Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000031a8ee000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000204f082c0 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 575 in __init__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1613 in remove_deleted_pointers
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1455 in __init__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2226 in process_changes
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3005 in command_trigger
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2899 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1522 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 55)


{"app_name":"ChimeraX","timestamp":"2024-11-26 11:37:00.00 -0800","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.1 (22C65)","roots_installed":0,"name":"ChimeraX","incident_id":"C2058FDC-62CF-4A14-8FA6-83870CBB77B1"}
{
  "uptime" : 510000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 650,
  "osVersion" : {
    "train" : "macOS 13.1",
    "build" : "22C65",
    "releaseType" : "User"
  },
  "captureTime" : "2024-11-26 11:36:55.1462 -0800",
  "incident" : "C2058FDC-62CF-4A14-8FA6-83870CBB77B1",
  "pid" : 93410,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-11-25 13:36:08.0975 -0800",
  "procStartAbsTime" : 11124120965651,
  "procExitAbsTime" : 12402837745736,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"8076F165-8627-5EEF-B587-5CCCDB1513AA","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "1A4B64E1-8B45-F009-B767-55D204EECFAE",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 6210,
  "sleepWakeUUID" : "7EA422CD-D801-449F-87B8-5792A42F1092",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140722726879063\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9025c000-7ffc99b2c000 [152.8M] r-x\/r-x SM=COW  ...t_id=7da4cf93",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140722726879063\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9025c000-7ffc99b2c000 [152.8M] r-x\/r-x SM=COW  ...t_id=7da4cf93",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "CFBundleShortVersionString" : "3.11.2, (c) 2001-2023 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 4079616,
    "uuid" : "24670b23-d78a-3eaa-bca8-22faf877f190",
    "path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.11.2"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703226953728,
    "size" : 40952,
    "uuid" : "f314b62b-98f4-3a7c-8296-8739f8b6855a",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703225028608,
    "size" : 184320,
    "uuid" : "f609f029-bcd0-3a54-b48a-99b3ce8378ce",
    "path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
    "name" : "libsystem_malloc.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 140703125041152,
    "size" : 196608,
    "uuid" : "d592bc4a-4a21-348f-a406-e12f9cd2f27c",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4634681344,
    "size" : 64094208,
    "uuid" : "9d768904-ac4b-327d-8126-cec11a08b966",
    "path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5342306304,
    "size" : 165052416,
    "uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
    "path" : "\/Applications\/ChimeraX-1.7.1.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" : "x86_64",
    "base" : 140703227170816,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4816896,
    "uuid" : "f3846a86-644b-3bcd-acce-fc7b751105c1",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.300"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703278313472,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 16809984,
    "uuid" : "00f4aa78-a19f-3a8e-9650-9f90b7beefd6",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299.30.116"
  }
],
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000025
    },
    {
      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

      },
      "deploymentId" : 240000002
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
      "experimentId" : "6643969b3099cf28e049862f",
      "deploymentId" : 400000007
    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jeff/Research/phenix/Refine_498/CrTE_refine_498_renum.pdb

Summary of feedback from opening
/Users/jeff/Research/phenix/Refine_498/CrTE_refine_498_renum.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (277 )  
  
Chain information for CrTE_refine_498_renum.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="HOH"

8 atoms, 8 residues, 1 model selected  

> show sel atoms

> select clear

> ui tool show "Crystal Contacts"

> crystalcontacts #1

3 pairs of asymmetric units of CrTE_refine_498_renum.pdb contact at distance
3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        17     0      7      0  0  0      0         1
         9     0      4      1  0  0      0         1
         5     0      4      0  0  0      0         1
    

  

> select #2.1

2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> show sel atoms

> hide sel atoms

> select clear

> select ::name="HOH"

32 atoms, 32 residues, 4 models selected  

> show sel atoms

> select clear

> hide atoms

> show cartoons

> hide cartoons

> undo

> select #2.2

2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #2.3

2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> select ::name="HOH"

32 atoms, 32 residues, 4 models selected  

> show sel atoms

> hide sel atoms

> color sel bychain

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for CrTE_refine_498_renum.pdb_B SES surface #1.2: minimum,
0.00, mean 0.00, maximum 0.00  
Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 7_B SES surface
#2.1.2: minimum, 0.00, mean 0.00, maximum 0.00  
Coulombic values for CrTE_refine_498_renum.pdb 1 0 0 sym 4_B SES surface
#2.2.2: minimum, 0.00, mean 0.00, maximum 0.00  
Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 4_B SES surface
#2.3.2: minimum, 0.00, mean 0.00, maximum 0.00  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select clear

