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Opened 21 months ago
Closed 21 months ago
#14494 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-14.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002ef713000 (most recent call first):
File "/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002ee707000 (most recent call first):
File "/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002ed6fb000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.7.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002ec6ef000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002eb6e3000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002ea6d7000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e96cb000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e86bf000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e76b3000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e66a7000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e569b000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e468f000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e3683000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e2677000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e166b000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002e065f000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002df653000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e0585ec0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3468 in __call__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2929 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.7.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.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.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.surface._surface, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw (total: 60)
{"app_name":"ChimeraX","timestamp":"2024-01-28 23:50:08.00 -0800","app_version":"1.7.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.1 (23B2073)","roots_installed":0,"name":"ChimeraX","incident_id":"20F6BE02-9AC4-48DE-9BFD-73F9680C0D68"}
{
"uptime" : 670000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,10",
"coalitionID" : 14361,
"osVersion" : {
"train" : "macOS 14.1",
"build" : "23B2073",
"releaseType" : "User"
},
"captureTime" : "2024-01-28 23:49:58.7343 -0800",
"codeSigningMonitor" : 1,
"incident" : "20F6BE02-9AC4-48DE-9BFD-73F9680C0D68",
"pid" : 80158,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-26 16:48:38.9519 -0800",
"procStartAbsTime" : 14743438243490,
"procExitAbsTime" : 16296490907592,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"83522F7A-B239-5B86-904C-63BD8ADD44D5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "87812259-AF0E-8539-4F2F-A6A431E997DD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 5643,
"sleepWakeUUID" : "B7D8E0C5-481B-4C22-87DC-B2CBD144BBC8",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 105554726879063\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600060000000-600080000000 [512.0M] rw-\/rwx SM=PRV ",
"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":80158},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 105554726879063\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600060000000-600080000000 [512.0M] rw-\/rwx SM=PRV ",
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"logWritingSignature" : "034b5bafde17d5392c431e68c56a6abf05277eab",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62745b8e85854550ad70b6e4",
"factorPackIds" : {
"SIRI_TTS_DEVICE_TRAINING" : "650a28170efd3c4addfc7355"
},
"deploymentId" : 240000073
},
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : {
},
"deploymentId" : 240000011
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/woori/Downloads/view_alphafold_hairpin_sk2o_sf.cxs
Log from Fri Jan 26 16:25:48 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/woori/Downloads/hsk2o_2M.pdb format pdb
Chain information for hsk2o_2M.pdb #1
---
Chain | Description
A C E G | No description available
B D F H | No description available
> hide atoms
> show cartoons
> open /Users/woori/Downloads/charmm-gui-0553074370/step5_assembly.pdb
Summary of feedback from opening /Users/woori/Downloads/charmm-
gui-0553074370/step5_assembly.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON JAN, 18.
2024. JOB
Ignored bad PDB record found on line 2
REMARK INPUT GENERATION
Ignored bad PDB record found on line 3
REMARK DATE: 1/18/24 20:53: 9 CREATED BY USER: apache
Ignored bad PDB record found on line 307118
TER 307115 CLA 381
Chain information for step5_assembly.pdb #2
---
Chain | Description
? | No description available
> hide #1 models
> hide #2 atoms
> show #2 cartoons
> show #1 models
> hide #2 models
> select add #1
33923 atoms, 34116 bonds, 2195 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/C #1/E #1/G
Alignment identifier is 1
> select clear
> select #1/A:2-3/C:527-528/E:1052-1053/G:1577-1578
164 atoms, 160 bonds, 8 residues, 1 model selected
> select #1/A:1-2/C:526-527/E:1051-1052/G:1576-1577
180 atoms, 180 bonds, 8 residues, 1 model selected
> select
> #1/A:1-2,324-379/C:526-527,849-904/E:1051-1052,1374-1429/G:1576-1577,1899-1954
4000 atoms, 4016 bonds, 232 residues, 1 model selected
> select #1 /A
6190 atoms, 6250 bonds, 379 residues, 1 model selected
> select #1 /b,c,d,e,f,d,h
21300 atoms, 21468 bonds, 1342 residues, 1 model selected
> hide sel
