Opened 6 days ago

Closed 6 days ago

#20499 closed defect (fixed)

Crash showing symmetry

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

Description

The following bug report has been submitted:
Platform:        macOS-26.5.1-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000000030704f000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x0000000306043000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x0000000305037000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000030402b000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000030301f000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x0000000301007000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000017f99b000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000017e98f000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000017d983000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000017c977000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000017b96b000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x000000017a95f000 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Current thread 0x00000001f7e15e80 (most recent call first):
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/place.py", line 807 in __mul__
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/sym.py", line 238 in show_symmetry
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/sym.py", line 107 in sym
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245 in run
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 322 in execute
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 147 in keyPressEvent
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
  File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath (total: 48)


{"app_name":"ChimeraX","timestamp":"2026-06-16 09:27:59.00 +0200","app_version":"1.12.0","slice_uuid":"544eb719-b770-3601-b425-1ceb237637ac","build_version":"1.12.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.5.1 (25F80)","roots_installed":0,"name":"ChimeraX","incident_id":"E37420AB-4195-4D09-863E-CA709A133020"}
{
  "uptime" : 91000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,1",
  "coalitionID" : 6969,
  "osVersion" : {
    "train" : "macOS 26.5.1",
    "build" : "25F80",
    "releaseType" : "User"
  },
  "captureTime" : "2026-06-16 09:27:45.1711 +0200",
  "codeSigningMonitor" : 2,
  "incident" : "E37420AB-4195-4D09-863E-CA709A133020",
  "pid" : 9041,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procLaunch" : "2026-06-15 08:29:24.4133 +0200",
  "procStartAbsTime" : 1125919226247,
  "procExitAbsTime" : 2189120092804,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.12.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.12.0","CFBundleVersion":"1.12.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"204A0FD2-B76B-5F99-BB2A-061A3C38C678","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F1ABBE62-2CCF-87EE-9985-1C56AEAC878E",
  "appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","assetIsNotReady"]},
  "developerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "DE5EF6B3-5567-4041-8001-49BD9CFEDB4A",
  "wakeTime" : 3909,
  "sleepWakeUUID" : "398E91E5-D0A2-451D-9DDB-344761EE2B87",
  "sip" : "enabled",
  "vmRegionInfo" : "0x6c00001280 is in 0x1000000000-0x7000000000;  bytes after start: 395136995968  bytes before end: 17179864447
      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL
      commpage (reserved)         fc0000000-1000000000   [  1.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)
--->  GPU Carveout (reserved)    1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)
      MALLOC_LARGE               7000000000-7008000000   [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000002, 0x0000006c00001280","rawCodes":[2,463856472704],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000006c00001280"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":9041},
  "vmregioninfo" : "0x6c00001280 is in 0x1000000000-0x7000000000;  bytes after start: 395136995968  bytes before end: 17179864447
      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL
      commpage (reserved)         fc0000000-1000000000   [  1.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)
--->  GPU Carveout (reserved)    1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)
      MALLOC_LARGE               7000000000-7008000000   [128.0M] rw-\/rwx SM=PRV  ",
  "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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    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    "name" : "_ribbons.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5253300224,
    "size" : 16384,
    "uuid" : "4125b296-a3be-3343-9e1c-fe687ea3bf9e",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
    "name" : "_graphics.cpython-311-darwin.so"
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  {
    "source" : "P",
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    "base" : 5256380416,
    "size" : 376832,
    "uuid" : "2ab16016-8716-388e-ada0-33f46a29576a",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    "name" : "mmcif.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5255249920,
    "size" : 376832,
    "uuid" : "f0b958ae-cf48-3682-8bf2-e30217be027d",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    "name" : "_mmcif.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5214896128,
    "size" : 49152,
    "uuid" : "5bd21324-288d-31d8-a98b-f8c1776ff590",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
    "name" : "nones_formathandler.cpython-311-darwin.so"
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  {
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    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imaging.cpython-311-darwin.so",
    "name" : "_imaging.cpython-311-darwin.so"
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    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libtiff.6.dylib",
    "name" : "libtiff.6.dylib"
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    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libjpeg.62.4.0.dylib",
    "name" : "libjpeg.62.4.0.dylib"
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    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libopenjp2.2.5.3.dylib",
    "name" : "libopenjp2.2.5.3.dylib"
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  {
    "source" : "P",
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    "uuid" : "5be17d28-46cf-3336-bfae-f315e9891018",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libz.1.3.1.zlib-ng.dylib",
    "name" : "libz.1.3.1.zlib-ng.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5318000640,
    "size" : 163840,
    "uuid" : "6fa02d7f-daaa-3c79-8b0d-c5319e003f3d",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libxcb.1.1.0.dylib",
    "name" : "libxcb.1.1.0.dylib"
  },
  {
    "source" : "P",
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    "size" : 262144,
    "uuid" : "8dfe23b8-ad17-3d21-8c5e-5525cd8953db",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/liblzma.5.dylib",
    "name" : "liblzma.5.dylib"
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    "uuid" : "32a172ad-f11b-381b-9270-3f9a195cbe7f",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libXau.6.dylib",
    "name" : "libXau.6.dylib"
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    "uuid" : "7c43df7b-5e3e-3a91-9bc6-b8f9ebd02ec2",
    "path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
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    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "CFBundleIdentifier" : "com.apple.AppKit",
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},
  "vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)
Writable regions: Total=80.0G written=1.2G(1%) resident=15.1M(0%) swapped_out=1.2G(1%) unallocated=78.8G(99%)

