Opened 4 months ago

Last modified 4 months ago

#18005 feedback defect

Crash using color editor

Reported by: teija.suhas@… 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-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202506032143 (2025-06-03 21:43:02 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x0000000100e54580 (most recent call first):
  File "/Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
  File "/Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
  File "/Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 56)


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{
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  "procLaunch" : "2025-06-16 13:05:16.4563 -0700",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "procStartAbsTime" : 1954557837858,
  "coalitionID" : 481,
  "osVersion" : {
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    "build" : "21D62",
    "releaseType" : "User"
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  "captureTime" : "2025-06-16 13:47:08.4540 -0700",
  "incident" : "4EFA2101-3B13-4EC6-A6F4-8D8A1B58BCE7",
  "bug_type" : "309",
  "pid" : 19049,
  "procExitAbsTime" : 1968492923669,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"86FD63A1-6418-56AA-BB8E-6AB5B6ADC8B6","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BFFC62EA-90DD-CCB8-F5D7-871EE09AFB91",
  "wakeTime" : 327,
  "sleepWakeUUID" : "347849F6-2EA5-45CB-843A-9EAB0FCBBBB1",
  "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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    "CFBundleIdentifier" : "com.apple.Foundation",
    "size" : 4120576,
    "uuid" : "f3ab29ba-726d-3d0b-8125-ceb1a79cd832",
    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    "name" : "Foundation",
    "CFBundleVersion" : "1856.107"
  },
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    "source" : "P",
    "arch" : "arm64e",
    "base" : 6945435648,
    "CFBundleShortVersionString" : "1.22",
    "CFBundleIdentifier" : "com.apple.HIServices",
    "size" : 393216,
    "uuid" : "fa16e436-5162-3c47-9f8d-9060502d5310",
    "path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
    "name" : "HIServices"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4987813888,
    "size" : 688128,
    "uuid" : "7e60f9ac-4ed3-3c71-9933-7b053de2a9b0",
    "path" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
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    "source" : "P",
    "arch" : "arm64",
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    "path" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
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    "arch" : "arm64",
    "base" : 4649156608,
    "size" : 3112960,
    "uuid" : "30fa1f27-f16b-3107-a7e0-821600076792",
    "path" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
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    "arch" : "arm64",
    "base" : 4305977344,
    "CFBundleShortVersionString" : "1.10.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
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    "path" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.10.0.0"
  },
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    "arch" : "arm64e",
    "base" : 4309499904,
    "size" : 393216,
    "uuid" : "d21a73ea-79cd-36eb-8ac9-2c5cf5181a27",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 11141120000,
    "size" : 181551104,
    "uuid" : "0d838d1a-cf25-3467-baee-ca40f59e38ba",
    "path" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4424482816,
    "size" : 21299200,
    "uuid" : "9854a721-2573-3169-81ec-19ea40ce8077",
    "path" : "\/Applications\/ChimeraX-1.10-rc2025.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  }
],
  "sharedCache" : {
  "base" : 6845087744,
  "size" : 3091218432,
  "uuid" : "296eb28e-6aeb-3129-8fa6-feb92261a4eb"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1152K        9 \nActivity Tracing                   256K        1 \nCG backing stores                 2192K        5 \nCG image                          1632K       34 \nColorSync                          656K       29 \nCoreAnimation                     3680K       92 \nCoreGraphics                        32K        2 \nCoreImage                           32K        2 \nCoreUI image data                 5168K       40 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             1.2G      159 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         728.0M        8         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                        608K       38 \nStack                            200.3M       39 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      295.0M      263 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__AUTH                            2624K      336 \n__AUTH_CONST                      20.5M      541 \n__CTF                               759        1 \n__DATA                            27.1M      683 \n__DATA_CONST                      29.4M      690 \n__DATA_DIRTY                      1952K      242 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       605.3M      148 \n__OBJC_CONST                      3929K      310 \n__OBJC_RO                         82.1M        1 \n__OBJC_RW                         3104K        1 \n__TEXT                           762.2M      708 \n__UNICODE                          588K        1 \ndyld private memory               1072K        3 \nmapped file                      215.1M       50 \nshared memory                     3200K       29 \n===========                     =======  ======= \nTOTAL                              4.7G     4490 \nTOTAL, minus reserved VM space     3.5G     4490 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
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  "experiments" : [

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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506032143 (2025-06-03)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/teijasuhas/Desktop/Reiter Lab/Electrostatic Potential Maps.cxs"
> format session

No such file/path: /Users/teijasuhas/Desktop/Reiter Lab/Electrostatic
Potential Maps.cxs  

> open "/Users/teijasuhas/Desktop/Reiter Lab/Ciliary Electrostatic Potential
> Maps.cxs"

