Opened 3 years ago

Last modified 3 years ago

#7994 feedback defect

Crash in color chooser

Reported by: afrance2@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Platform 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x000070001c4ae000 (most recent call first):
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x0000000105d03600 (most recent call first):
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 332 in event_loop
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Users/amandaghilardi/Desktop/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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{
  "uptime" : 61000,
  "procLaunch" : "2022-11-09 17:06:42.4390 -0500",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 504,
  "deployVersion" : 210,
  "modelCode" : "iMac20,1",
  "procStartAbsTime" : 111482171929,
  "coalitionID" : 481,
  "osVersion" : {
    "train" : "macOS 12.0.1",
    "build" : "21A559",
    "releaseType" : "User"
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  "captureTime" : "2022-11-10 10:09:51.7925 -0500",
  "incident" : "8A460229-71DA-4AF4-8DD1-AB81F0C1A410",
  "bug_type" : "309",
  "pid" : 747,
  "procExitAbsTime" : 61501573026615,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "B648F3E9-3C05-5922-1609-51E501149E1F",
  "bridgeVersion" : {"build":"19P549","train":"6.0"},
  "sip" : "enabled",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "asi" : {"libsystem_c.dylib":["Assertion failed: (backingScaleFactor > 0.f), function drawnFocusRingBitmapForTime, file NSAutomaticFocusRing.m, line 346."]},
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  "faultingThread" : 0,
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    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/OpenGL",
    "name" : "OpenGL",
    "CFBundleVersion" : "19.1.1"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5000785920,
    "size" : 165068800,
    "uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
    "path" : "\/Users\/USER\/Desktop\/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"
  }
],
  "sharedCache" : {
  "base" : 140703515795456,
  "size" : 15213641728,
  "uuid" : "3d05845f-3f65-358f-9ebf-2236e772ac01"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               896K        7 \nActivity Tracing                   256K        1 \nCG backing stores                 3844K        5 \nCG image                          1632K       43 \nColorSync                          244K       29 \nCoreAnimation                     6252K       98 \nCoreGraphics                        12K        2 \nCoreImage                           12K        1 \nCoreUI image data                 5120K       41 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.1G     1119 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        156K       39 \nStack                            178.3M       40 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      149.8M      185 \nVM_ALLOCATE (reserved)           160.0M        1         reserved VM address space (unallocated)\n__DATA                            55.8M      659 \n__DATA_CONST                      30.2M      345 \n__DATA_DIRTY                      1639K      218 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       665.0M      138 \n__OBJC_RO                         81.5M        1 \n__OBJC_RW                         3120K        2 \n__TEXT                           776.3M      663 \n__UNICODE                          588K        1 \ndyld private memory               1184K        3 \nmapped file                      215.8M       51 \nshared memory                     2980K       27 \n===========                     =======  ======= \nTOTAL                              3.8G     3741 \nTOTAL, minus reserved VM space     3.2G     3741 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "61ef3bd729647d394933a0a6"
      },
      "deploymentId" : 240000416
    },
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "614a34c5eae97a2111628dc5"
      },
      "deploymentId" : 240000305
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

      },
      "deploymentId" : 240000026
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000215
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000537
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000020
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/amandaghilardi/Desktop/orai/for Anh Tuan/AE-13/ae-13.mol2"

Summary of feedback from opening /Users/amandaghilardi/Desktop/orai/for Anh
Tuan/AE-13/ae-13.mol2  
---  
warnings | line 10: ignoring section 'DICT'  
line 24893: bad substructure data  
line 24893: ignore unexpected line '1 UNK 1 GROUP 0 **** 0 ROOT'  
  
Chain information for Model of AAH15369.2 based on 7KR5 - prepared_A, 7KR5 -
prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 - prepared_E, 7KR5 -
prepared_F-1 - prepared #1.1  
---  
Chain | Description  
A B C D E F | No description available  
  
