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Opened 13 months ago
Closed 13 months ago
#15994 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000032363b000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000322638000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000321635000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000320632000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031f62f000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031e62c000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d629000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c626000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b623000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a620000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031961d000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031861a000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000204a93600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py", line 283 in data_as
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1188 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2225 in process_changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, chimerax.surface._surface, 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, PIL._imagingmath, 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 (total: 57)
{"app_name":"ChimeraX","timestamp":"2024-09-23 14:34:50.00 +0100","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.5.1 (21G83)","incident_id":"56B7911D-F7F0-4345-A61C-DEC98C737C0D","name":"ChimeraX"}
{
"uptime" : 120000,
"procLaunch" : "2024-09-20 12:17:49.7194 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"procStartAbsTime" : 2370486740012,
"coalitionID" : 2424,
"osVersion" : {
"train" : "macOS 12.5.1",
"build" : "21G83",
"releaseType" : "User"
},
"captureTime" : "2024-09-23 14:34:46.9388 +0100",
"incident" : "56B7911D-F7F0-4345-A61C-DEC98C737C0D",
"bug_type" : "309",
"pid" : 20611,
"procExitAbsTime" : 3082181366416,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5A474F56-37F1-5EAE-AE4A-716C4B8E9ECA","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "05C48EED-39CC-5B24-BB62-5216644C543A",
"wakeTime" : 813,
"sleepWakeUUID" : "6CE54190-846A-4F0C-8ACB-0019D73F9765",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722790416215\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc93ef4000-7ffc94530000 [ 6384K] r-x\/r-x SM=COW ...t_id=de16d401",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140722790416215\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc93ef4000-7ffc94530000 [ 6384K] r-x\/r-x SM=COW ...t_id=de16d401",
"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,
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"source" : "P",
"arch" : "x86_64",
"base" : 4632363008,
"size" : 64094208,
"uuid" : "9d768904-ac4b-327d-8126-cec11a08b966",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703457984512,
"size" : 19331678208,
"uuid" : "f3387257-f96f-3907-b94c-1d7f0ebef98b"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 2176K 4 \nCG image 844K 41 \nColorSync 232K 28 \nCoreAnimation 1156K 21 \nCoreGraphics 12K 2 \nCoreUI image data 4348K 32 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.7G 461 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 640.0M 7 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 24K 6 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1352K 335 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1000K 100 \nRosetta Thread Context 1000K 100 \nSTACK GUARD 44K 11 \nStack 353.7M 50 \nStack Guard 56.2M 39 \nVM_ALLOCATE 298.4M 362 \nVM_ALLOCATE (reserved) 128.1M 16 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 47.5M 710 \n__DATA_CONST 31.1M 345 \n__DATA_DIRTY 1646K 214 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 744.3M 188 \n__OBJC_RO 82.8M 1 \n__OBJC_RW 3200K 2 \n__TEXT 830.2M 709 \n__UNICODE 592K 1 \ndyld private memory 1280K 3 \nmapped file 5.4G 1270 \nshared memory 3136K 24 \nunshared pmap 11.2M 9 \n=========== ======= ======= \nTOTAL 10.7G 5119 \nTOTAL, minus reserved VM space 9.7G 5119 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000029
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{
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"experiments" : [
{
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"experimentId" : "6639bc6ba73d460582162323",
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}
}
===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_0.cif
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_1.cif
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_2.cif
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_3.cif
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_4.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_0.cif #1
---
Chain | Description
A B C | .
D | .
Chain information for fold_2024_09_20_myadm_trail_trimer_model_1.cif #2
---
Chain | Description
A B C | .
D | .
Chain information for fold_2024_09_20_myadm_trail_trimer_model_2.cif #3
---
Chain | Description
A B C | .
D | .
Chain information for fold_2024_09_20_myadm_trail_trimer_model_3.cif #4
---
Chain | Description
A B C | .
D | .
Chain information for fold_2024_09_20_myadm_trail_trimer_model_4.cif #5
---
Chain | Description
A B C | .
D | .
