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Opened 3 months ago
Closed 3 months ago
#18612 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202312120034 (2023-12-12 00:34:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000289ab000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000279a8000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000269a5000 (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 930 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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000259a2000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002499f000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002399c000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700022999000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700021996000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700020993000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001f990000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001e98d000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001d98a000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001c987000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001b984000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001a981000 (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 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff855e0a700 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.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.pdb_lib._load_libs, 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.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.mlp._mlp, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 58)
{"app_name":"ChimeraX","timestamp":"2025-08-25 14:53:31.00 +0800","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.1 (22G90)","roots_installed":0,"name":"ChimeraX","incident_id":"3E0206E0-C8F0-458C-8AEB-81DD0F4CEC26"}
{
"uptime" : 1100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 24957,
"osVersion" : {
"train" : "macOS 13.5.1",
"build" : "22G90",
"releaseType" : "User"
},
"captureTime" : "2025-08-25 14:53:29.1518 +0800",
"incident" : "3E0206E0-C8F0-458C-8AEB-81DD0F4CEC26",
"pid" : 74775,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-15 10:06:06.2526 +0800",
"procStartAbsTime" : 236643532956161,
"procExitAbsTime" : 1117855711105210,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F5180E70-A43E-5BE1-8346-0820A82A8824","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DF6A6BB5-FAE6-B42D-516A-3A14CBCBB1F5",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"bridgeVersion" : {"build":"20P6072","train":"7.6"},
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487859543\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff87000-7ffffff88000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":74775},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487859543\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff87000-7ffffff88000 [ 4K] r-x\/r-x SM=SHM ",
"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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"base" : 140703434608640,
"size" : 624112,
"uuid" : "31e1c182-e611-3883-97a3-4334a21c90bd",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
}
],
"sharedCache" : {
"base" : 140703433986048,
"size" : 21474836480,
"uuid" : "08a60487-01b2-3cd1-a713-ab9ca254667b"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=3.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 4512K 8 \nCG image 3452K 41 \nColorSync 264K 30 \nCoreAnimation 10.9M 36 \nCoreGraphics 24K 4 \nCoreGraphics (reserved) 16K 2 reserved VM address space (unallocated)\nCoreServices 624K 2 \nCoreUI image data 3844K 29 \nDispatch continuations 96.0M 1 \nFoundation 44K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.7G 558 \nMALLOC guard page 48K 11 \nMALLOC_MEDIUM (reserved) 960.0M 12 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 172K 43 \nStack 404.8M 44 \nStack Guard 56.0M 1 \nVM_ALLOCATE 522.9M 383 \nVM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 49.1M 778 \n__DATA_CONST 52.1M 397 \n__DATA_DIRTY 1802K 225 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 203.4M 154 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 933.8M 777 \ndyld private memory 420K 4 \nmapped file 526.4M 83 \nshared memory 3036K 40 \n=========== ======= ======= \nTOTAL 5.5G 3684 \nTOTAL, minus reserved VM space 4.5G 3684 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "1047e1d48f5cf4a4a782105e5337d8c924ccba02",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
},
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/liuxuelei/Downloads/8g2o.cif
8g2o.cif title:
Fab structure - Anti-ApoE-7C11 antibody [more info...]
Chain information for 8g2o.cif #1
---
Chain | Description
H | anti-ApoE-7C11 heavy chain
L | anti-ApoE-7C11 light chain
Non-standard residues in 8g2o.cif #1
---
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)
> open /Users/liuxuelei/Downloads/8g2o.cif
8g2o.cif title:
Fab structure - Anti-ApoE-7C11 antibody [more info...]
Chain information for 8g2o.cif #2
---
Chain | Description
H | anti-ApoE-7C11 heavy chain
L | anti-ApoE-7C11 light chain
Non-standard residues in 8g2o.cif #2
---
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)
> ui tool show Registration
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Alignment identifier is 1/H
> sequence chain #1/L
Alignment identifier is 1/L
> open /Users/liuxuelei/Downloads/7fcr.cif
7fcr.cif title:
Crystal structure of the N-terminal domain of mutants of Human
Apolipoprotein-E (ApoE) [more info...]
