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Opened 2 days ago
#19407 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202511122144 (2025-11-12 21:44:22 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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017fa1b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017ea0f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017da03000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017c9f7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017b9eb000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017a9df000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000001799d3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000001789c7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000001eff76080 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 146 in render
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 115 in _redraw
File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.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, PIL._imaging, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54)
{"app_name":"ChimeraX","timestamp":"2025-11-21 13:01:12.00 +0000","app_version":"1.11.0","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.1 (25B78)","roots_installed":0,"name":"ChimeraX","incident_id":"F3B99729-58DA-4B67-BB90-C8ECACDFF3C3"}
{
"uptime" : 130000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 3860,
"osVersion" : {
"train" : "macOS 26.1",
"build" : "25B78",
"releaseType" : "User"
},
"captureTime" : "2025-11-21 13:01:04.8056 +0000",
"codeSigningMonitor" : 2,
"incident" : "F3B99729-58DA-4B67-BB90-C8ECACDFF3C3",
"pid" : 92642,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-20 10:43:49.0632 +0000",
"procStartAbsTime" : 2428120746459,
"procExitAbsTime" : 3138699170735,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8330DCBC-A847-5780-B99F-5EE3831D3E46","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4B8D0552-F25E-3117-5FC1-7C04C199AF25",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "5BFC8FC6-F9E6-4AB5-B703-0BDAF9626BAD",
"wakeTime" : 4,
"sleepWakeUUID" : "2548C9E8-F622-4B11-8C92-0C9BC4A21851",
"sip" : "enabled",
"vmRegionInfo" : "0xb00001d00 is in 0x878000000-0xb69400000; bytes after start: 10871643392 bytes before end: 1765794559
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 60e000000-60e294000 [ 2640K] rw-\/rwx SM=PRV
GAP OF 0x269d6c000 BYTES
---> commpage (reserved) 878000000-b69400000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL b69400000-b69800000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000b00001d00","rawCodes":[2,47244647680],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000b00001d00"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":92642},
"vmregioninfo" : "0xb00001d00 is in 0x878000000-0xb69400000; bytes after start: 10871643392 bytes before end: 1765794559
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 60e000000-60e294000 [ 2640K] rw-\/rwx SM=PRV
GAP OF 0x269d6c000 BYTES
---> commpage (reserved) 878000000-b69400000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL b69400000-b69800000 [ 4096K] 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" : [{
"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":49279711896},{"value":80},{"value":97},{"value":0},{"value":0},{"value":17932822431628264112},{"value":17932822428898779696},{"value":14757395258967641293},{"value":4294967286},{"value":49279711826},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8343983072},{"value":0},{"value":10},{"value":259},{"value":8320934240 ,"symbolLocation":224,"symbol": "_main_thread"},{"value":0},{"value":1},{"value":4350297656 ,"symbolLocation":0,"symbol": "faulthandler_handlers"},{"value":1},{"value":4330017000},{"value":4346985272 ,"symbolLocation":0,"symbol": "cfunction_call"},{"value":4353920216}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6498719880},"cpsr":{"value":1073741824},"fp":{"value":49279711968},"sp":{"value":49279711936},"esr":{"value":1442840704,"description":"(Syscall)"},"pc":{"value":6498481584,"matchesCrashFrame":1},"far":{"value":0}},"id":1925155,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[
{"imageOffset":38320,"symbol": "__pthread_kill" ,"symbolLocation":8,"imageIndex":137},
{"imageOffset":26760,"symbol": "pthread_kill" ,"symbolLocation":296,"imageIndex":138},
{"imageOffset":269616,"symbol": "raise" ,"symbolLocation":32,"imageIndex":139},
{"imageOffset":2447420,"symbol": "faulthandler_fatal_error" ,"symbolLocation":392,"imageIndex":1},
{"imageOffset":14148,"symbol": "_sigtramp" ,"symbolLocation":56,"imageIndex":140},
{"imageOffset":16151172,"symbol": "-[NSSoftwareSurface frontBuffer]" ,"symbolLocation":576,"imageIndex":141},
{"imageOffset":16145676,"symbol": "-[NSCGLSurface flushRect:]" ,"symbolLocation":512,"imageIndex":141},
{"imageOffset":16144988,"symbol": "NSCGLSurfaceFlush" ,"symbolLocation":132,"imageIndex":141},
{"imageOffset":106048,"symbol": "glSwap_Exec" ,"symbolLocation":256,"imageIndex":142},
{"imageOffset":55032,"symbol": "CGLFlushDrawable" ,"symbolLocation":64,"imageIndex":143},
{"imageOffset":1392988,"symbol": "-[NSOpenGLContext flushBuffer]" ,"symbolLocation":28,"imageIndex":141},
{"imageOffset":512676,"imageIndex":71},
{"imageOffset":3679112,"symbol": "QOpenGLContext::swapBuffers(QSurface*)" ,"symbolLocation":236,"imageIndex":49},
