Opened 3 years ago

Closed 3 years ago

#8427 closed defect (can't reproduce)

Unsupported scale factor (0.000000) detected on Display0

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

Description 

The following bug report has been submitted:
Platform:        macOS-13.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202301280224 (2023-01-28 02:24:25 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 0x00000001f31e7a80 (most recent call first):
  File "/private/var/folders/th/hvr39ggj7ws1fg_m600c2gnr0000gn/T/AppTranslocation/D2C65C2F-17D9-4D41-B50D-0327E361DEA4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
  File "/private/var/folders/th/hvr39ggj7ws1fg_m600c2gnr0000gn/T/AppTranslocation/D2C65C2F-17D9-4D41-B50D-0327E361DEA4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/private/var/folders/th/hvr39ggj7ws1fg_m600c2gnr0000gn/T/AppTranslocation/D2C65C2F-17D9-4D41-B50D-0327E361DEA4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/private/var/folders/th/hvr39ggj7ws1fg_m600c2gnr0000gn/T/AppTranslocation/D2C65C2F-17D9-4D41-B50D-0327E361DEA4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/th/hvr39ggj7ws1fg_m600c2gnr0000gn/T/AppTranslocation/D2C65C2F-17D9-4D41-B50D-0327E361DEA4/d/ChimeraX_Daily.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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  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
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  "modelCode" : "MacBookPro18,1",
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  "captureTime" : "2023-02-02 00:50:27.9925 -0800",
  "incident" : "AEC385BD-77C3-4BCE-9FC6-7251027158EF",
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  "procLaunch" : "2023-02-01 22:50:12.5413 -0800",
  "procStartAbsTime" : 2724164512710,
  "procExitAbsTime" : 2897329583713,
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "parentPid" : 1,
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  "crashReporterKey" : "0E87F8DE-9969-30DB-F909-D0E1A2D30D1C",
  "throttleTimeout" : 2147483647,
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  "sleepWakeUUID" : "EF00D03D-E3C7-4CAF-99D0-39E732C95448",
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    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4687593472,
    "size" : 622592,
    "uuid" : "d3d12a1e-d996-3265-885a-a8e474f79f50",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
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    "arch" : "arm64e",
    "base" : 6897168384,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15773696,
    "uuid" : "dbbd4dea-6c68-3200-a81b-79b6a62f4669",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299.30.116"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6968745984,
    "CFBundleShortVersionString" : "1.11",
    "CFBundleIdentifier" : "com.apple.QuartzCore",
    "size" : 3559424,
    "uuid" : "8ccb450e-ab2b-3fce-931e-70986187d2e0",
    "path" : "\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore",
    "name" : "QuartzCore",
    "CFBundleVersion" : "1042.24.1"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6843920384,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5079040,
    "uuid" : "fd16d6d9-10c0-323b-b43b-9781c4a4d268",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.300"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6859829248,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.Foundation",
    "size" : 10719232,
    "uuid" : "f1f5f857-8c3c-36d5-bc27-7702d6795468",
    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    "name" : "Foundation",
    "CFBundleVersion" : "1953.300"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6924259328,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 4292608,
    "uuid" : "c1288dc8-1ec1-31aa-915b-6dcd0f99b264",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6841917440,
    "size" : 294912,
    "uuid" : "191028d2-0477-3ebc-9eef-a85acafc7193",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7002398720,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3358720,
    "uuid" : "f1e0f4f6-dd7b-3d16-a622-5ee94a20fcaa",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4316332032,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2555904,
    "uuid" : "5ee765c2-b52f-3980-9781-73db1abd2bde",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4308025344,
    "CFBundleShortVersionString" : "1.6.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "a5992708-d5b4-36ec-ac0a-e525f6105b56",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.6.0.0"
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  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6840197120,
    "size" : 568164,
    "uuid" : "487cfdeb-9b07-39bf-bfb9-970b61aea2d1",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4351295488,
    "size" : 20709376,
    "uuid" : "6b8373ed-7142-34ea-9b4b-9f502e8a6f33",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5701337088,
    "size" : 154746880,
    "uuid" : "3bb8485a-3fbc-3d6e-81e9-c7f5635b6909",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 3904K        8 \nCG image                           752K       33 \nColorSync                          560K       28 \nCoreAnimation                      336K       21 \nCoreGraphics                        48K        3 \nCoreUI image data                 4544K       33 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                           622.3M      299 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)           1.1G       10         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        528K       33 \nStack                            152.8M       34 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      162.6M      332 \nVM_ALLOCATE (reserved)           224.0M        3         reserved VM address space (unallocated)\n__AUTH                            1933K      360 \n__AUTH_CONST                      24.8M      588 \n__CTF                               756        1 \n__DATA                            19.9M      717 \n__DATA_CONST                      37.6M      726 \n__DATA_DIRTY                      1983K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       794.3M      137 \n__OBJC_CONST                      4752K      325 \n__OBJC_RO                         65.4M        1 \n__OBJC_RW                         1986K        1 \n__TEXT                           819.6M      747 \ndyld private memory                256K        1 \nmapped file                      516.2M       80 \nshared memory                     3264K       32 \n===========                     =======  ======= \nTOTAL                              4.9G     4810 \nTOTAL, minus reserved VM space     3.2G     4810 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "61fd92db295c182621ececc3",
      "factorPackIds" : {