Chain information for 7fcr.cif #3
---
Chain | Description | UniProt
A | Apolipoprotein E | APOE_HUMAN 1-191
Non-standard residues in 7fcr.cif #3
---
NA — sodium ion
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> open /Users/liuxuelei/Downloads/2l7b.cif
2l7b.cif title:
NMR Structure of full length apoE3 [more info...]
Chain information for 2l7b.cif
---
Chain | Description | UniProt
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A
4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | Apolipoprotein E |
APOE_HUMAN 1-299
> hide #!3 models
> select #4.1/A
4792 atoms, 4819 bonds, 299 residues, 1 model selected
> select ~sel & ##selected
Nothing selected
> hide #4.1-20 cartoons
> select #4.5/A
4792 atoms, 4819 bonds, 299 residues, 1 model selected
> show sel cartoons
> rainbow sel
> select clear
> mlp #4.1-20
Map values for surface "2l7b.cif_A SES surface": minimum -29.81, mean -3.209,
maximum 25.85
Map values for surface "2l7b.cif_A SES surface": minimum -26.77, mean -3.221,
maximum 25.68
Map values for surface "2l7b.cif_A SES surface": minimum -28.72, mean -3.17,
maximum 24.69
Map values for surface "2l7b.cif_A SES surface": minimum -27.66, mean -3.03,
maximum 25.29
Map values for surface "2l7b.cif_A SES surface": minimum -27.36, mean -3.418,
maximum 24.15
Map values for surface "2l7b.cif_A SES surface": minimum -26.9, mean -3.401,
maximum 24.9
Map values for surface "2l7b.cif_A SES surface": minimum -28.17, mean -3.313,
maximum 25.74
Map values for surface "2l7b.cif_A SES surface": minimum -27.7, mean -3.315,
maximum 24.52
Map values for surface "2l7b.cif_A SES surface": minimum -29.94, mean -3.096,
maximum 25.11
Map values for surface "2l7b.cif_A SES surface": minimum -29.82, mean -3.331,
maximum 24.1
Map values for surface "2l7b.cif_A SES surface": minimum -28, mean -2.946,
maximum 24.2
Map values for surface "2l7b.cif_A SES surface": minimum -26.42, mean -3.265,
maximum 24.34
Map values for surface "2l7b.cif_A SES surface": minimum -28.12, mean -3.268,
maximum 24.34
Map values for surface "2l7b.cif_A SES surface": minimum -27.99, mean -3.39,
maximum 24.55
Map values for surface "2l7b.cif_A SES surface": minimum -29.26, mean -3.549,
maximum 26.22
Map values for surface "2l7b.cif_A SES surface": minimum -28.53, mean -3.199,
maximum 24.96
Map values for surface "2l7b.cif_A SES surface": minimum -27, mean -3.421,
maximum 24.52
Map values for surface "2l7b.cif_A SES surface": minimum -27.27, mean -3.116,
maximum 24.5
Map values for surface "2l7b.cif_A SES surface": minimum -30.69, mean -3.199,
maximum 25.24
Map values for surface "2l7b.cif_A SES surface": minimum -28.31, mean -3.294,
maximum 24.12
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!4.1-20
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
2l7b.cif #4.1/A HIS 299
2l7b.cif #4.2/A HIS 299
2l7b.cif #4.3/A HIS 299
2l7b.cif #4.4/A HIS 299
2l7b.cif #4.5/A HIS 299
2l7b.cif #4.6/A HIS 299
2l7b.cif #4.7/A HIS 299
2l7b.cif #4.8/A HIS 299
2l7b.cif #4.9/A HIS 299
2l7b.cif #4.10/A HIS 299
2l7b.cif #4.11/A HIS 299
2l7b.cif #4.12/A HIS 299
2l7b.cif #4.13/A HIS 299
2l7b.cif #4.14/A HIS 299
2l7b.cif #4.15/A HIS 299
2l7b.cif #4.16/A HIS 299
2l7b.cif #4.17/A HIS 299
2l7b.cif #4.18/A HIS 299
