hide #!9#!4.1-2#!5.1-2 cartoons

Drag select of 1 atoms  

> hide (#!5.2 & sel) target a

Drag select of 1 atoms  

> hide sel target a

Drag select of 1 atoms  

> hide sel target a

Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> hide (#!9 & sel) target a

Drag select of 2 atoms  

> hide (#!9 & sel) target a

> select clear

Drag select of 5 atoms, 4 bonds  

> hide sel target a

Drag select of 1 atoms  

> hide sel target a

Drag select of 1 atoms  

> hide (#!9 & sel) target a

Drag select of 7 atoms, 6 bonds  
Drag select of 4 atoms, 2 bonds  

> hide (#!5.1 & sel) target ab

Drag select of 2 atoms  

> hide (#!5.1 & sel) target a

Drag select of 9 atoms, 10 bonds  

> hide (#!9#!5.1 & sel) target a

> show sel cartoons

> select #10/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> select #10/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> select #9/A

1607 atoms, 1641 bonds, 204 residues, 1 model selected  

> show sel cartoons

> select clear

> select

19848 atoms, 20290 bonds, 212 pseudobonds, 2426 residues, 25 models selected  

> show sel & #!9#!4.1-2#!5.1-2 cartoons

> select clear

> select add #5.1

2114 atoms, 2164 bonds, 259 residues, 2 models selected  

> show #!1.1 models

> show #!1.2 models

> show #!2 models

> show #!2.1 models

> show #!2.2 models

> show #!3 models

> show #!3.1 models

> show #!3.2 models

> select clear

> show #!7 models

> show #!10 models

> hide #!7 models

Drag select of 94 residues  
Drag select of 11 residues  

> select clear

> ui tool show "Side View"

> help help:user/tools/sideview.html

Drag select of 2 residues  
Drag select of 172 residues, 1 pseudobonds  

> ui tool show "Side View"

> select clear

> ui tool show "Side View"

> ui autostart true "Side View"

> ui tool show "Side View"

Drag select of 47 residues  

> show (#!1.1#!2.1#!3.1#!4.2#!5.2 & sel) target ab

> select clear

> ui tool show "Side View"

> hide #6 models

> show #6 models

> hide #6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> ui tool show "Side View"

> hide #!7 models

> ui tool show "Side View"

> select #4.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select #5.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select clear

> select #5.1/B

2114 atoms, 2164 bonds, 259 residues, 1 model selected  

> select clear

> ui tool show "Side View"

Drag select of 121 atoms, 64 residues, 104 bonds  

> style sel sphere

Changed 524 atom styles  

> hide (#!2.1#!3.1#!4.1#!5.2 & sel) target a


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-22.1.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
      OS Loader Version: 580~743

Software:

    System Software Overview:

      System Version: macOS 14.1.1 (23B81)
      Kernel Version: Darwin 23.1.0
      Time since boot: 3 days, 10 hours, 53 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        MT5531:
          Resolution: 1360 x 768
          UI Looks like: 1360 x 768 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7,55


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
    ChimeraX-AddH: 2.2.4
    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: 1.6rc202304150037
    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: 2.7.1
    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: 1.10.2
    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: 6.4.1
    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: 3.2.0
    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: 6.2
    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 Eric Pettersen, 2 years ago

Component: UnassignedGraphics
Description: modified (diff)
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionGraphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 2 years ago

Resolution: nonchimerax
Status: assignedclosed
Summary: Graphics hardware encountered an error and was resetGraphics crash, macOS 14.1.1, Intel Iris Plus Graphics 655

Apple Intel graphics driver crash.

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