      },
      "deploymentId" : 240000247
    },
    {
      "rolloutId" : "62fe74515312cd4599bd3c80",
      "factorPackIds" : {
        "MYRIAD_BOOSTS" : "62fe74805312cd4599bd3c81"
      },
      "deploymentId" : 240000006
    }
  ],
  "experiments" : [

  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202301280224 (2023-01-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/minhanhpham/Downloads/PAPA1_CARPA_cut.eq.1.pdb format pdb

Chain information for PAPA1_CARPA_cut.eq.1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/minhanhpham/Downloads/protein_28_928d3.result/protein_28_928d3_unrelaxed_rank_1_model_3.pdb

Chain information for protein_28_928d3_unrelaxed_rank_1_model_3.pdb #2  
---  
Chain | Description  
A | No description available  
  

> 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 PAPA1_CARPA_cut.eq.1.pdb, chain A (#1) with
protein_28_928d3_unrelaxed_rank_1_model_3.pdb, chain A (#2), sequence
alignment score = 624.1  
RMSD between 190 pruned atom pairs is 0.928 angstroms; (across all 208 pairs:
1.729)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:361

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

> select #2/A:355-361

51 atoms, 52 bonds, 7 residues, 1 model selected  

> select #2/A:361

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

> select #2/A:354-361

57 atoms, 58 bonds, 8 residues, 1 model selected  

> select #1/A:212

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:204-212

144 atoms, 146 bonds, 9 residues, 1 model selected  

> select #1/A:212

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:205-212

130 atoms, 132 bonds, 8 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:25

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

> select #1/A:25-37

191 atoms, 193 bonds, 13 residues, 1 model selected  

> select #1/A:42-43

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #1/A:38-43

105 atoms, 104 bonds, 6 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:42

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:25-42

289 atoms, 291 bonds, 18 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:42

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:25-42

289 atoms, 291 bonds, 18 residues, 1 model selected  

> color sel red

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:56-57

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:53-57

72 atoms, 71 bonds, 5 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:52

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:52,53-56,97

90 atoms, 89 bonds, 6 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:77-78

38 atoms, 38 bonds, 2 residues, 1 model selected  

> select #1/A:76-78

48 atoms, 48 bonds, 3 residues, 1 model selected  

> select #1/A:77

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:68-77

157 atoms, 159 bonds, 10 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:77

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:68-77

157 atoms, 159 bonds, 10 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:127

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:118-127

145 atoms, 145 bonds, 10 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:142

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:139-142

71 atoms, 71 bonds, 4 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:199

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:199-201

33 atoms, 32 bonds, 3 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:56

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

> select #1/A:52,53-56,97

90 atoms, 89 bonds, 6 residues, 1 model selected  

> select #1/A:77-78

38 atoms, 38 bonds, 2 residues, 1 model selected  

> select #1/A:76-78

48 atoms, 48 bonds, 3 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:77

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:68-77

157 atoms, 159 bonds, 10 residues, 1 model selected  

> select #1/A:127

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:118-127

145 atoms, 145 bonds, 10 residues, 1 model selected  

> select #1/A:142

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:139-142

71 atoms, 71 bonds, 4 residues, 1 model selected  

> select #1/A:199

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:199-201

33 atoms, 32 bonds, 3 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:112

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:109-112

64 atoms, 63 bonds, 4 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:134

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:130-134

78 atoms, 77 bonds, 5 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:134

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:130-134

78 atoms, 77 bonds, 5 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:166

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:159-166

108 atoms, 109 bonds, 8 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:166