2l7b.cif #4.19/A HIS 299
2l7b.cif #4.20/A HIS 299
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2l7b.cif_A SES surface #4.1.1: minimum, -16.93, mean
-0.64, maximum 13.18
Coulombic values for 2l7b.cif_A SES surface #4.2.1: minimum, -21.34, mean
-0.39, maximum 22.73
Coulombic values for 2l7b.cif_A SES surface #4.3.1: minimum, -18.00, mean
-0.47, maximum 13.63
Coulombic values for 2l7b.cif_A SES surface #4.4.1: minimum, -17.34, mean
-0.44, maximum 11.97
Coulombic values for 2l7b.cif_A SES surface #4.5.1: minimum, -17.87, mean
-0.08, maximum 30.65
Coulombic values for 2l7b.cif_A SES surface #4.6.1: minimum, -14.82, mean
-0.50, maximum 14.65
Coulombic values for 2l7b.cif_A SES surface #4.7.1: minimum, -18.74, mean
-0.30, maximum 17.17
Coulombic values for 2l7b.cif_A SES surface #4.8.1: minimum, -24.03, mean
-0.42, maximum 15.91
Coulombic values for 2l7b.cif_A SES surface #4.9.1: minimum, -17.05, mean
-0.44, maximum 25.90
Coulombic values for 2l7b.cif_A SES surface #4.10.1: minimum, -25.33, mean
-0.50, maximum 12.43
Coulombic values for 2l7b.cif_A SES surface #4.11.1: minimum, -20.88, mean
-0.32, maximum 17.58
Coulombic values for 2l7b.cif_A SES surface #4.12.1: minimum, -19.63, mean
-0.45, maximum 14.75
Coulombic values for 2l7b.cif_A SES surface #4.13.1: minimum, -16.31, mean
-0.47, maximum 32.72
Coulombic values for 2l7b.cif_A SES surface #4.14.1: minimum, -16.85, mean
-0.56, maximum 21.60
Coulombic values for 2l7b.cif_A SES surface #4.15.1: minimum, -18.27, mean
-0.42, maximum 18.17
Coulombic values for 2l7b.cif_A SES surface #4.16.1: minimum, -17.97, mean
-0.46, maximum 18.64
Coulombic values for 2l7b.cif_A SES surface #4.17.1: minimum, -18.91, mean
-0.67, maximum 13.21
Coulombic values for 2l7b.cif_A SES surface #4.18.1: minimum, -21.26, mean
-0.60, maximum 21.31
Coulombic values for 2l7b.cif_A SES surface #4.19.1: minimum, -18.26, mean
-0.32, maximum 14.26
Coulombic values for 2l7b.cif_A SES surface #4.20.1: minimum, -23.82, mean
-0.47, maximum 13.60
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!4.1-20 surfaces
> select clear
> select #1/H:1-218
1613 atoms, 1655 bonds, 1 pseudobond, 211 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> save "/Users/liuxuelei/Downloads/anti-APOE-7C11 HC" format fasta alignment
> 1/H
> select #1/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/L:1-212
1624 atoms, 1663 bonds, 212 residues, 1 model selected
> select clear
> select #1/L:1-215
1654 atoms, 1694 bonds, 215 residues, 1 model selected
> save "/Users/liuxuelei/Downloads/anti-APOE-7C11 LC" format fasta alignment
> 1/L
> select #1/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/L:1-57
435 atoms, 445 bonds, 57 residues, 1 model selected
> open /Users/liuxuelei/Downloads/PTCHD1/PTCHD4/Alphafold3/WANGWEI/DS.json
Failed opening file
/Users/liuxuelei/Downloads/PTCHD1/PTCHD4/Alphafold3/WANGWEI/DS.json:
DS.json does not look like Mole Online json file, does not contain Channels.
> open /Users/liuxuelei/Downloads/model.cif
Chain information for model.cif #5
---
Chain | Description
A | .
> hide #!4 models
> lighting soft
> open /Users/liuxuelei/Downloads/pibh8_dimer/seed-1_sample-2/model.cif
Chain information for model.cif #6
---
Chain | Description
A B | .