> hide sel cartoons
> select #1 /g
6190 atoms, 6250 bonds, 379 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/A:379/C:904/E:1429/G:1954
60 atoms, 56 bonds, 4 residues, 1 model selected
> select #1/A:324-379/C:849-904/E:1374-1429/G:1899-1954
3820 atoms, 3836 bonds, 224 residues, 1 model selected
> select #1/A:283-284/C:808-809/E:1333-1334/G:1858-1859
128 atoms, 124 bonds, 8 residues, 1 model selected
> select #1/A:283-379/C:808-904/E:1333-1429/G:1858-1954
6640 atoms, 6680 bonds, 388 residues, 1 model selected
> select #1/A:281/C:806/E:1331/G:1856
76 atoms, 72 bonds, 4 residues, 1 model selected
> select #1/A:281-379/C:806-904/E:1331-1429/G:1856-1954
6772 atoms, 6812 bonds, 396 residues, 1 model selected
> save /Users/woori/Downloads/seq_hsk2o format fasta alignment 1
> select #1/A:280/C:805/E:1330/G:1855
60 atoms, 56 bonds, 4 residues, 1 model selected
> select #1/A:226-280/C:751-805/E:1276-1330/G:1801-1855
3260 atoms, 3284 bonds, 220 residues, 1 model selected
> select #1/A:280-281/C:805-806/E:1330-1331/G:1855-1856
136 atoms, 132 bonds, 8 residues, 1 model selected
> select #1/A:192-281/C:717-806/E:1242-1331/G:1767-1856
5500 atoms, 5556 bonds, 360 residues, 1 model selected
> select #1/A:191-192/C:716-717/E:1241-1242/G:1766-1767
100 atoms, 100 bonds, 8 residues, 1 model selected
> select #1/A:188-192/C:713-717/E:1238-1242/G:1763-1767
300 atoms, 300 bonds, 20 residues, 1 model selected
> select
> #1/A:2-82,87-90,93-106,129-131,135-158,160-162,165-174,180-190,192-214,227-238,251-278,283-319,324-361,363-378/C:527-607,612-615,618-631,654-656,660-683,685-687,690-699,705-715,717-739,752-763,776-803,808-844,849-886,888-903/E:1052-1132,1137-1140,1143-1156,1179-1181,1185-1208,1210-1212,1215-1224,1230-1240,1242-1264,1277-1288,1301-1328,1333-1369,1374-1411,1413-1428/G:1577-1657,1662-1665,1668-1681,1704-1706,1710-1733,1735-1737,1740-1749,1755-1765,1767-1789,1802-1813,1826-1853,1858-1894,1899-1936,1938-1953
20144 atoms, 20272 bonds, 1216 residues, 1 model selected
> select #1/A:191/C:716/E:1241/G:1766
44 atoms, 40 bonds, 4 residues, 1 model selected
> select #1/A:160-191/C:685-716/E:1210-1241/G:1735-1766
2076 atoms, 2084 bonds, 128 residues, 1 model selected
> select #1/A:100-107/C:625-632/E:1150-1157/G:1675-1682
480 atoms, 476 bonds, 32 residues, 1 model selected
> select #1/A:99-107/C:624-632/E:1149-1157/G:1674-1682
556 atoms, 552 bonds, 36 residues, 1 model selected
> select #1/A:160/C:685/E:1210/G:1735
88 atoms, 84 bonds, 4 residues, 1 model selected
> select #1/A:160-191/C:685-716/E:1210-1241/G:1735-1766
2076 atoms, 2084 bonds, 128 residues, 1 model selected
> select #1/A:159/C:684/E:1209/G:1734
44 atoms, 40 bonds, 4 residues, 1 model selected
> select #1/A:92-159/C:617-684/E:1142-1209/G:1667-1734
4468 atoms, 4532 bonds, 272 residues, 1 model selected
> select #1/A:91/C:616/E:1141/G:1666
68 atoms, 64 bonds, 4 residues, 1 model selected
> select #1/A:1-91/C:526-616/E:1051-1141/G:1576-1666
6020 atoms, 6076 bonds, 364 residues, 1 model selected
> select #1/A:64-65/C:589-590/E:1114-1115/G:1639-1640
104 atoms, 100 bonds, 8 residues, 1 model selected
> select #1/A:56-65/C:581-590/E:1106-1115/G:1631-1640
628 atoms, 624 bonds, 40 residues, 1 model selected
> select #1/A:84-85/C:609-610/E:1134-1135/G:1659-1660
88 atoms, 84 bonds, 8 residues, 1 model selected
> select #1/A:1-85/C:526-610/E:1051-1135/G:1576-1660
5596 atoms, 5644 bonds, 340 residues, 1 model selected
> open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb
AF-Q9H2S1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for small conductance calcium- activated
potassium channel protein 2 (Q9H2S1) [more info...]
Chain information for AF-Q9H2S1-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | small conductance calcium-activated potassium channel protein 2 |
KCNN2_HUMAN 1-579
> delete #1, 2
> open /Users/woori/Downloads/hsk2o_2M.pdb
Chain information for hsk2o_2M.pdb #1
---
Chain | Description
A C E G | No description available
B D F H | No description available
> mmaker #1 to 3
> matchmaker #1 to 3
Invalid "to" argument: invalid atoms specifier
> mmaker #1 to #3 /A
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 AF-Q9H2S1-F1-model_v4.pdb, chain A (#3) with hsk2o_2M.pdb, chain E
(#1), sequence alignment score = 1901.9
RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs:
4.437)
> show cartoons
> hide atoms
> hide #3 models
> show #3 models
> open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb
AF-Q9H2S1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for small conductance calcium- activated
potassium channel protein 2 (Q9H2S1) [more info...]
Chain information for AF-Q9H2S1-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | small conductance calcium-activated potassium channel protein 2 |
KCNN2_HUMAN 1-579
> open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb
AF-Q9H2S1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for small conductance calcium- activated
potassium channel protein 2 (Q9H2S1) [more info...]
Chain information for AF-Q9H2S1-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | small conductance calcium-activated potassium channel protein 2 |
KCNN2_HUMAN 1-579
> open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb
AF-Q9H2S1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for small conductance calcium- activated
potassium channel protein 2 (Q9H2S1) [more info...]