{"imageOffset":977256,"symbol": "meth_QOpenGLContext_swapBuffers(_object*, _object*)" ,"symbolLocation":104,"imageIndex":51},
{"imageOffset":998296,"symbol": "cfunction_call" ,"symbolLocation":96,"imageIndex":1},
{"imageOffset":586556,"symbol": "_PyObject_MakeTpCall" ,"symbolLocation":128,"imageIndex":1},
{"imageOffset":1798332,"symbol": "_PyEval_EvalFrameDefault" ,"symbolLocation":54032,"imageIndex":1},
{"imageOffset":1820600,"symbol": "_PyEval_Vector" ,"symbolLocation":156,"imageIndex":1},
{"imageOffset":603732,"symbol": "method_vectorcall" ,"symbolLocation":164,"imageIndex":1},
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REGION TYPE SIZE COUNT (non-coalesced)
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Accelerate framework 256K 2
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 192K 8
ColorSync 160K 10
CoreAnimation 5024K 72
CoreGraphics 32K 2
CoreUI image data 2288K 36
Dispatch continuations 96.0M 1
Foundation 48K 2
Kernel Alloc Once 112K 3
MALLOC 1.7G 347
MALLOC guard page 3680K 4
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 1072K 67
Stack 440.7M 68
Stack Guard 56.0M 1
VM_ALLOCATE 216.8M 192
VM_ALLOCATE (reserved) 256.0M 2 reserved VM address space (unallocated)
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__TEXT 1.5G 1204
__TEXT (graphics) 912K 2
__TPRO_CONST 128K 2
dyld private memory 1072K 11
mapped file 354.7M 61
page table in kernel 2243K 1
shared memory 3664K 24
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TOTAL 5.5G 7195
TOTAL, minus reserved VM space 5.2G 7195
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202511122144 (2025-11-12)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
No sequence chosen for AlphaFold match
> open alphafold P11388
'alphafold' has no suffix
Fetching compressed P11388 UniProt info from
https://www.uniprot.org/uniprot/P11388.xml
> alphafold match P11388
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold P11388 from
https://alphafold.ebi.ac.uk/files/AF-P11388-F1-model_v6.cif
1 AlphaFold model found using UniProt identifier: P11388 (UniProt P11388)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P11388 | P11388 | 100.0 | 100.0
Opened 1 AlphaFold model
> sequence chain #1Alignment identifier is 1/A
> select /A:11917 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:1-11919625 atoms, 9814 bonds, 1191 residues, 1 model selected
> color sel red> background whiteUnknown command: background white
> set bgColor white> select up12261 atoms, 12495 bonds, 1531 residues, 1 model
> selected
> select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected
> select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected
> select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected
> select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected
> select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected
> select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected
> select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected
> select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected
> select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected
> color sel black> select /A:1275-1320376 atoms, 384 bonds, 46 residues, 1
> model selected
> select /A:136-13209539 atoms, 9723 bonds, 1185 residues, 1 model selected
> select /A:13579 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1357-1402345 atoms, 352 bonds, 46 residues, 1 model selected
> open /Users/johnsor2/Downloads/emd_49171.mapOpened emd_49171.map as #2, grid
> size 480,480,480, pixel 1.4, shown at level 0.0271, step 2, values float32
> close #1> close> open /Users/johnsor2/Downloads/emd_49171.mapOpened
> emd_49171.map as #1, grid size 480,480,480, pixel 1.4, shown at level
> 0.0271, step 2, values float32
> volume #1 level 0.02004> volume #1 level 0.01769> volume #1 level 0.009239> volume #1 level 0.01323> volume #1 style image> volume #1 style mesh> volume #1 style image maximumIntensityProjection true> volume #1 maximumIntensityProjection false> volume #1 region 0,0,238,479,479,238 step 1 showOutlineBox true> volume #1 region 0,0,0,479,479,479 step 2> volume #1 region 0,0,0,479,479,479 step 1 colorMode opaque8 orthoplanes xyz positionPlanes 239,239,239 imageMode orthoplanes> volume #1 imageMode "box faces"> volume #1 region 0,0,0,479,479,479 step 2 colorMode auto8 imageMode "tilted slab" tiltedSlabAxis 0.2958,0.05286,-0.9538 tiltedSlabOffset -236.5 tiltedSlabSpacing 1.402 tiltedSlabPlaneCount 48> volume #1 style surface> volume #1 change image level -0.002962,0 level 0.02707,0.8 level 0.1141,1> volume #1 level 0.04139> volume #1 level 0.02755> volume #1 level 0.0259> volume #1 step 1> volume #1 level 0.03061> volume #1 step 4> volume #1 step 2> volume #1 level 0.03038> volume #1 level 0.02709> volume #1 level 0.01582> open 9N9J | Summary of feedback from opening 9N9J fetched from pdb
---
warnings | Atom HO5' is not in the residue template for C /L5:1
Atom HO5' is not in the residue template for C /L8:1
notes | Fetching compressed mmCIF 9n9j from http://files.rcsb.org/download/9n9j.cif
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif
Fetching CCD ELU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/ELU/ELU.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD NDG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NDG/NDG.cif
9n9j title:
Structure of a GRP94 folding intermediate engaged with a CCDC134- and
FKBP11-bound secretory translocon [more info...]