                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               128K        1 
Activity Tracing                   256K        1 
AttributeGraph Data               1024K        1 
CG image                          6336K       17 
CG raster data                    3296K        7 
ColorSync                          112K        6 
CoreAnimation                     3200K      128 
CoreGraphics                        32K        2 
CoreServices                       352K        2 
CoreUI image data                 4864K       37 
Foundation                          32K        2 
Kernel Alloc Once                   96K        2 
MALLOC                            22.0G     1325 
MALLOC guard page                 3856K        4 
MALLOC_LARGE (reserved)           53.4G        1         reserved VM address space (unallocated)
Mach message                        64K        4 
Memory Tag 22                     64.0M        1 
OpenGL GLSL                        256K        3 
PROTECTED_MEMORY                    16K        1 
STACK GUARD                        912K       57 
Stack                            419.4M       58 
Stack Guard                       56.0M        1 
VM_ALLOCATE                        4.0G     3317 
VM_ALLOCATE (reserved)           128.0M        2         reserved VM address space (unallocated)
__AUTH                            6024K      634 
__AUTH_CONST                      89.9M     1026 
__CTF                               824        1 
__DATA                            41.9M     1105 
__DATA_CONST                      61.8M     1158 
__DATA_DIRTY                      8351K      881 
__FONT_DATA                        2352        1 
__GLSLBUILTINS                    5176K        1 
__LINKEDIT                       603.5M      129 
__OBJC_RO                         79.1M        1 
__OBJC_RW                         2599K        1 
__TEXT                             1.5G     1180 
__TPRO_CONST                       128K        2 
dyld private memory                304K        5 
mapped file                      314.1M       72 
page table in kernel              15.1M        1 
shared memory                     3696K       24 
===========                     =======  ======= 
TOTAL                             82.8G    11202 
TOTAL, minus reserved VM space    29.2G    11202 
",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
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},
  "logWritingSignature" : "01581d00a27b63f7382ba7c69f0e879bb9097664",
  "bug_type" : "309",
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  "trialInfo" : {
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}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/CORSAIR/Dima/Plasmid and Primers/AAV5 plasmid with
> mutations/7kp3.pdb"

7kp3.pdb title:  
Adeno-associated virus serotype 5 At 2.1 angstroms resolution, AAV5 [more
info...]  
  
Chain information for 7kp3.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein | Q9YIJ1_9VIRU 2-724  
  

> hide cartoons

> show cartoons

> hide atoms

> show atoms

> hide atoms

> transparency 60 surfaces

> info models

model id #1 type AtomicStructure name 7kp3.pdb  

> open 7kp4 assemply 1

'assemply' has no suffix  

> info models

model id #1 type AtomicStructure name 7kp3.pdb  

> info chains

chain id /A chain_id A  

> open /Users/dima/Downloads/9DC7-assembly1.cif.gz

File reader requires uncompressed file;
'/Users/dima/Downloads/9DC7-assembly1.cif.gz' is compressed  

> open /Users/dima/Downloads/7KP3.pdb1.gz

7KP3.pdb1.gz title:  
Adeno-associated virus serotype 5 At 2.1 angstroms resolution, AAV5 [more
info...]  
  