Chain information for AF-Q9H2S1-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | small conductance calcium-activated potassium channel protein 2 |
KCNN2_HUMAN 1-579
> mmaker #3 to #1 /B
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 hsk2o_2M.pdb, chain B (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 63.2
RMSD between 7 pruned atom pairs is 1.290 angstroms; (across all 122 pairs:
38.453)
> mmaker #3 to #1 /C
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 hsk2o_2M.pdb, chain C (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 1896.2
RMSD between 186 pruned atom pairs is 1.091 angstroms; (across all 379 pairs:
5.394)
> mmaker #4 to #1 /E
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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 1901.9
RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs:
4.437)
> mmaker #4 to #1 /E
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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 1901.9
RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs:
4.437)
> mmaker #4 to #1 /F
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 hsk2o_2M.pdb, chain F (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 63.2
RMSD between 8 pruned atom pairs is 1.529 angstroms; (across all 122 pairs:
38.041)
> mmaker #4 to #1 /E
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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 1901.9
RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs:
4.437)
> mmaker #5 to #1 /G
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 hsk2o_2M.pdb, chain G (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 1859.3
RMSD between 184 pruned atom pairs is 1.254 angstroms; (across all 379 pairs:
4.882)
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #2 models
> show #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> mmaker #4 to #1 /E
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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 1901.9
RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs:
4.437)
> mmaker #2 to #1 /A
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 hsk2o_2M.pdb, chain A (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#2), sequence alignment score = 1893.5
RMSD between 195 pruned atom pairs is 1.230 angstroms; (across all 379 pairs:
6.673)
> mmaker #3 to #1 /C
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 hsk2o_2M.pdb, chain C (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 1896.2
RMSD between 186 pruned atom pairs is 1.091 angstroms; (across all 379 pairs:
5.394)
> mmaker #4 to #1 /E
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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#4), sequence alignment score = 1901.9
RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs:
4.437)
> mmaker #5 to #1 /G
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 hsk2o_2M.pdb, chain G (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 1859.3
RMSD between 184 pruned atom pairs is 1.254 angstroms; (across all 379 pairs:
4.882)
> show #4 models
> show #5 models
> hide #3 models
> hide #4 models
> hide #5 models
> select #1 /b,c,d,e,f,g,h
27490 atoms, 27718 bonds, 1721 residues, 1 model selected
> hide sel
> hide sel cartoons
> select clear
> select #1/A:136
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/C #1/E #1/G
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #2/A #4/A #5/A
Alignment identifier is 2
> select #1/A:136
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #2/A:254
23 atoms, 21 bonds, 2 residues, 2 models selected
> save /Users/woori/Downloads/seq_sk2_alphafold format fasta alignment 2
> select
> #3/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
> #2/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
> #4/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
> #5/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
11648 atoms, 11792 bonds, 1444 residues, 4 models selected
> select #3/A:234-240,247-253 #2/A:234-240,247-253 #4/A:234-240,247-253
> #5/A:234-240,247-253
436 atoms, 444 bonds, 56 residues, 4 models selected
> select
> #3/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
> #2/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
> #4/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
> #5/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554
11648 atoms, 11792 bonds, 1444 residues, 4 models selected
> select clear
> select #1/A:41
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:158
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/A:158
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:165
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:243
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #2/A:362
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:363
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:245
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select #2/A:242
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:241
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #2/A:246
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/A:245
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #3/A:234-240,247-253 #2/A:234-240,247-253 #4/A:234-240,247-253
> #5/A:234-240,247-253
436 atoms, 444 bonds, 56 residues, 4 models selected
> select clear
> select #3/A:234-240,247-253 #2/A:234-240,247-253 #4/A:234-240,247-253
> #5/A:234-240,247-253
436 atoms, 444 bonds, 56 residues, 4 models selected
> select clear
> select #2/A:247
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:240
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:245@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:362
4 atoms, 3 bonds, 1 residue, 1 model selected
Drag select of 11 atoms, 13 residues, 4 bonds
> hide sel atoms
> select clear