Opened ae-13.mol2 containing 2 structures (11981 atoms, 12127 bonds)  

> set bgColor white

> graphics silhouettes true

> style stick

Changed 11981 atom styles  

> show cartoons

> hide protein

> select #1.1/A

1992 atoms, 2016 bonds, 127 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1.1/B

1990 atoms, 2014 bonds, 127 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1.2

36 atoms, 38 bonds, 1 residue, 1 model selected  

> select sel : show sel

> hide H

> select clear

> select #1.1/D

1990 atoms, 2014 bonds, 127 residues, 1 model selected  

> color sel #fbfeffff

> color sel #fbfdffff

> color sel #fafbffff

> color sel #fbf9ffff

> color sel #fcf7ffff

> color sel #fdf6ffff

> color sel #fdf5ffff

> color sel #fdf4ffff

> color sel #fef3ffff

> color sel #fef2ffff

> color sel #fff1ffff

> color sel #fff0ffff

> color sel #ffeeffff

> color sel #ffecfdff

> color sel #ffe9fcff

> color sel #ffe6faff

> color sel #ffe4f9ff

> color sel #ffe3f8ff

> color sel #ffe2f8ff

> color sel #ffe1f7ff

> color sel #ffddf6ff

> color sel #ffd6f3ff

> color sel #ffd1f1ff

> color sel #ffcef0ff

> color sel #ffcbefff

> color sel #ffcaeeff

> color sel #ffc9eeff

> color sel #ffc8edff

> color sel #ffc7edff

> color sel #ffc7ecff

> color sel #ffc6ecff

> color sel #ffc5ecff

> color sel #ffc4ecff

> color sel #ffc3ecff

> color sel #ffc2ecff

> color sel #ffc2edff

> color sel #ffc1edff

> color sel #ffc0edff

> color sel #ffbfedff

> color sel #ffbdeeff

> color sel #ffbceeff

> color sel #ffbbefff

> color sel #ffbaefff

> color sel #ffb9efff

> color sel #ffb6efff

> color sel #ffb3edff

> color sel #ffb2edff

> color sel #ffb1ecff

> color sel #ffb0ecff

> color sel #ffafecff

> color sel #ffaeecff

> color sel #ffacecff

> color sel #ffa9ecff

> color sel #ffa7ebff

> color sel #ffa6ebff

> color sel #ffa6eaff

> color sel #ffa8eaff

> color sel #ffa9e9ff

> color sel #ffaae8ff

> color sel #fface8ff

> color sel #ffade8ff

> color sel #ffaee8ff

> color sel #ffafe7ff

> color sel #ffb0e7ff

> color sel #ffb1e7ff

> color sel #ffb2e7ff

> color sel #ffb3e7ff

> color sel #ffb2e7ff

> select clear

> select #1.1/E

1991 atoms, 2015 bonds, 127 residues, 1 model selected  

> color sel #ffc1ecff

> color sel #ffc2ecff

> color sel #ffc3ecff

> color sel #ffc6ecff

> color sel #ffc7ecff

> color sel #ffc8ecff

> color sel #ffcaedff

> color sel #ffcdefff

> color sel #ffd0f1ff

> color sel #ffd3f4ff

> color sel #ffd7f7ff

> color sel #ffdafaff

> color sel #ffddfeff

> color sel #fde0ffff

> color sel #f9e3ffff

> color sel #f3e5ffff

> color sel #ede6ffff

> color sel #e5e4ffff

> color sel #dde8ffff

> color sel #d7e9ffff

> color sel #d0eaffff

> color sel #c9ebffff

> color sel #c4ecffff

> color sel #c1ecffff

> color sel #bfecffff

> color sel #beecffff

> color sel #bdecffff

> color sel #bbecffff

> color sel #b9ecffff

> color sel #b6ebffff

> color sel #b4ebffff

> color sel #b1ebffff

> color sel #afebffff

> color sel #acecffff

> color sel #aaebffff

> color sel #a9ebffff

> color sel #a7ebffff

> color sel #a6ebffff

> color sel #a5ebffff