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json
> color bfactor #1 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 14.7 to 92.7
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_1.json
> color bfactor #2 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_2.json
> color bfactor #3 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 15.1 to 92.6
> ui tool show "AlphaFold Error Plot"
> alphafold pae #4 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_3.json
> color bfactor #4 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.5
> ui tool show "AlphaFold Error Plot"
> alphafold pae #5 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_4.json
> color bfactor #5 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 13.1 to 92.3
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select add #1
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-64.035,0,1,0,159.1,0,0,1,202.23
> select add #2
19620 atoms, 20106 bonds, 2468 residues, 2 models selected
> select subtract #1
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models #2,1,0,0,-29.522,0,1,0,80.841,0,0,1,112.05
> ui mousemode right "rotate selected models"
> select subtract #2
Nothing selected
> select add #3
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models
> #3,-0.62242,-0.66271,0.41642,-38.429,0.68585,-0.20548,0.69813,27.644,-0.3771,0.72013,0.58242,-15.639
> view matrix models
> #3,-0.8027,-0.49839,0.32754,-44.503,0.52147,-0.32004,0.79098,24.217,-0.28939,0.80572,0.51679,-14.006
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.8027,-0.49839,0.32754,-79.739,0.52147,-0.32004,0.79098,68.85,-0.28939,0.80572,0.51679,-20.478
> select subtract #3
Nothing selected
> select add #4
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models #4,1,0,0,-53.542,0,1,0,15.432,0,0,1,-137.68
> select subtract #4
Nothing selected
> select add #5
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models #5,1,0,0,-55.302,0,1,0,-39.326,0,0,1,-277.06
> select subtract #5
Nothing selected
> select add #1
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99991,0.0052477,0.012504,-63.852,-0.0050364,0.99984,-0.016871,159.16,-0.012591,0.016807,0.99978,202.96
> view matrix models
> #1,0.51581,-0.11468,0.84899,-51.246,-0.64161,0.60497,0.47153,167.41,-0.56769,-0.78795,0.23846,193.99
> view matrix models
> #1,0.57816,-0.067393,0.81313,-51.793,-0.67842,0.51396,0.52497,166.31,-0.4533,-0.85516,0.25143,189.51
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.57816,-0.067393,0.81313,-54.698,-0.67842,0.51396,0.52497,177.96,-0.4533,-0.85516,0.25143,208.42
> select subtract #1
Nothing selected
> select add #2
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.55254,-0.76613,0.32826,-23.543,0.68278,-0.19017,0.70544,85.978,-0.47804,0.61391,0.62817,109.57
> view matrix models
> #2,-0.93131,0.092752,0.35223,-27.932,0.36423,0.23232,0.90187,83.802,0.0018215,0.96821,-0.25014,107.84
> view matrix models
> #2,-0.92496,0.13026,0.35705,-28.157,0.37644,0.18443,0.9079,84.051,0.052406,0.97418,-0.21963,107.71
> select subtract #2
Nothing selected
> select add #3
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models
> #3,-0.35948,0.39377,-0.846,-77.594,0.91934,-0.0059472,-0.39341,72.625,-0.15994,-0.91919,-0.35987,-12.309
> view matrix models
> #3,-0.40798,0.58935,-0.69729,-79.207,0.91038,0.20485,-0.35952,71.48,-0.069041,-0.78147,-0.62011,-11.73
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.40798,0.58935,-0.69729,-83.953,0.91038,0.20485,-0.35952,78.989,-0.069041,-0.78147,-0.62011,-10.347
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.41859,0.61249,-0.67055,-84.233,0.89926,0.17631,-0.40032,78.649,-0.12697,-0.77056,-0.62459,-11.98
> select subtract #3
Nothing selected
> select add #2
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models
> #2,-0.96191,0.20294,0.18315,-28.345,0.23299,0.25816,0.93759,83.788,0.14299,0.94455,-0.29561,107.84