> select #1/A:244
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel ball
Changed 7 atom styles
> show sel atoms
[Repeated 1 time(s)]
> style sel ball
Changed 7 atom styles
> show sel atoms
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> show sel atoms
> select clear
> select #2/A:240
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> select #2 :363
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> select #2/A:243@CA
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> style sel stick
Changed 1 atom style
> select #2/A:243@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 11 atom styles
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select #1 :363
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1 :245
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel sphere
Changed 12 atom styles
> hide #2 models
> show sel atoms
> show #2 models
> select #1 :245, 770, 1295, 1820
48 atoms, 44 bonds, 4 residues, 1 model selected
> select #1 :245, 770, 1295, 1820
48 atoms, 44 bonds, 4 residues, 1 model selected
> show sel atoms
> open /Users/woori/Downloads/rank-001-modified-hsk2o-mmseq2-enc.pdb
Chain information for rank-001-modified-hsk2o-mmseq2-enc.pdb #6
---
Chain | Description
A B C D | No description available
E F G H | No description available
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> show #1-2,6 cartoons
> hide #1-2,6 atoms
> mmaker #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 hsk2o_2M.pdb, chain E (#1) with rank-001-modified-
hsk2o-mmseq2-enc.pdb, chain A (#6), sequence alignment score = 1882.7
RMSD between 293 pruned atom pairs is 1.019 angstroms; (across all 379 pairs:
4.110)
> select /b,c,d,e,f,g,h
41974 atoms, 42433 bonds, 3538 residues, 2 models selected
> hide sel cartoons
> select #6 /e
1173 atoms, 1185 bonds, 149 residues, 1 model selected
> show sel cartoons
> select #6 /c
3264 atoms, 3325 bonds, 407 residues, 1 model selected
> show sel cartoons
> select #6 /a,b,d,e,f,g,h
14484 atoms, 14715 bonds, 1817 residues, 1 model selected
> hide sel cartoons
> hide #2 models
> delete #2,3,4,5
> mmaker #6 /C :157-144 to #1 /a :149-136
No 'to' model specified
> mmaker #6 /C :157-144 to #1 /A :149-136
No 'to' model specified
> align #6 /C :157-144 toAtoms #1 /A :149-136
No atoms paired for alignment
> align #6 /C :157-144 & #1 /A :149-136
Missing required "to_atoms" argument
> align #6 /C :157-144 toAtoms #1 /A :149-136
No atoms paired for alignment
> ui tool show Matchmaker
> help help:user/tools/matchmaker.html
> align #6 /C :157-144 toAtoms #1 /A :149-136
No atoms paired for alignment
> align #6 /C :144-157 toAtoms #1 /A :136-149
Unequal number of atoms to pair, 118 and 249
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A #6/B #6/C #6/D
Alignment identifier is 2
> select #6/A-D:144-145
60 atoms, 56 bonds, 8 residues, 1 model selected
> select #6/A-D:144-161
600 atoms, 608 bonds, 72 residues, 1 model selected
> select #6/A-D:157
48 atoms, 48 bonds, 4 residues, 1 model selected
> select #6/A-D:144-157
472 atoms, 480 bonds, 56 residues, 1 model selected
> align #6 /C :144-157 toAtoms #1 /A :136-149
Unequal number of atoms to pair, 118 and 249
> align #6 /C :144-157 toAtoms #1 /A :136-149
Unequal number of atoms to pair, 118 and 249
> select #6 /C :144-157
118 atoms, 120 bonds, 14 residues, 1 model selected
> select #1 /A :136-149
249 atoms, 251 bonds, 14 residues, 1 model selected
> mmaker #6 /C :144-157 to #1 /A :136-149
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 hsk2o_2M.pdb, chain A (#1) with rank-001-modified-
hsk2o-mmseq2-enc.pdb, chain C (#6), sequence alignment score = 72.8
RMSD between 14 pruned atom pairs is 0.481 angstroms; (across all 14 pairs:
0.481)
> select clear
> select #1/A:93
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/C:115
26 atoms, 25 bonds, 2 residues, 2 models selected
> select add #1/A:107
36 atoms, 34 bonds, 3 residues, 2 models selected
> mmaker #6 /C :101-115 to #1 /A :93-107
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 hsk2o_2M.pdb, chain A (#1) with rank-001-modified-
hsk2o-mmseq2-enc.pdb, chain C (#6), sequence alignment score = 79.4
RMSD between 15 pruned atom pairs is 0.253 angstroms; (across all 15 pairs:
0.253)
> select up
798 atoms, 812 bonds, 57 residues, 2 models selected
> mmaker #6 /C :101-115, 144-157 to #1 /A :93-107, 136-149
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 hsk2o_2M.pdb, chain A (#1) with rank-001-modified-
hsk2o-mmseq2-enc.pdb, chain C (#6), sequence alignment score = 152.2
RMSD between 29 pruned atom pairs is 0.499 angstroms; (across all 29 pairs:
0.499)
> select #1 /A :93-107, 136-149
507 atoms, 511 bonds, 29 residues, 1 model selected
> select #1 /A :108-135
425 atoms, 434 bonds, 28 residues, 1 model selected
> select #1 /A :107-135
435 atoms, 444 bonds, 29 residues, 1 model selected
> select #1 /A :106-135
446 atoms, 455 bonds, 30 residues, 1 model selected
> select #1 /A :106-136
462 atoms, 471 bonds, 31 residues, 1 model selected
> select #1 /A :106-137
474 atoms, 483 bonds, 32 residues, 1 model selected
> select #1 /A :106-137, #6 /c :114-145
Expected a keyword
> select #1 /A :106-137 and #6 /c :114-145
Expected a keyword
> select #1 /A :106-137 & #6 /c :114-145
Nothing selected
> select #1 /A :106-137
474 atoms, 483 bonds, 32 residues, 1 model selected
> select #6 /c :114-145
246 atoms, 255 bonds, 32 residues, 1 model selected
> select #1 /A :106-137
474 atoms, 483 bonds, 32 residues, 1 model selected
> select #1 /A :106-137
474 atoms, 483 bonds, 32 residues, 1 model selected
> select clear
> hide #1 models
> select #6/C:133
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #6/C:130
22 atoms, 21 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 22 atom styles
> style sel ball
Changed 22 atom styles