Chain information for 9n9j #2
---
Chain | Description | UniProt
5 | Translocon-associated protein subunit alpha | SSRA_HUMAN 1-286
6 | Translocon-associated protein subunit beta | SSRB_HUMAN 1-183
7 | Translocon-associated protein subunit gamma | SSRG_HUMAN 1-185
8 | Translocon-associated protein subunit delta | SSRD_HUMAN 1-173
A | Peptidyl-prolyl cis-trans isomerase FKBP11 | FKB11_HUMAN -26-174
B | Coiled-coil domain-containing protein 134 | CC134_HUMAN 1-229
D | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_HUMAN 1-476
E | Protein transport protein Sec61 subunit beta | SC61B_HUMAN 1-96
F | Protein transport protein Sec61 subunit gamma | SC61G_HUMAN 1-68
G | Stress-associated endoplasmic reticulum protein 1 | SERP1_HUMAN 1-66
I | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A | STT3A_HUMAN 1-705
J | Oligosaccharyltransferase complex subunit OSTC | OSTC_HUMAN 1-149
K2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 | OST4_HUMAN 1-37
L2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258 | TM258_HUMAN 1-79
L5 | 28S ribosomal RNA |
L7 | 5S ribosomal RNA |
L8 | 5.8S ribosomal RNA |
LA | 60S ribosomal protein L8 | RL8_HUMAN 1-257
LB | 60S ribosomal protein L3 | RL3_HUMAN 1-403
LC | Large ribosomal subunit protein uL4 | RL4_HUMAN 1-427
LD | Large ribosomal subunit protein uL18 | RL5_HUMAN 1-297
LE | Large ribosomal subunit protein eL6 | RL6_HUMAN 1-288
LF | 60S ribosomal protein L7 | RL7_HUMAN 1-248
LG | Large ribosomal subunit protein eL8 | RL7A_HUMAN 1-266
LH | Large ribosomal subunit protein uL6 | RL9_HUMAN 1-192
LI | Ribosomal protein uL16-like | RL10L_HUMAN 1-214
LJ | Large ribosomal subunit protein uL5 | RL11_HUMAN 1-178
LL | Large ribosomal subunit protein eL13 | RL13_HUMAN 1-211
LM | Large ribosomal subunit protein eL14 | RL14_HUMAN 1-215
LN | Large ribosomal subunit protein eL15 | RL15_HUMAN 1-204
LO | Large ribosomal subunit protein uL13 | RL13A_HUMAN 1-203
LP | Large ribosomal subunit protein uL22 | RL17_HUMAN 1-184
LQ | Large ribosomal subunit protein eL18 | RL18_HUMAN 1-188
LR | Large ribosomal subunit protein eL19 | RL19_HUMAN 1-196
LS | Large ribosomal subunit protein eL20 | RL18A_HUMAN 1-176
LT | Large ribosomal subunit protein eL21 | RL21_HUMAN 1-160
LU | Large ribosomal subunit protein eL22 | RL22_HUMAN 1-128
LV | Large ribosomal subunit protein uL14 | RL23_HUMAN 1-140
LW | Large ribosomal subunit protein eL24 | RL24_HUMAN 1-157
LX | Large ribosomal subunit protein uL23 | RL23A_HUMAN 1-156
LY | Large ribosomal subunit protein uL24 | RL26_HUMAN 1-145
LZ | Large ribosomal subunit protein eL27 | RL27_HUMAN 1-136
La | 60S ribosomal protein L27a | RL27A_HUMAN 1-148
Lb | 60S ribosomal protein L29 | RL29_HUMAN 1-159
Lc | Large ribosomal subunit protein eL30 | RL30_HUMAN 1-115
Ld | Large ribosomal subunit protein eL31 | RL31_HUMAN 1-125
Le | Large ribosomal subunit protein eL32 | RL32_HUMAN 1-135
Lf | Large ribosomal subunit protein eL33 | RL35A_HUMAN 1-110
Lg | Large ribosomal subunit protein eL34 | RL34_HUMAN 1-117
Lh | Large ribosomal subunit protein uL29 | RL35_HUMAN 1-123
Li | Large ribosomal subunit protein eL36 | RL36_HUMAN 1-105
Lj | Large ribosomal subunit protein eL37 | RL37_HUMAN 1-97
Lk | Large ribosomal subunit protein eL38 | RL38_HUMAN 1-70
Ll | Large ribosomal subunit protein eL39 | RL39_HUMAN 1-51
Lm | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN 1-128
Ln | Small ribosomal subunit protein eS32 | RS32_HUMAN 1-25
Lo | Large ribosomal subunit protein eL42 | RL36A_HUMAN 1-106
Lp | Large ribosomal subunit protein eL43 | RL37A_HUMAN 1-92
Lr | 60S ribosomal protein L28 | RL28_HUMAN 1-137
Ls | 60S acidic ribosomal protein P0 | RLA0_HUMAN 1-317
Lt | 60S ribosomal protein L12 | RL12_HUMAN 1-165
Lz | 60S ribosomal protein L10a | RL10A_HUMAN 1-217
M2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 | DAD1_HUMAN 1-113
N | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 | KTAP2_HUMAN 1-136
N2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit | OST48_HUMAN 1-456