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.96191,0.20294,0.18315,-24.617,0.23299,0.25816,0.93759,79.439,0.14299,0.94455,-0.29561,110.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.93343,0.26988,0.23636,-25.085,0.32759,0.37264,0.86823,78.741,0.14624,0.88787,-0.43624,110.6
> view matrix models
> #2,-0.92616,0.29433,0.23579,-25.232,0.33199,0.3397,0.87999,78.91,0.17891,0.89329,-0.41233,110.5
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.92616,0.29433,0.23579,-24.109,0.33199,0.3397,0.87999,77.515,0.17891,0.89329,-0.41233,111.01
> select clear
> select add #4
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.54039,0.79371,0.27928,-58.39,0.30795,0.12232,-0.94351,22.765,-0.78303,0.59587,-0.17832,-137
> view matrix models
> #4,0.61563,0.1901,0.76476,-57.675,0.78347,-0.25196,-0.56806,23.636,0.084704,0.94888,-0.30405,-136.51
> view matrix models
> #4,-0.85968,0.00082882,0.51083,-58.416,-0.34877,-0.7316,-0.58577,23.728,0.37324,-0.68173,0.62923,-133.07
> view matrix models
> #4,-0.79069,0.5399,0.28866,-59.598,-0.51557,-0.33294,-0.78952,22.642,-0.33016,-0.77308,0.5416,-133.54
> view matrix models
> #4,-0.88225,0.37591,0.28342,-59.089,-0.36399,-0.16286,-0.91705,22.688,-0.29857,-0.91223,0.28051,-132.01
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.88225,0.37591,0.28342,-29.863,-0.36399,-0.16286,-0.91705,4.9703,-0.29857,-0.91223,0.28051,-82.9
> select add #2
19620 atoms, 20106 bonds, 2468 residues, 2 models selected
> select subtract #4
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models
> #2,-0.92616,0.29433,0.23579,-21.209,0.33199,0.3397,0.87999,99.203,0.17891,0.89329,-0.41233,161.14
> select subtract #2
Nothing selected
> select add #3
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models
> #3,-0.41859,0.61249,-0.67055,-76.011,0.89926,0.17631,-0.40032,110.52,-0.12697,-0.77056,-0.62459,72.983
> select subtract #3
Nothing selected
> select add #4
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models
> #4,-0.88225,0.37591,0.28342,-46.116,-0.36399,-0.16286,-0.91705,22.307,-0.29857,-0.91223,0.28051,30.649
> select subtract #4
Nothing selected
> select add #5
9810 atoms, 10053 bonds, 1234 residues, 1 model selected
> view matrix models #5,1,0,0,-78.202,0,1,0,-14.935,0,0,1,-88.375
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.7302,-0.64342,-0.22981,-80.205,0.071363,0.40634,-0.91093,-18.378,0.6795,0.64876,0.34262,-88.384
> view matrix models
> #5,0.38045,-0.8959,-0.2294,-79.636,0.5015,0.40828,-0.76276,-20.855,0.77702,0.17515,0.60462,-91.676
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.38045,-0.8959,-0.2294,-67.166,0.5015,0.40828,-0.76276,-18.449,0.77702,0.17515,0.60462,-67.906
> select clear
> ui mousemode right zoom
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D #2/D #3/D #4/D #5/D
Alignment identifier is 1
> select #1/D:64-65 #2/D:64-65 #3/D:64-65 #4/D:64-65 #5/D:64-65
60 atoms, 55 bonds, 10 residues, 5 models selected
> select #1/D:64-69 #2/D:64-69 #3/D:64-69 #4/D:64-69 #5/D:64-69
240 atoms, 245 bonds, 30 residues, 5 models selected
. [ID: 1] region 5 chains [64-69] RMSD: 194.332
> select #1/D:29 #2/D:29 #3/D:29 #4/D:29 #5/D:29
35 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/D:29-32 #2/D:29-32 #3/D:29-32 #4/D:29-32 #5/D:29-32
155 atoms, 155 bonds, 20 residues, 5 models selected
. [ID: 1] region 5 chains [29-32] RMSD: 194.559
> select #1/D:35 #2/D:35 #3/D:35 #4/D:35 #5/D:35
35 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/D:35-58 #2/D:35-58 #3/D:35-58 #4/D:35-58 #5/D:35-58
855 atoms, 860 bonds, 120 residues, 5 models selected
. [ID: 1] region 5 chains [35-58] RMSD: 194.914
> select #1/D:63 #2/D:63 #3/D:63 #4/D:63 #5/D:63
30 atoms, 25 bonds, 5 residues, 5 models selected
> select #1/D:63-80 #2/D:63-80 #3/D:63-80 #4/D:63-80 #5/D:63-80
740 atoms, 770 bonds, 90 residues, 5 models selected
. [ID: 1] region 5 chains [63-80] RMSD: 193.861
> select #1/D:289 #2/D:289 #3/D:289 #4/D:289 #5/D:289