Opened charge_D1 as #1.2, grid size 97,97,97, pixel 3.12, shown at step 1,
values float32  
Opened charge_GPR161.dx as #2.2, grid size 97,97,97, pixel 3.12, shown at
level -9.45e-07,9.45e-07, step 1, values float32  
Opened charge_HTR6 as #3.2, grid size 97,97,97, pixel 3.12, shown at level
-1.5e-06,1.5e-06, step 1, values float32  
Opened charge_KISS1R.dx as #4.2, grid size 97,97,97, pixel 3.12, shown at step
1, values float32  
Opened charge_MC4R.dx as #5.2, grid size 97,97,97, pixel 3.12, shown at step
1, values float32  
Opened charge_NPY2R.dx as #6.2, grid size 97,97,97, pixel 3.12, shown at step
1, values float32  
Opened charge_PRLHR.dx as #7.2, grid size 97,97,97, pixel 3.12, shown at step
1, values float32  
Opened charge_SSTR3.dx as #8.2, grid size 97,97,97, pixel 3.12, shown at step
1, values float32  
Opened charge_V2_Vasopressin.dx as #9.2, grid size 97,97,97, pixel 3.12, shown
at step 1, values float32  
Map values for surface "NPY2R.orient1.pqr_ SES surface": minimum -0.004707,
mean -7.533e-05, maximum 0.004297  
Map values for surface "KISS1R.orient1.pqr_ SES surface": minimum -0.004159,
mean 8.59e-05, maximum 0.004196  
Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  
Map values for surface "5HT6_ SES surface": minimum -0.004124, mean
-1.203e-05, maximum 0.004183  
Map values for surface "MC4R.orient1.pqr_ SES surface": minimum -0.006654,
mean -0.0002477, maximum 0.004246  
Map values for surface "V2_Vasopressin.orient1.pqr_ SES surface": minimum
-0.004533, mean 2.588e-05, maximum 0.004124  
Map values for surface "SSTR3.orient1.pqr_ SES surface": minimum -0.004478,
mean 9.326e-05, maximum 0.003706  
Map values for surface "GPR161_ SES surface": minimum -0.004668, mean
4.56e-05, maximum 0.005357  
Map values for surface "PRLHR.orient1.pqr_ SES surface": minimum -0.006505,
mean -3.528e-05, maximum 0.003743  

> view name session-start

opened ChimeraX session  

> ui tool show "Surface Color"

> color electrostatic #1.1.2 map #1.2 palette
> -0.007,#ff0000:0,#ffffff:0.007,#0000ff outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> color electrostatic #1.1.2 map #1.2 palette
> -0.009,#ff0000:-0.0045,#ffff00:0,#00ff00:0.0045,#00ffff:0.009,#0000ff
> outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> color electrostatic #1.1.2 map #1.2 palette
> -0.009,#ff0000:-0.0045,#ffff00:0,#ffffff:0.0045,#00ffff:0.009,#0000ff
> outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> color electrostatic #1.1.2 map #1.2 palette
> -0.005,#ff0000:-0.0025,#ffff00:0,#ffffff:0.0025,#00ffff:0.005,#0000ff
> outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> color electrostatic #1.1.2 map #1.2 palette
> -0.005,#ff0000:-0.0025,#ffff00:0,#ffffff:0.0025,#43fd43:0.005,#0000ff
> outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> color electrostatic #1.1.2 map #1.2 palette
> -0.007,#ff0000:-0.0035,#ffff00:0,#ffffff:0.0035,#43fd43:0.007,#0000ff
> outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> key red:-0.007 yellow:-0.004 white:0.000 #43fd43:0.004 blue:0.007 showTool
> true

> ui mousemode right "color key"

> key fontSize 12

> color electrostatic #1.1.2 map #1.2 palette
> -0.007,#ff0000:-0.0035,#ffff00:0,#ffffff:0.0035,#00b0f2:0.007,#5300f5
> outsideColor #808080

Map values for surface "D1.orient1.pqr_ SES surface": minimum -0.005791, mean
5.054e-05, maximum 0.004006  

> key red:-0.007 yellow:-0.004 white:0.000 #00b0f2:0.004 #5300f5:0.007
> showTool true

> ui mousemode right "color key"

> key red:-0.007 yellow:-0.004 white:0.000 #00b0f2:0.004 #5300f5:0.007

> color electrostatic #2.1.2 map #2.2 palette
> -0.007,#ff0000:0,#ffffff:0.007,#0000ff outsideColor #808080

Map values for surface "GPR161_ SES surface": minimum -0.004668, mean
4.56e-05, maximum 0.005357  


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

Log:
UCSF ChimeraX version: 1.10rc202506032143 (2025-06-03)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 9 days 17:24

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506032143
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.1
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.0
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 4 months 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 → Crash using color editor

comment:2 by Eric Pettersen, 4 months ago

Status: accepted → feedback

Hi Teija,

Thanks for reporting this problem. Looking at the information in the bug report, it seems like you were using the Mac color editor at the time, perhaps dragging or dropping a color. Is that right? If not, do you remember what you were doing when the crash occurred?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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