> color sel byhetero
> select clear
> select #6/C:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select clear
> select #6/C:252
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 4 atom styles
> color sel byhetero
> show sel atoms
[Repeated 1 time(s)]
> style sel ball
Changed 4 atom styles
> show sel atoms
> style sel sphere
Changed 4 atom styles
> style sel ball
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel ball
Changed 4 atom styles
> show sel atoms
> select add #6/C:248
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
87 atoms, 88 bonds, 12 residues, 1 model selected
> select down
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
87 atoms, 88 bonds, 12 residues, 1 model selected
> select down
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #6/C:251
22 atoms, 20 bonds, 3 residues, 1 model selected
> select add #6/C:250
26 atoms, 23 bonds, 4 residues, 1 model selected
> select add #6/C:249
34 atoms, 30 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 34 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> show sel atoms
> select O
6466 atoms, 4398 residues, 2 models selected
> select clear
> select #6/C:253@CA
1 atom, 1 residue, 1 model selected
> select add #6/C:252
5 atoms, 3 bonds, 2 residues, 1 model selected
> select add #6/C:251@CA
6 atoms, 3 bonds, 3 residues, 1 model selected
> select add #6/C:250
10 atoms, 6 bonds, 4 residues, 1 model selected
> select add #6/C:249
18 atoms, 13 bonds, 5 residues, 1 model selected
> select add #6/C:248
24 atoms, 18 bonds, 6 residues, 1 model selected
> select add #6/C:247
32 atoms, 25 bonds, 7 residues, 1 model selected
> select sel & O
6 atoms, 5 residues, 1 model selected
> color sel & O red
> hide sel cartoons
> select #6 /b,c,d
9792 atoms, 9975 bonds, 1221 residues, 1 model selected
> select #6 /a,b,d
9792 atoms, 9975 bonds, 1221 residues, 1 model selected
> show sel cartoons
> select clear
> select #6 :114-145
2012 atoms, 2052 bonds, 256 residues, 1 model selected
> select ~sel
49659 atoms, 50088 bonds, 4163 residues, 2 models selected
> select #6 :1-113, 146-407
15736 atoms, 15972 bonds, 1968 residues, 1 model selected
> delete sel
> select #6 /e,f,g,h
1028 atoms, 1032 bonds, 128 residues, 1 model selected
> show sel cartoons
> open /Users/woori/Downloads/rank-001-modified-hsk2o-mmseq2-enc.pdb
Chain information for rank-001-modified-hsk2o-mmseq2-enc.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #2 models
> show #2 models
> hide #6 models
> hide #2 atoms
> show #2 cartoons
> select #6 /e,f,g,h
1028 atoms, 1032 bonds, 128 residues, 1 model selected
> show #2 cartoons
[Repeated 2 time(s)]
> show #2 atoms
> show #2 cartoons
> hide #2 atoms
> select #6 /e,f,g,h
1028 atoms, 1032 bonds, 128 residues, 1 model selected
> show #2 atoms
> hide #2 atoms
> show #2 cartoons
> show #6 models
> delete #6 /e,f,g,h
> hide #2 models
> mmaker #2 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 hsk2o_2M.pdb, chain E (#1) with rank-001-modified-
hsk2o-mmseq2-enc.pdb, chain A (#2), sequence alignment score = 1882.7
RMSD between 293 pruned atom pairs is 1.019 angstroms; (across all 379 pairs:
4.110)
> show #2 models
> hide #2 models
> select #6 :130, 133
88 atoms, 84 bonds, 8 residues, 1 model selected
> style sel ball
Changed 88 atom styles
> show sel atoms
> color sel byhetero
> select clear
> show #1 models
> select #1 :228-257
444 atoms, 449 bonds, 30 residues, 1 model selected
> select #1 /a,c,e,g :228-257
444 atoms, 449 bonds, 30 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #1
33923 atoms, 34116 bonds, 2195 residues, 1 model selected
> show sel cartoons
> select clear
> select #1 :228-257
444 atoms, 449 bonds, 30 residues, 1 model selected
> select #1 :228-257, 753-782, 1278-1307, 1803-1832
1788 atoms, 1804 bonds, 124 residues, 1 model selected
> select #1 :1-226, 257-379, 526-751, 782-904, 1051-1276, 1307-1429,
> 1575-1801, 1832-1954
23148 atoms, 23292 bonds, 1460 residues, 1 model selected
> hide sel cartoons
> select ~sel & ##selected
10775 atoms, 10824 bonds, 735 residues, 1 model selected
> select up
10784 atoms, 10824 bonds, 744 residues, 1 model selected
> select #1 :b,d,f,h
Nothing selected
> hide #1,6 cartoons
> show #1,6 cartoons
> select #1 :1-226, 257-379, 526-751, 782-904, 1051-1276, 1307-1429,
> 1575-1801, 1832-1954
23148 atoms, 23292 bonds, 1460 residues, 1 model selected
> hide sel cartoons
> select up
23494 atoms, 23642 bonds, 1485 residues, 1 model selected
> select down
23148 atoms, 23292 bonds, 1460 residues, 1 model selected
> select down
10775 atoms, 10824 bonds, 735 residues, 1 model selected
> select #1 /b,d,f,h
8920 atoms, 8968 bonds, 584 residues, 1 model selected
> hide sel cartoons
> select #1/C:764
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/C:752
39 atoms, 38 bonds, 2 residues, 1 model selected
> select up
370 atoms, 375 bonds, 24 residues, 1 model selected
> select down
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #1/A:227-228/C:752-753/E:1277-1278/G:1802-1803
156 atoms, 156 bonds, 8 residues, 1 model selected
> select #1/A:227-237/C:752-762/E:1277-1287/G:1802-1812
716 atoms, 724 bonds, 44 residues, 1 model selected
> hide sel cartoons
> select #1/C:781
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1/C:772
32 atoms, 30 bonds, 2 residues, 1 model selected
> select #1/A:247-248/C:772-773/E:1297-1298/G:1822-1823
120 atoms, 120 bonds, 8 residues, 1 model selected
> select #1/A:247-256/C:772-781/E:1297-1306/G:1822-1831
564 atoms, 568 bonds, 40 residues, 1 model selected
> hide sel cartoons
> save /Users/woori/Downloads/view_alphafold_hairpin_sk2o_sf.cxs
> select #1/G:1819
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/G:1815
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:240/C:765/E:1290/G:1815
44 atoms, 40 bonds, 4 residues, 1 model selected