25 atoms, 20 bonds, 5 residues, 5 models selected
> select #1/D:289-296 #2/D:289-296 #3/D:289-296 #4/D:289-296 #5/D:289-296
345 atoms, 350 bonds, 40 residues, 5 models selected
. [ID: 1] region 5 chains [289-296] RMSD: 197.040
> select
> #1/D:29-31,35-57,63-87,90-93,101-127,132-158,168-170,172-192,194-196,201-225,229-231,236-263,265-267,273-275,277-279,289-316
> #2/D:29-31,35-57,63-87,90-93,101-127,132-158,168-170,172-192,194-196,201-225,229-231,236-263,265-267,273-275,277-279,289-316
> #3/D:29-31,35-57,63-87,90-93,101-127,132-158,168-170,172-192,194-196,201-225,229-231,236-263,265-267,273-275,277-279,289-316
> #4/D:29-31,35-57,63-87,90-93,101-127,132-158,168-170,172-192,194-196,201-225,229-231,236-263,265-267,273-275,277-279,289-316
> #5/D:29-31,35-57,63-87,90-93,101-127,132-158,168-170,172-192,194-196,201-225,229-231,236-263,265-267,273-275,277-279,289-316
8930 atoms, 9105 bonds, 1145 residues, 5 models selected
> select #1/D:289 #2/D:289 #3/D:289 #4/D:289 #5/D:289
25 atoms, 20 bonds, 5 residues, 5 models selected
> select #1/D:289-316 #2/D:289-316 #3/D:289-316 #4/D:289-316 #5/D:289-316
1085 atoms, 1105 bonds, 140 residues, 5 models selected
. [ID: 1] region 5 chains [289-316] RMSD: 197.950
> select #1/D:236 #2/D:236 #3/D:236 #4/D:236 #5/D:236
55 atoms, 55 bonds, 5 residues, 5 models selected
> select #1/D:236-260 #2/D:236-260 #3/D:236-260 #4/D:236-260 #5/D:236-260
960 atoms, 990 bonds, 125 residues, 5 models selected
. [ID: 1] region 5 chains [236-260] RMSD: 198.025
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_summary_confidences_0.json
Failed opening file
/Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_summary_confidences_0.json:
User did not choose format
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_summary_confidences_1.json
Failed opening file
/Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_summary_confidences_1.json:
User did not choose format
> close #4
> close
> open /Users/joe/Downloads/overlay_MD_vs_XRC.pse
Unrecognized file suffix '.pse'
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_0.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_0.cif #1
---
Chain | Description
A B C | .
D | .
> select clear
> close
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_1.json
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_1.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_1.cif #1
---
Chain | Description
A B C | .
D | .
> close
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/apo_depoKP36_c3_chainA_WIP.pdb
Chain information for apo_depoKP36_c3_chainA_WIP.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J113_004_volume_map_C1_apo.mrc
Opened cryosparc_P4_J113_004_volume_map_C1_apo.mrc as #2, grid size
336,336,336, pixel 1.05, shown at level 0.0741, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3392
> fitmap #1 inMap #2
Fit molecule apo_depoKP36_c3_chainA_WIP.pdb (#1) to map
cryosparc_P4_J113_004_volume_map_C1_apo.mrc (#2) using 10542 atoms
average map value = 0.3604, steps = 112
shifted from previous position = 6.01
rotated from previous position = 11.1 degrees
atoms outside contour = 5906, contour level = 0.33924
Position of apo_depoKP36_c3_chainA_WIP.pdb (#1) relative to
cryosparc_P4_J113_004_volume_map_C1_apo.mrc (#2) coordinates:
Matrix rotation and translation
0.99609750 -0.06946173 0.05445031 -0.87878229
0.05903330 0.98296974 0.17402746 -33.94933995
-0.06561125 -0.17013394 0.98323426 45.46911358
Axis -0.89048451 0.31064775 0.33246853
Axis point 0.00000000 234.36773024 227.57141502
Rotation angle (degrees) 11.14215530
Shift along axis 5.35330538
> select add #1
10542 atoms, 10642 bonds, 706 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9961,-0.069462,0.05445,4.3135,0.059033,0.98297,0.17403,-30.309,-0.065611,-0.17013,0.98323,41.483
> view matrix models
> #1,0.9961,-0.069462,0.05445,11.036,0.059033,0.98297,0.17403,-29.487,-0.065611,-0.17013,0.98323,41.911