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:159-166

108 atoms, 109 bonds, 8 residues, 1 model selected  

> select #1/A:174

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:170-174

100 atoms, 100 bonds, 5 residues, 1 model selected  

> select #1/A:190

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:186-190

105 atoms, 105 bonds, 5 residues, 1 model selected  

> select #1/A:174

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:170-174

100 atoms, 100 bonds, 5 residues, 1 model selected  

> select #1/A:190

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:188-190

65 atoms, 64 bonds, 3 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:190

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:186-190

105 atoms, 105 bonds, 5 residues, 1 model selected  

> select #1/A:210

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:207-210

71 atoms, 73 bonds, 4 residues, 1 model selected  

> select #1/A:112

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:109-112

64 atoms, 63 bonds, 4 residues, 1 model selected  

> select #1/A:134

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:130-134

78 atoms, 77 bonds, 5 residues, 1 model selected  

> select #1/A:166

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:159-166

108 atoms, 109 bonds, 8 residues, 1 model selected  

> select #1/A:174

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:171-174

79 atoms, 78 bonds, 4 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:174

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:170-174

100 atoms, 100 bonds, 5 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:174

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:170-174

100 atoms, 100 bonds, 5 residues, 1 model selected  

> select #1/A:109-112,130-134,159-166,170-174,186-190,207-210

526 atoms, 527 bonds, 31 residues, 1 model selected  

> select #1/A:190

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:186-190

105 atoms, 105 bonds, 5 residues, 1 model selected  

> select #1/A:210

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:207-210

71 atoms, 73 bonds, 4 residues, 1 model selected  

> select
> #2/A:42-69,76-98,116-123,172-189,197-203,210-212,216-226,263-270,284-287,349-351

896 atoms, 905 bonds, 113 residues, 1 model selected  

> select #2/A:104-106,254-257,275-279,289-292,304-313,319-324,336-340,357-360

331 atoms, 334 bonds, 41 residues, 1 model selected  

> select #2/A:106

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

> select #2/A:104-106

27 atoms, 27 bonds, 3 residues, 1 model selected  

> select #1/A:1-2

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select #1/A:1-2

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select #2/A:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:1

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

> select #2/A:1

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

> select #2/A:2-3

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:1-3

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #2/A:361

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

> select #2/A:360-361

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #2/A:361

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

> select #2/A:357-361

37 atoms, 38 bonds, 5 residues, 1 model selected  

> select #1/A:212

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:209-212

67 atoms, 67 bonds, 4 residues, 1 model selected  

> select #1/A:25-42,52,53-56,68-77,97,118-127,139-142,199-201

785 atoms, 787 bonds, 51 residues, 1 model selected  

> select #1/A:25

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

> select #1/A:25

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

> select #1/A:25,159

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select #1/A:25,159,195

42 atoms, 40 bonds, 3 residues, 1 model selected  

> select #1/A:25

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

> select #1/A:25

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

> select #1/A:25,159

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select #1/A:25,159,175

42 atoms, 40 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 42 atom styles  

> show sel atoms

> style sel sphere

Changed 42 atom styles  

> style sel stick

Changed 42 atom styles  

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


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

Log:
UCSF ChimeraX version: 1.6.dev202301280224 (2023-01-28)  
© 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 M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 3 days, 23 hours, 10 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 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: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL S2419NX:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.7
    ChimeraX-AtomicLibrary: 10.0.3
    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: 2.7.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.1
    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.dev202301280224
    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: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2.1
    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: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.11
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    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-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10
    ChimeraX-PDB: 2.6.13
    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: 1.0
    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: 2.8.1
    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: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    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: 1.26
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    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: 0.4.5
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    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: 6.0.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.5
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    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: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.2
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.4.0
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.3
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.8.0
    typing-extensions: 4.4.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.12.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Unsupported scale factor (0.000000) detected on Display0

comment:2 by Eric Pettersen, 3 years ago

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

*Possibly* the same as #8226. The user does have two displays.

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