> color sel #a4ebffff

> color sel #a2ebffff

> color sel #a1ebffff

> color sel #a0eaffff

> color sel #a0e9ffff

> color sel #9fe8ffff

> color sel #9fe7ffff

> color sel #9ee7ffff

> color sel #9de7ffff

> color sel #9ce7ffff

> color sel #9be7ffff

> color sel #9ae6ffff

> color sel #98e6ffff

> color sel #96e6ffff

> color sel #94e6ffff

> color sel #93e6ffff

> color sel #92e6ffff

> color sel #91e6ffff

> color sel #90e5ffff

> color sel #8ee5ffff

> color sel #8de4ffff

> color sel #8ce4ffff

> color sel #8fe7ffff

> color sel #91e7ffff

> color sel #92e7ffff

> color sel #93e7ffff

> color sel #94e7ffff

> color sel #95e7ffff

> color sel #96e7ffff

> color sel #97e6ffff

> color sel #9ae6ffff

> color sel #9ce6ffff

> color sel #9de5ffff

> color sel #9ee5ffff

> color sel #9fe5ffff

> color sel #a0e5ffff

> color sel #a1e5ffff

> color sel #a4e5ffff

> color sel #a5e5ffff

> color sel #a7e5ffff

> color sel #a8e5ffff

> color sel #a8e4ffff

> color sel #a7e4ffff

> color sel #a7e3ffff

> select clear

> select protein

7963 atoms, 8059 bonds, 508 residues, 1 model selected  

> color sel byhetero

> select clear

> select #1.2

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel surfaces

> transparency (#!1.2 & sel) 70

> select clear

> select #1.2

36 atoms, 38 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 36 atom styles  

> select clear

> ui mousemode right distance

> hide surfaces

> select add #1.2/?:1@C13

1 atom, 1 residue, 1 model selected  

> select add #1.1/F:651@CZ

2 atoms, 2 residues, 3 models selected  

> ui tool show Distances

> distance #1.2/?:1@C13 #1.1/F:651@CZ

Distance between ae-13 #1.2/? UNK 1 C13 and Model of AAH15369.2 based on 7KR5
- prepared_A, 7KR5 - prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 -
prepared_E, 7KR5 - prepared_F-1 - prepared #1.1/F PHE9 651 CZ: 3.814Å  

> select clear

> select add #1.2/?:1@C3

1 atom, 1 residue, 1 model selected  

> select add #1.1/E:527@CG1

2 atoms, 2 residues, 3 models selected  

> distance #1.2/?:1@C3 #1.1/E:527@CG1

Distance between ae-13 #1.2/? UNK 1 C3 and Model of AAH15369.2 based on 7KR5 -
prepared_A, 7KR5 - prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 -
prepared_E, 7KR5 - prepared_F-1 - prepared #1.1/E VAL1 527 CG1: 3.581Å  

> select clear

> select add #1.1/E:524@CZ

1 atom, 1 residue, 1 model selected  

> select add #1.2/?:1@N1

2 atoms, 2 residues, 2 models selected  

> distance #1.1/E:524@CZ #1.2/?:1@N1

Distance between Model of AAH15369.2 based on 7KR5 - prepared_A, 7KR5 -
prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 - prepared_E, 7KR5 -
prepared_F-1 - prepared #1.1/E PHE9 524 CZ and ae-13 #1.2/? UNK 1 N1: 4.825Å  

> select clear

> select add #1.2/?:1@N4

1 atom, 1 residue, 1 model selected  

> select add #1.1/C:277@OE2

2 atoms, 2 residues, 3 models selected  

> distance #1.2/?:1@N4 #1.1/C:277@OE2

Distance between ae-13 #1.2/? UNK 1 N4 and Model of AAH15369.2 based on 7KR5 -
prepared_A, 7KR5 - prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 -
prepared_E, 7KR5 - prepared_F-1 - prepared #1.1/C GLU1 277 OE2: 4.840Å  