> select #1/A:240-244/C:765-769/E:1290-1294/G:1815-1819
260 atoms, 260 bonds, 20 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 260 atom styles
> color sel byhetero
> hide sel cartoons
> select clear
> select #1/A:242/C:767/E:1292/G:1817
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #1/A:242-244/C:767-769/E:1292-1294/G:1817-1819
140 atoms, 140 bonds, 12 residues, 1 model selected
> select #1/A:240-241/C:765-766/E:1290-1291/G:1815-1816
120 atoms, 116 bonds, 8 residues, 1 model selected
> select #1/A:240-241/C:765-766/E:1290-1291/G:1815-1816
120 atoms, 116 bonds, 8 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> save /Users/woori/Downloads/view_alphafold_hairpin_sk2o_sf.cxs
\u2014\u2014\u2014 End of log from Fri Jan 26 16:25:48 2024 \u2014\u2014\u2014
opened ChimeraX session
> show #1,6 cartoons
> show #2 models
> select clear
> ui tool show "Change Chain IDs"
> select add #6
984 atoms, 1020 bonds, 128 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel A E
Chain IDs of 32 residues changed
> changechains sel C A
Chain IDs of 32 residues changed
> changechains sel B C
Chain IDs of 32 residues changed
> changechains sel D G
Chain IDs of 32 residues changed
> changechains sel D G
No residues specified have any of the 'from' chain IDs
> select subtract #6
Nothing selected
> hide #2 models
> select #1 :1-226, 257-379, 526-751, 782-904, 1051-1276, 1307-1429,
> 1575-1801, 1832-1954
23148 atoms, 23292 bonds, 1460 residues, 1 model selected
> hide sel cartoons
> select up
23494 atoms, 23642 bonds, 1485 residues, 1 model selected
> select down
23148 atoms, 23292 bonds, 1460 residues, 1 model selected
> select down
23148 atoms, 23292 bonds, 1460 residues, 1 model selected
> select #1 /b,d,f,h
8920 atoms, 8968 bonds, 584 residues, 1 model selected
> hide sel cartoons
> save /Users/woori/Desktop/revised_chainid_truncated_hairpinloop.pdb models
> #6
> select #1/A:227
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #1/A:238
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1/A:227-228/C:752-753/E:1277-1278/G:1802-1803
156 atoms, 156 bonds, 8 residues, 1 model selected
> select #1/A:227-239/C:752-764/E:1277-1289/G:1802-1814
872 atoms, 884 bonds, 52 residues, 1 model selected
> hide sel cartoons
> select #1/A:247
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:246/C:771/E:1296/G:1821
68 atoms, 64 bonds, 4 residues, 1 model selected
> select #1/A:246-253/C:771-778/E:1296-1303/G:1821-1828
452 atoms, 456 bonds, 32 residues, 1 model selected
> hide sel cartoons
> select #1/A:256-257/C:781-782/E:1306-1307/G:1831-1832
108 atoms, 104 bonds, 8 residues, 1 model selected
> select #1/A:251-257/C:776-782/E:1301-1307/G:1826-1832
376 atoms, 376 bonds, 28 residues, 1 model selected
> hide sel cartoons
> select #1/A:240-241/C:765-766/E:1290-1291/G:1815-1816
120 atoms, 116 bonds, 8 residues, 1 model selected
> select #1/A:240-245/C:765-770/E:1290-1295/G:1815-1820
308 atoms, 308 bonds, 24 residues, 1 model selected
> hide sel atoms
> select
> #1/A:2-82,87-90,93-106,129-131,135-158,160-162,165-174,180-190,192-214,227-238,251-278,283-319,324-361,363-378/C:527-607,612-615,618-631,654-656,660-683,685-687,690-699,705-715,717-739,752-763,776-803,808-844,849-886,888-903/E:1052-1132,1137-1140,1143-1156,1179-1181,1185-1208,1210-1212,1215-1224,1230-1240,1242-1264,1277-1288,1301-1328,1333-1369,1374-1411,1413-1428/G:1577-1657,1662-1665,1668-1681,1704-1706,1710-1733,1735-1737,1740-1749,1755-1765,1767-1789,1802-1813,1826-1853,1858-1894,1899-1936,1938-1953
20144 atoms, 20272 bonds, 1216 residues, 1 model selected
> select #1/A:240-245/C:765-770/E:1290-1295/G:1815-1820
308 atoms, 308 bonds, 24 residues, 1 model selected
> select clear
> select #1/A:245/C:770/E:1295/G:1820
48 atoms, 44 bonds, 4 residues, 1 model selected
> select #1/A:244-245/C:769-770/E:1294-1295/G:1819-1820
76 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 76 atom styles
> color sel byhetero
> hide sel cartoons
> select clear
> select #6/A:130
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
rank-001-modified-hsk2o-mmseq2-enc.pdb #6/A ARG 130: phi -98.2, psi 128.8
trans
Changed 600 bond radii
> select clear
> ui mousemode right zoom
> select #!6/A:130@NH1
1 atom, 1 residue, 1 model selected
> select add #1/G:1820@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/A ARG 130 NH1 and
hsk2o_2M.pdb #1/G ASP 1820 OD2: 4.375Å
> select clear
> select #!6/C:130@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3
trans
Changed 600 bond radii
> ui mousemode right translate
> select #6.2.60/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:245@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 60 #6.2.60/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245
OD2: 2.990Å
> select #6.2.58/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:245@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 58 #6.2.58/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245
OD2: 3.615Å
> select up
21 atoms, 19 bonds, 2 residues, 2 models selected
> select up
180 atoms, 180 bonds, 13 residues, 2 models selected
> select up
6199 atoms, 6258 bonds, 380 residues, 2 models selected
> select down
180 atoms, 180 bonds, 13 residues, 2 models selected
> swapaa #!6/C:130 ARG criteria 60 rotLib Dunbrack retain false
Using Dunbrack library
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3
trans
Applying ARG rotamer (chi angles: 57.4 85.0 174.5 173.5) to rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/C ARG 130
> select #1/A:245@O
1 atom, 1 residue, 1 model selected
> select add #!6/C:130@NH1
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/A ASP 245 O and rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/C ARG 130 NH1: 5.651Å
> select #1/A:245@OD2
1 atom, 1 residue, 1 model selected