Chain information for 7KP3.pdb1.gz  
---  
Chain | Description  
2.1/A | No description available  
2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A 2.21/A 2.22/A 2.23/A 2.24/A 2.25/A 2.26/A 2.27/A 2.28/A 2.29/A 2.30/A 2.31/A 2.32/A 2.33/A 2.34/A 2.35/A 2.36/A 2.37/A 2.38/A 2.39/A 2.40/A 2.41/A 2.42/A 2.43/A 2.44/A 2.45/A 2.46/A 2.47/A 2.48/A 2.49/A 2.50/A 2.51/A 2.52/A 2.53/A 2.54/A 2.55/A 2.56/A 2.57/A 2.58/A 2.59/A 2.60/A | No description available  
  

> hide #!2 models

> show #!2 models

> hide #1 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> hide #1 target m

> select 587

Expected an objects specifier or a keyword  

> select :587

488 atoms, 427 bonds, 61 residues, 61 models selected  

> color red sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red sel steyle sel sphere

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red sel steyle sel sphere

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style sel sphere

Changed 488 atom styles  

> color red sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red sel atoms

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red atoms

> style atoms sphere

Expected a keyword  

> style sel atoms sphere

Expected a keyword  

> style sel atom sphere

Expected a keyword  

> select :587

488 atoms, 427 bonds, 61 residues, 61 models selected  

> color red sel atoms

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style :587 sphere

Changed 488 atom styles  

> show #1 models

> hide #1 models

> color red :587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red :587 atoms

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style :587 sphere

Changed 488 atom styles  

> surface transparency 40 surface

Expected a keyword  

> surface transparency 40 surface color lightgray surface

Expected a keyword  

> surface

> transparency 40 surfaces

> color lightgray surfaces

> color red :587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style :587 sphere

Changed 488 atom styles  

> color red :263,531,587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style :263,531,587 sphere

Changed 1586 atom styles  

> select #1:587

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

> color red #1:587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select #1:587

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

> color red sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red #1:587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red :587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color :587

> color A:587

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A:587

> color red /A:587

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color /A:587 red

> surface tranparency 60 surface

Expected an atoms specifier or a keyword  

> surface color lightgray surface tranparency 60 surface

Expected a keyword  

> size sphere 2.0 / A:587

Expected a keyword  

> size sphere / A:587

Expected a keyword  

> size sphere / A : 587

Expected a keyword  

> size sphere /A : 587

Expected a keyword  

> size sphere /A : 587

Expected a keyword  

> size sphere 2.0 /A:587

Expected a keyword  

> size sphere /A:587

Expected a keyword  

> size /A:587

> style /A:587 sphere

Changed 488 atom styles  

> transparency 60 surfaces

> symmetry axes

Unknown command: symmetry axes  

> sym #1 i

Made 60 graphical clones for 7kp3.pdb symmetry i  

> symmetry show true

Unknown command: symmetry show true  

> measure symmetry #1

No volume specified  

> sym #1 i

Made 60 graphical clones for 7kp3.pdb symmetry i  

> transparency 30 surfaces

> transparency 60 surfaces

> transparency 20 surfaces

> transparency 30 surfaces

> symmetry axes

Unknown command: symmetry axes  

> sym #1 i

Made 60 graphical clones for 7kp3.pdb symmetry i  

> show sym

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> symmetry #1

Unknown command: symmetry #1  

> sym #1 i

Made 60 graphical clones for 7kp3.pdb symmetry i  

> sym #1 i


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

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK183D/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 Performance and 2 Efficiency)
      Memory: 16 GB
      System Firmware Version: 18000.120.36
      OS Loader Version: 18000.120.36

Software:

    System Software Overview:

      System Version: macOS 26.5.1 (25F80)
      Kernel Version: Darwin 25.5.0
      Time since boot: 4 days, 9 hours, 53 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 4
      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: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    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: 1.2.2
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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
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    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
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    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2

Change History (3)

comment:1 by Eric Pettersen, 6 days ago

Component: UnassignedHigher-Order Structure
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionCrash showing symmetry

comment:2 by Tom Goddard, 6 days ago

The user ran "sym #1 i" five times, each time multiplying the number of graphical instances by 60 with no visual change, for about 800 million instances. Then it likely ran out of memory. The same user error was made in #20117.

Not clear how to avoid this. It is sometimes useful to apply multiple symmetries with two or more commands. The distinguishing feature of this case is that the copies just end up on top of other copies. That is a pain to check for since it involves floating point tolerances. I could simply log a warning when you create new instances from old, although the user may not see the warning in the log.

comment:3 by Tom Goddard, 6 days ago

Resolution: fixed
Status: assignedclosed

I added a warning message when sym command makes graphical clones from existing graphical clones. Suggested using "sym clear" command to remove clones. Hopefully user will see this. Has been reported 3 times in the last 8 years going back to ChimeraX 1.2.

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