> select clear

> ui mousemode right translate

> select add #1.2/?:1@C11

1 atom, 1 residue, 1 model selected  

> select add #1.1/F:654@CG1

2 atoms, 2 residues, 3 models selected  

> distance #1.2/?:1@C11 #1.1/F:654@CG1

Distance between ae-13 #1.2/? UNK 1 C11 and Model of AAH15369.2 based on 7KR5
- prepared_A, 7KR5 - prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 -
prepared_E, 7KR5 - prepared_F-1 - prepared #1.1/F VAL1 654 CG1: 4.166Å  

> select clear

> select #1.2

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel surfaces

> select clear

> color #2.1 black models transparency 0

> save /Users/amandaghilardi/Desktop/image1.png supersample 3

> show surfaces

> select #1.1/C

1992 atoms, 2016 bonds, 127 residues, 1 model selected  

> select clear

> select #1.1/D

1990 atoms, 2014 bonds, 127 residues, 1 model selected  

> color (#!1.1 & sel) #000000ff

> color (#!1.1 & sel) #050401ff

> color (#!1.1 & sel) #181507ff

> color (#!1.1 & sel) #463e15ff

> color (#!1.1 & sel) #63581eff

> color (#!1.1 & sel) #7c6e26ff

> color (#!1.1 & sel) #857629ff

> color (#!1.1 & sel) #91812cff

> color (#!1.1 & sel) #9f8e31ff

> color (#!1.1 & sel) #af9b36ff

> color (#!1.1 & sel) #bca739ff

> color (#!1.1 & sel) #bda83aff

> color (#!1.1 & sel) #bda434ff

> color (#!1.1 & sel) #bda436ff

> color (#!1.1 & sel) #bda53aff

> color (#!1.1 & sel) #bda74cff

> color (#!1.1 & sel) #bda65dff

> color (#!1.1 & sel) #bda36dff

> color (#!1.1 & sel) #bda07aff

> color (#!1.1 & sel) #bd9f84ff

> color (#!1.1 & sel) #bd9f8cff

> color (#!1.1 & sel) #bd9e90ff

> color (#!1.1 & sel) #bd9d92ff

> color (#!1.1 & sel) #bd9d93ff

> color (#!1.1 & sel) #bd9b94ff

> color (#!1.1 & sel) #bd9a97ff

> color (#!1.1 & sel) #bd9899ff

> color (#!1.1 & sel) #bd999fff

> color (#!1.1 & sel) #bd99a2ff

> color (#!1.1 & sel) #bd98a6ff

> color (#!1.1 & sel) #bd95a9ff

> color (#!1.1 & sel) #bd92acff

> color (#!1.1 & sel) #bd8eaeff

> color (#!1.1 & sel) #bd8bb0ff

> color (#!1.1 & sel) #bd8ab0ff

> color (#!1.1 & sel) #bd8cb1ff

> color (#!1.1 & sel) #bd8fb3ff

> color (#!1.1 & sel) #bd91b5ff

> color (#!1.1 & sel) #bd92b7ff

> color (#!1.1 & sel) #bd93b8ff

> color (#!1.1 & sel) #bc99bdff

> color (#!1.1 & sel) #b69ebdff

> color (#!1.1 & sel) #b59fbdff

> color (#!1.1 & sel) #b49fbdff

> color (#!1.1 & sel) #b4a0bdff

> color (#!1.1 & sel) #b1a2bdff

> color (#!1.1 & sel) #afa4bdff

> color (#!1.1 & sel) #aea5bdff

> color (#!1.1 & sel) #afa6bdff

> color (#!1.1 & sel) #b0a8bdff

> color (#!1.1 & sel) #b0aabdff

> color (#!1.1 & sel) #b1abbdff

> color (#!1.1 & sel) #b2abbdff

> color (#!1.1 & sel) #b3acbdff

> color (#!1.1 & sel) #b7acbdff

> color (#!1.1 & sel) #bbabbdff

> color (#!1.1 & sel) #bda9bbff

> color (#!1.1 & sel) #bda8baff

> color (#!1.1 & sel) #bda7b9ff

> color (#!1.1 & sel) #bda4b6ff

> color (#!1.1 & sel) #bda1b2ff

> color (#!1.1 & sel) #bda1b1ff

> color (#!1.1 & sel) #bea2b2ff