> select add #!6/C:130@NH2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/A ASP 245 OD2 and rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/C ARG 130 NH2: 2.990Å
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
No rotamers for ALA in Dunbrack rotamer library
> select up
23 atoms, 21 bonds, 2 residues, 2 models selected
> select clear
> select #!6/C:130
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3
trans
Changed 600 bond radii
> select clear
> select #6.2.30/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:245@O
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 30 #6.2.30/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245
O: 5.181Å
> select add #6.2.11/A:1@NH2
3 atoms, 3 residues, 3 models selected
> select subtract #1/A:245@O
2 atoms, 2 residues, 2 models selected
> select add #1/A:245@O
3 atoms, 3 residues, 3 models selected
> distance sel
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects
> select clear
> select add #1/A:245@O
1 atom, 1 residue, 1 model selected
> select add #6.2.11/A:1@NH2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/A ASP 245 O and rotamer 11 #6.2.11/A ARG 1
NH2: 5.048Å
> select clear
> select #1/A:245@O
1 atom, 1 residue, 1 model selected
> distance sel
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects
> select clear
> select add #1/A:245@O
1 atom, 1 residue, 1 model selected
> select add #6.2.51/A:1@NH2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/A ASP 245 O and rotamer 51 #6.2.51/A ARG 1
NH2: 4.367Å
> select add #6.2.65/A:1@NH2
3 atoms, 3 residues, 3 models selected
> select clear
> select #6.2.65/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:245@O
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 65 #6.2.65/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245
O: 4.232Å
> select #6.2.7/A:1@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:245@O
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 7 #6.2.7/A ARG 1 NH1 and hsk2o_2M.pdb #1/A ASP 245 O:
4.575Å
> select clear
> select #!6/G:130
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/G ARG 130: phi -100.0, psi 129.7
trans
Changed 600 bond radii
> select #1/E:1295@OD2
1 atom, 1 residue, 1 model selected
> select add #6.3.60/A:1@NH1
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/E ASP 1295 OD2 and rotamer 60 #6.3.60/A ARG 1
NH1: 6.113Å
> select clear
> select #1/E:1295@OD2
1 atom, 1 residue, 1 model selected
> select add #6.3.39/A:1@NH1
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/E ASP 1295 OD2 and rotamer 39 #6.3.39/A ARG 1
NH1: 6.134Å
> select #6.3.66/A:1@NH1
1 atom, 1 residue, 1 model selected
> select add #1/E:1295@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 66 #6.3.66/A ARG 1 NH1 and hsk2o_2M.pdb #1/E ASP 1295
OD2: 6.759Å
> select up
21 atoms, 19 bonds, 2 residues, 2 models selected
> select up
180 atoms, 180 bonds, 13 residues, 2 models selected
> select up
6199 atoms, 6258 bonds, 380 residues, 2 models selected
> select up
33932 atoms, 34124 bonds, 2196 residues, 2 models selected
> select up
34598 atoms, 34716 bonds, 2270 residues, 76 models selected
> select up
34598 atoms, 34716 bonds, 2270 residues, 77 models selected
> swapaa #!6/G:130 ARG criteria 60 rotLib Dunbrack retain false
Using Dunbrack library
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/G ARG 130: phi -100.0, psi 129.7
trans
Applying ARG rotamer (chi angles: 57.4 85.0 174.5 173.5) to rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/G ARG 130
> select add #!6/G:130@NH1
33924 atoms, 34116 bonds, 2196 residues, 2 models selected
> select clear
> select add #1/E:1295@OD2
1 atom, 1 residue, 1 model selected
> select add #!6/G:130@NH1
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/E ASP 1295 OD2 and rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/G ARG 130 NH1: 6.113Å
> select clear
> select #!6/E:130@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/E ARG 130: phi -98.8, psi 128.7
trans
Changed 600 bond radii
> select clear
> select #6.3.60/A:1@NH1
1 atom, 1 residue, 1 model selected
> select add #1/C:770@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 60 #6.3.60/A ARG 1 NH1 and hsk2o_2M.pdb #1/C ASP 770
OD2: 5.454Å
> select clear
> select add #6.3.39/A:1@NH1
1 atom, 1 residue, 1 model selected
> select add #1/C:770@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 39 #6.3.39/A ARG 1 NH1 and hsk2o_2M.pdb #1/C ASP 770
OD2: 5.293Å
> show #2 models
> select clear
> ui tool show "Show Sequence Viewer"
> select #2 :248-255
228 atoms, 228 bonds, 32 residues, 1 model selected
> select #2 :1-247,255-407
17548 atoms, 17832 bonds, 2196 residues, 1 model selected
> hide sel cartoons
> select #2 :248
24 atoms, 20 bonds, 4 residues, 1 model selected
> select #2 :256
28 atoms, 28 bonds, 4 residues, 1 model selected
> select #2 :258
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #2 :251
48 atoms, 48 bonds, 4 residues, 1 model selected
> select #2 :250
16 atoms, 12 bonds, 4 residues, 1 model selected
> select #2 :252
16 atoms, 12 bonds, 4 residues, 1 model selected
> select #2 :253
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 32 atom styles
> select clear
> swapaa #!6/A:130 ARG criteria 60 rotLib Dunbrack retain false
Using Dunbrack library
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/A ARG 130: phi -98.2, psi 128.8
trans
Applying ARG rotamer (chi angles: 57.4 85.0 174.5 173.5) to rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/A ARG 130
> swapaa #!6/C:130 ARG criteria 65 rotLib Dunbrack retain false
Using Dunbrack library
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3
trans
Applying ARG rotamer (chi angles: 59.3 92.1 71.9 -159.5) to rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/C ARG 130
> select #1/C:770@OD2
1 atom, 1 residue, 1 model selected