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for CrTE_refine_498_renum.pdb_A SES surface #1.3: minimum,
-14.22, mean -1.14, maximum 12.95  
Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 7_A SES surface
#2.1.3: minimum, -14.22, mean -1.14, maximum 12.95  
Coulombic values for CrTE_refine_498_renum.pdb 1 0 0 sym 4_A SES surface
#2.2.3: minimum, -14.22, mean -1.14, maximum 12.95  
Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 4_A SES surface
#2.3.3: minimum, -14.22, mean -1.14, maximum 12.95  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #2.2,2.3

2291 atoms, 290 residues, 1 model selected  

> hide sel surfaces

> select #2.2,#2.3

Expected an objects specifier or a keyword  

> hide sel surfaces

> select #2.3

2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected  

> hide sel surfaces

> select clear

> hide surfaces

> select add #2.2

2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected  

> select add #2.3

4598 atoms, 4686 bonds, 2 pseudobonds, 596 residues, 6 models selected  

> close #2.2

> close #2.3

> hide #!2 models

> ui tool show "Selection Inspector"

> setattr =sel p display false

Assigning display attribute to 1 item  

> undo

> redo

No redo action is available  

> redo

No redo action is available  

> hide #!2 models

> select clear

Drag select of 19 residues  

> ui tool show "Selection Inspector"