> color (#!1.1 & sel) #c3a6b7ff

> color (#!1.1 & sel) #debdd0ff

> color (#!1.1 & sel) #eecbdfff

> color (#!1.1 & sel) #fbd6ebff

> color (#!1.1 & sel) #ffd9efff

> color (#!1.1 & sel) #ffd8efff

> color (#!1.1 & sel) #fbd5ebff

> color (#!1.1 & sel) #f9d3e9ff

> color (#!1.1 & sel) #f7d2e8ff

> color (#!1.1 & sel) #f6d1e7ff

> color (#!1.1 & sel) #f2cee3ff

> color (#!1.1 & sel) #f2d0d5ff

> color (#!1.1 & sel) #f2cfd5ff

> color (#!1.1 & sel) #f2cdd5ff

> color (#!1.1 & sel) #f2ccd4ff

> color (#!1.1 & sel) #f2cbd4ff

> color (#!1.1 & sel) #f2cad4ff

> color (#!1.1 & sel) #f2cad5ff

> color (#!1.1 & sel) #f2c9d4ff

> color (#!1.1 & sel) #f2c9d5ff

> color (#!1.1 & sel) #f2c8d5ff

> color (#!1.1 & sel) #f2c7d5ff

> color (#!1.1 & sel) #f2c5d5ff

> color (#!1.1 & sel) #f2c4d5ff

> color (#!1.1 & sel) #f2c3d5ff

> color (#!1.1 & sel) #f2c2d5ff

> color (#!1.1 & sel) #f2c1d6ff

> color (#!1.1 & sel) #f2c0d5ff

> color (#!1.1 & sel) #f2bed5ff

> color (#!1.1 & sel) #f2bed6ff

> color (#!1.1 & sel) #f2bdd6ff


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

Log:
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/amandaghilardi/Desktop/orai/for Anh Tuan/AE-13/ae-13.mol2"

Summary of feedback from opening /Users/amandaghilardi/Desktop/orai/for Anh
Tuan/AE-13/ae-13.mol2  
---  
warnings | line 10: ignoring section 'DICT'  
line 24893: bad substructure data  
line 24893: ignore unexpected line '1 UNK 1 GROUP 0 **** 0 ROOT'  
  
Chain information for Model of AAH15369.2 based on 7KR5 - prepared_A, 7KR5 -
prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 - prepared_E, 7KR5 -
prepared_F-1 - prepared #1.1  
---  
Chain | Description  
A B C D E F | No description available  
  
Opened ae-13.mol2 containing 2 structures (11981 atoms, 12127 bonds)  




OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 8-Core Intel Core i7
      Processor Speed: 3.8 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0)
      OS Loader Version: 540.40.4~45

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 17:06

Graphics/Displays:

    AMD Radeon Pro 5500 XT:

      Chipset Model: AMD Radeon Pro 5500 XT
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0041
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XT-011
      Option ROM Version: 113-D322A1XT-011
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.2
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.5.dev202206100131
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.20.4
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in color chooser

comment:2 by Eric Pettersen, 3 years ago

Status: accepted → feedback

Hi Amanda,

Thanks for reporting this problem. Were you using the color-chooser dialog when this happened? Specifically, dragging a color to one of the "favorite colors" boxes?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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