> hide #5 models
> select add #1
3657 atoms, 3364 bonds, 1 pseudobond, 803 residues, 2 models selected
> hide #6 models
> show #5 models
> show #6 models
> hide #5 models
> show #5 models
> hide #6 models
> close #1-4
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #5/A:211
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #5
9697 atoms, 9860 bonds, 1226 residues, 1 model selected
> select subtract #5
Nothing selected
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-3_sample-0/model.cif
Chain information for model.cif #1
---
Chain | Description
A | .
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-5_sample-3/model.cif
Chain information for model.cif #2
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2,5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#2), sequence
alignment score = 6148.2
RMSD between 888 pruned atom pairs is 0.681 angstroms; (across all 1226 pairs:
12.666)
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#5), sequence
alignment score = 6151.8
RMSD between 882 pruned atom pairs is 0.591 angstroms; (across all 1226 pairs:
10.083)
> hide #2 models
> show #2 models
> hide #2 models
> hide #5 models
> show #2 models
> show #5 models
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-1_sample-3/model.cif
Chain information for model.cif #3
---
Chain | Description
A | .
> close #6
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-6_sample-4/model.cif
Chain information for model.cif #4
---
Chain | Description
A | .
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-4_sample-3/model.cif
Chain information for model.cif #6
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2-6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#2), sequence
alignment score = 6148.2
RMSD between 888 pruned atom pairs is 0.681 angstroms; (across all 1226 pairs:
12.666)
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#3), sequence
alignment score = 6208.8
RMSD between 905 pruned atom pairs is 0.693 angstroms; (across all 1226 pairs:
7.782)
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#4), sequence
alignment score = 6201.6
RMSD between 856 pruned atom pairs is 0.455 angstroms; (across all 1226 pairs:
29.044)
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#5), sequence
alignment score = 6151.8
RMSD between 882 pruned atom pairs is 0.591 angstroms; (across all 1226 pairs:
10.083)
Matchmaker model.cif, chain A (#1) with model.cif, chain A (#6), sequence
alignment score = 6202.8
RMSD between 875 pruned atom pairs is 0.634 angstroms; (across all 1226 pairs:
18.064)
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:24
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:24-126
853 atoms, 870 bonds, 103 residues, 1 model selected
> color sel red
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> select clear
Drag select of 47 residues
> select clear
> select #1/A:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:212-363
1213 atoms, 1242 bonds, 152 residues, 1 model selected
> color sel forest green
> select #1/A:444-445
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:444-695
1991 atoms, 2019 bonds, 252 residues, 1 model selected
> color sel cornflower blue
> select #1/A:871
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:871-930
475 atoms, 486 bonds, 60 residues, 1 model selected
> color sel purple
> select clear
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-1_sample-4/model.cif
Chain information for model.cif #7
---
Chain | Description
A | .
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-2_sample-1/model.cif
Chain information for model.cif #8
---
Chain | Description
A | .
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-2_sample-1/model.cif
Chain information for model.cif #9
---
Chain | Description
A | .
> open /Users/liuxuelei/Downloads/pibh8_monomer/seed-7_sample-3/model.cif
Chain information for model.cif #10
---
Chain | Description
A | .
> ui tool show Matchmaker
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: iMac
Model Identifier: iMac20,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 72 GB
System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.5.1 (22G90)
Kernel Version: Darwin 22.6.0
Time since boot: 12 days, 22 hours, 31 minutes
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-011
Option ROM Version: 113-D322A1XL-011
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2723QX:
Resolution: 1890 x 3360
UI Looks like: 945 x 1680 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 28725P3
Mirror: Off
Online: Yes
Rotation: 90
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
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: 1.5.14
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.2
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: 1.51.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
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: 1.8.dev202312120034
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
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: 1.0.3
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: 1.2
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: 1.14.1
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: 1.33.4
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: 0.2.0
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: 4.46.0
funcparserlib: 2.0.0a0
glfw: 2.6.3
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: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
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: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.41
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
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: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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