> show sel atoms

> hide sel atoms

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A

Alignment identifier is 1  

> select #1:266,268,270

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

> show sel atoms

> select clear

> select #1:138

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

> show sel atoms

> hide sel atoms

> select clear

> select #1:306

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

> show sel atoms

> select clear

> color #1 cornflower blue

> select clear

> color #!1 byhetero

> select clear

> color #1 #f7fff8ff

> color #1 #f6fff8ff

> color #1 #f5fff8ff

> color #1 #eefff9ff

> color #1 #e7fffbff

> color #1 #e2fffcff

> color #1 #d5ffffff

> color #1 #cbfcffff

> color #1 #c9fbffff

> color #1 #c2f9ffff

> color #1 #baf6ffff

> color #1 #b7f5ffff

> color #1 #b3f2ffff

> color #1 #b2f2ffff

> color #1 #aff1ffff

> color #1 #acefffff

> color #1 #aaefffff

> color #1 #a9efffff

> color #1 #a8eeffff

> color #1 #a7eeffff

> color #1 #a5edffff

> color #1 #a2ebffff

> color #1 #a1eaffff

> color #1 #9fe8ffff

> color #1 #9fe7ffff

> color #1 #9ee6ffff

> color #1 #9ee5ffff

> color #1 #9de3ffff

> color #1 #9de2ffff

> color #1 #9de1ffff

> color #1 #9de0ffff

> color #1 #9dddffff

> color #1 #9ddcffff

> color #1 #9cd6ffff

> color #1 #9bd1ffff

> color #1 #9bcfffff

> color #1 #9acdffff

> color #1 #9acbffff

> color #1 #9acaffff

> color #1 #9ac8ffff

> color #1 #9ac7ffff

> color #1 #99c6ffff

> color #1 #99c5ffff

> color #1 #99c4ffff

> color #1 #98c3ffff

> color #1 #98c2ffff

> color #1 #97c0ffff

> color #1 #97bfffff

> color #1 #97beffff

> color #1 #96bdffff

> color #1 #96bcffff

> color #1 #96bbffff

> color #1 #95bcffff

> color #1 #95beffff

> color #1 #93c8ffff

> color #1 #92ccffff

> color #1 #8fd1ffff

> color #1 #8dd3ffff

> color #1 #8bd4ffff

> color #1 #89d5ffff

> color #1 #86d6ffff

> color #1 #81d7ffff

> color #1 #7fd7ffff

> color #1 #7dd7ffff

> color #1 #7dd8ffff

> color #1 #7cd8ffff

> color #1 #7cd9ffff

> color #1 #78dfffff

> color #1 #76e2ffff

> color #1 #73e4ffff

> color #1 #71e7ffff

> color #1 #6eeaffff

> color #1 #6decffff

> color #1 #6aefffff

> color #1 #69f1ffff

> color #1 #68f2ffff

> color #1 #68f1ffff

> color #1 #69f1ffff

> color #1 #6aeeffff

> color #1 #6aedffff

> color #1 #6beaffff

> color #1 #6ce9ffff

> color #1 #6ee6ffff

> color #1 #6fe4ffff

> color #1 #70e4ffff

> color #1 #70e3ffff

> color #1 #71e3ffff

> color #1 #70e1ffff

> color #1 #70deffff

> color #1 #70dcffff

> color #1 #6fdaffff

> color #1 #6fd7ffff

> color #1 #6fd6ffff

> color #1 #6ed4ffff

> color #1 #6ed3ffff

> color #1 #6ed4ffff

> color #1 #6dd4ffff

> color #1 #6bd5ffff

> color #1 #6ad6ffff

> color #1 #69d6ffff

> color #1 #69d7ffff

> color #1 #68d8ffff

> color #1 #68d9ffff

> color #1 #67daffff

> color #1 #67dbffff

> color #1 #67dcffff

> color #1 #66dcffff

> color #1 #67dcffff

> color #1 #66ddffff

> color #1 #66deffff

> color #1 #65dfffff

> color #1 #65e0ffff

> color #1 #65e1ffff

> color #1 #64e2ffff

> color #1 #64e4ffff

> color #1 #64e6ffff

> color #1 #63e8ffff

> color #1 #61ecffff

> color #1 #62edffff

> color #1 #61eeffff

> color #1 #61efffff

> color #1 #62f4ffff

> color #1 #62f7ffff

> color #1 #63fbffff

> color #1 #63fdffff

> color #1 #64fdffff

> color #1 #63fdffff

> color #1 #63feffff

> color #1 #5fffffff

> color #1 #5cfffeff

> color #1 #55fffbff

> color #1 #4cfff8ff

> color #1 #4afff7ff

> color #1 #45fff6ff

> color #1 #43fff6ff

> color #1 #40fff5ff

> color #1 #3efff5ff

> color #1 #3cfff5ff

> color #1 #3bfff5ff

> color #1 #37fff5ff

> color #1 #35fff5ff

> color #1 #33fff5ff

> color #1 #31fff5ff

> color #1 #2ffff5ff

> color #1 #2efff5ff

> color #1 #2dfff5ff

> color #1 #2cfff5ff

> color #1 #2afff5ff

> color #1 #29fff4ff

> color #1 #28fff4ff

> color #1 #27fff3ff

> color #1 #26fff1ff

> color #1 #26fff0ff

> color #1 #26ffefff

> color #1 #25ffeeff

> color #1 #25ffedff

> color #1 #25ffecff

> color #1 #26ffebff

> color #1 #26ffeaff

> color #1 #2affe1ff

> color #1 #34ffcbff

> color #1 #3dffb5ff

> color #1 #3fffb2ff

> color #1 #41ffaeff

> color #1 #42ffaeff

> color #1 #43ffaeff

> color #1 #47ffb0ff

> color #1 #49ffb2ff

> color #1 #4fffb6ff

> color #1 #54ffbbff

> color #1 #56ffbcff

> color #1 #5cffbfff

> color #1 #64ffc0ff

> color #1 #68ffc1ff

> color #1 #75ffc2ff

> color #1 #7affc3ff

> color #1 #80ffc3ff

> color #1 #83ffc3ff

> color #1 #85ffc3ff

> color #1 #85ffc1ff

> color #1 #86ffc1ff

> color #1 #87ffc1ff

> color #1 #89ffbeff

> color #1 #8bffbdff

> color #1 #8bffbcff

> color #1 #8bffbbff

> color #1 #8affb9ff

> color #1 #88ffb7ff

> color #1 #88ffb5ff

> color #1 #86ffb4ff

> color #1 #86ffb2ff

> color #1 #85ffb1ff

> color #1 #84ffb0ff

> color #1 #83ffb0ff

> color #1 #83ffafff

> color #1 #82ffaeff

> color #1 #81ffaeff

> color #1 #82ffafff

> color #1 #82ffb0ff

> color #1 #83ffb1ff

> color #1 #83ffb3ff

> color #1 #84ffb4ff

> color #1 #84ffb5ff

> color #1 #84ffb6ff

> color #1 #84ffb7ff

> color #1 #84ffb8ff

> color #1 #85ffb8ff

> color #1 #85ffb9ff

> color #1 #85ffbaff

> color #1 #86ffbaff

> color #1 #86ffbbff

> color #1 #86ffbcff

> color #1 #86ffbdff

> color #1 #87ffbdff

> color #1 #87ffbeff

> color #1 #87ffbfff

> color #1 #88ffbfff

> color #1 #88ffc0ff

> color #1 #89ffc1ff

> color #1 #8affc3ff

> color #1 #8affc4ff

> color #1 #8bffc7ff

> color #1 #8cffc9ff

> color #1 #8dffcaff

> color #1 #8dffc9ff

> color #1 #8cffc5ff

> color #1 #8bffc1ff

> color #1 #8bffc0ff

> color #1 #8affbfff

> color #1 #8affbeff

> color #1 #8affbdff

> color #1 #8bffbdff

> color #1 #8bffbcff

> color #1 #8bffbaff


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

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 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: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Unknown
      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: 22 days, 18 hours, 18 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: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2518D:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    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: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9