O2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | RPN1_HUMAN 1-607
P2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 | RPN2_HUMAN 1-631
u3 | tRNA |
v3 | tRNA |
y3 | Endoplasmin | ENPL_HUMAN 1-302
Non-standard residues in 9n9j #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
ELU — phosphono
[(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen
phosphate
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine;
2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE)
ZN — zinc ion
> volume #1 level 0.02028
> volume #1 level 0.01582
> show #2 ribbons
> hide #2
> select #1
3 models selected
> transparency sel 50
> transparency sel 80
> ~select
Nothing selected
> ui tool show "Side View"
> select #1
4 models selected
> transparency sel 40
> transparency sel 20
> hide #1
> select /LC:69
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
1053 atoms, 1067 bonds, 68 residues, 1 model selected
> select up
6031 atoms, 6085 bonds, 368 residues, 1 model selected
> select down
1053 atoms, 1067 bonds, 68 residues, 1 model selected
> select down
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
1053 atoms, 1067 bonds, 68 residues, 1 model selected
> select up
6031 atoms, 6085 bonds, 368 residues, 1 model selected
> select down
1053 atoms, 1067 bonds, 68 residues, 1 model selected
> select up
6031 atoms, 6085 bonds, 368 residues, 1 model selected
> select down
1053 atoms, 1067 bonds, 68 residues, 1 model selected
> select up
6031 atoms, 6085 bonds, 368 residues, 1 model selected
> select /y3:208
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
142 atoms, 141 bonds, 9 residues, 1 model selected
> select up
1413 atoms, 1430 bonds, 89 residues, 1 model selected
> invert sel
Unknown command: invert sel
> select invert
Expected an objects specifier or a keyword
> select ~sel
324694 atoms, 336815 bonds, 4350 pseudobonds, 16062 residues, 7 models
selected
> hide sel ribbons
> select
326107 atoms, 338245 bonds, 4352 pseudobonds, 16151 residues, 7 models
selected
Desktop color scheme is dark
Desktop color scheme is light
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202511122144 (2025-11-12)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: MX2H3B/A
Chip: Apple M4 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 4 days, 16 hours, 8 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL U2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.11.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.11.0
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.3
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: 1.61.1
ChimeraX-AtomicLibrary: 14.2.1
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
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202511122144
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: 2.5.3
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: 1.7.2
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
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: 1.4.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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: 0.2.6
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.48.4
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 8.3.0
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.11.3
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.60.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
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: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
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: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
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: 4.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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: 2.12.4
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.28.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
sniffio: 1.3.1
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.3
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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