> view matrix models
> #1,0.9961,-0.069462,0.05445,7.0925,0.059033,0.98297,0.17403,-22.883,-0.065611,-0.17013,0.98323,43.512
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.58493,-0.7461,0.31809,153.61,0.75308,0.64523,0.1286,-86.053,-0.30119,0.16433,0.9393,37.6
> view matrix models
> #1,0.555,-0.81546,0.16435,197.91,0.75532,0.57678,0.31115,-106.6,-0.34852,-0.048546,0.93604,83.492
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.555,-0.81546,0.16435,196.08,0.75532,0.57678,0.31115,-112.47,-0.34852,-0.048546,0.93604,72.178
> view matrix models
> #1,0.555,-0.81546,0.16435,194.4,0.75532,0.57678,0.31115,-115.6,-0.34852,-0.048546,0.93604,74.751
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.85532,-0.4773,0.2015,74.054,0.40311,0.85742,0.31991,-99.795,-0.32546,-0.1924,0.92577,96.939
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.85532,-0.4773,0.2015,73.795,0.40311,0.85742,0.31991,-102.93,-0.32546,-0.1924,0.92577,97.78
> view matrix models
> #1,0.85532,-0.4773,0.2015,74.381,0.40311,0.85742,0.31991,-103.46,-0.32546,-0.1924,0.92577,101.84
> view matrix models
> #1,0.85532,-0.4773,0.2015,58.384,0.40311,0.85742,0.31991,-110.81,-0.32546,-0.1924,0.92577,109.26
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.80573,-0.58088,-0.11566,140.75,0.59123,0.80044,0.098674,-97.388,0.035262,-0.14789,0.98838,23.623
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.80573,-0.58088,-0.11566,157.44,0.59123,0.80044,0.098674,-85.121,0.035262,-0.14789,0.98838,21.66
> view matrix models
> #1,0.80573,-0.58088,-0.11566,157.47,0.59123,0.80044,0.098674,-85.681,0.035262,-0.14789,0.98838,20.109
> volume #2 level 0.4183
> fitmap #1 inMap #2
Fit molecule apo_depoKP36_c3_chainA_WIP.pdb (#1) to map
cryosparc_P4_J113_004_volume_map_C1_apo.mrc (#2) using 10542 atoms
average map value = 0.5573, steps = 120
shifted from previous position = 1.85
rotated from previous position = 7.45 degrees
atoms outside contour = 4193, contour level = 0.41831
Position of apo_depoKP36_c3_chainA_WIP.pdb (#1) relative to
cryosparc_P4_J113_004_volume_map_C1_apo.mrc (#2) coordinates:
Matrix rotation and translation
0.81658487 -0.57718429 -0.00688782 134.77703355
0.57710733 0.81611843 0.02996385 -74.56539665
-0.01167339 -0.02844304 0.99952725 7.06151501
Axis -0.05053469 0.00414056 0.99871372
Axis point 184.88488312 174.74999679 0.00000000
Rotation angle (degrees) 35.30221223
Shift along axis -0.06722600
> volume #2 level 0.302
> close #2
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J161_004_volume_map_C1_EPS.mrc
Opened cryosparc_P4_J161_004_volume_map_C1_EPS.mrc as #2, grid size
336,336,336, pixel 1.1, shown at level 0.0303, step 2, values float32
> volume #2 step 1
> volume #2 level 0.2036
> volume #2 level 0.289
> volume #2 level 0.17
> view matrix models
> #1,0.81658,-0.57718,-0.0068878,173.58,0.57711,0.81612,0.029964,-92.667,-0.011673,-0.028443,0.99953,5.4587
> close
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J161_004_volume_map_C1_EPS.mrc
> format mrc
Opened cryosparc_P4_J161_004_volume_map_C1_EPS.mrc as #1, grid size
336,336,336, pixel 1.1, shown at level 0.0303, step 2, values float32
> volume #1 level 0.1842
> volume #1 step 1
> volume #1 level 0.3032
> volume #1 level 0.1402
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/EPS_depoKP36_c3_chainA.pdb
Chain information for EPS_depoKP36_c3_chainA.pdb #2
---
Chain | Description
A | No description available
> select add #2
10554 atoms, 10654 bonds, 707 residues, 1 model selected
> view matrix models #2,1,0,0,0.69164,0,1,0,5.1447,0,0,1,-12.551
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac14,7
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 10 days 21:25
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| 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 , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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