> select add #6.3.37/A:1@NH2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between hsk2o_2M.pdb #1/C ASP 770 OD2 and rotamer 37 #6.3.37/A ARG 1
NH2: 6.498Å
> select #6.3.65/A:1@NH1
1 atom, 1 residue, 1 model selected
> select add #1/C:770@OD2
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between rotamer 65 #6.3.65/A ARG 1 NH1 and hsk2o_2M.pdb #1/C ASP 770
OD2: 5.726Å
> select down
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 2 models selected
> swapaa #!6/E:130 ARG criteria 65 rotLib Dunbrack retain false
Using Dunbrack library
rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/E ARG 130: phi -98.8, psi 128.7
trans
Applying ARG rotamer (chi angles: 59.3 92.1 71.9 -159.5) to rank-001-modified-
hsk2o-mmseq2-enc.pdb #!6/E ARG 130
> select clear
> save
> /Users/woori/Desktop/revised_rotamer_revised_chainid_truncated_hairpinloop.pdb
> models #6
> select clear
Drag select of 2 atoms, 9 residues, 1 bonds
> select up
99 atoms, 65 bonds, 10 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 99 atom styles
> color sel byhetero
> select clear
> save /Users/woori/Downloads/view_alphafold_revised_hairpin_sk2o_sf.cxs
> hide #6 models
Drag select of 47 atoms, 22 residues, 43 bonds
> select clear
Drag select of 44 atoms, 22 residues, 39 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 4 atoms, 2 bonds
> hide sel atoms
Drag select of 24 atoms, 11 residues, 22 bonds
> hide sel atoms
> hide sel cartoons
> hide #2 models
> show sel & #1 cartoons
> select clear
> show #1 cartoons
> hide #1 atoms
> select :272
32 atoms, 27 bonds, 5 residues, 2 models selected
> select #1/A:272/C:797/E:1322/G:1847
64 atoms, 60 bonds, 4 residues, 1 model selected
> select #1/A:272/C:797/E:1322/G:1847
64 atoms, 60 bonds, 4 residues, 1 model selected
> open /Users/woori/Downloads/hsk2n_2M.pdb
Chain information for hsk2n_2M.pdb #4
---
Chain | Description
A C E G | No description available
B D F H | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/C #1/E #1/G #4/A #4/C #4/E #4/G
Alignment identifier is 3
> select #4 :390
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1 :272, 727, 1322, 1847
59 atoms, 55 bonds, 4 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> hide #!3 models
> hide #3.1 models
> hide #4 models
> select #1 :272, 797, 1322, 1847
64 atoms, 60 bonds, 4 residues, 1 model selected
> show sel atoms
> open
> /Users/woori/Downloads/expanse_result/sk4_control_pore_restraint/6cno_2M_v2.pdb
Summary of feedback from opening
/Users/woori/Downloads/expanse_result/sk4_control_pore_restraint/6cno_2M_v2.pdb
---
warning | PDB SEQRES record for chain H is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for 6cno_2M_v2.pdb #5
---
Chain | Description
A B C D | No description available
E F G H | No description available
> delete #4
> delete #3
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #1 models
> hide #5 models
> show #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A #5/B #5/C #5/D
Alignment identifier is 3
> select
> #5/A:2-42,47-81,88-91,94-108,117-123,126-128,140-162,169-178,184-193,196-218,229-240,253-281,289-322,326-360,365-377/B:380-420,425-459,466-469,472-486,495-501,504-506,518-540,547-556,562-571,574-596,607-618,631-659,667-700,704-738,743-755/C:758-798,803-837,844-847,850-864,873-879,882-884,896-918,925-934,940-949,952-974,985-996,1009-1037,1045-1078,1082-1116,1121-1133/D:1136-1176,1181-1215,1222-1225,1228-1242,1251-1257,1260-1262,1274-1296,1303-1312,1318-1327,1330-1352,1363-1374,1387-1415,1423-1456,1460-1494,1499-1511
9264 atoms, 9404 bonds, 1176 residues, 1 model selected
> select clear
> show #5 cartoons
> hide #5 atoms
> select #5 :274
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #5
> show #1 models
> show #2 models
> ui mousemode right rotate
> hide #1-2 atoms
> show #1-2 cartoons
> hide #2 models
> show #6 models
> show #2 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #2 models
> show #2 models
> hide #2 models
> delete #2
> select #1/A:108/C:633/E:1158/G:1683
76 atoms, 72 bonds, 4 residues, 1 model selected
> select #1/A:108/C:633/E:1158/G:1683
76 atoms, 72 bonds, 4 residues, 1 model selected
> select #1/A:108-135/C:633-660/E:1158-1185/G:1683-1710
1700 atoms, 1736 bonds, 112 residues, 1 model selected
> color sel red
> select clear
> open /Users/woori/Downloads/rank-001-modified-hsk2o-mmseq2-enc.pdb
Chain information for rank-001-modified-hsk2o-mmseq2-enc.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> show cartoons
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #6/E #6/C #6/A #6/G #2/A #2/B #2/C #2/D
Alignment identifier is 2
> select #6/E,C,A,G:124 #2/A-D:124
56 atoms, 48 bonds, 8 residues, 2 models selected
> select #6/E,C,A,G:124-143 #2/A-D:124-143
1248 atoms, 1288 bonds, 160 residues, 2 models selected
2 [ID: 2] region 8 chains [124-143] RMSD: 62.767
> mmaker #2 :124-143 to #6
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,10
Model Number: MRX53LL/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B2073)
Kernel Version: Darwin 23.1.0
Time since boot: 37 days, 18 hours, 46 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
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: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
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-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
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: 1.5.13
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: 1.1
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: 1.12.3
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: 1.33.2
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: 4.47.0
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: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
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: 3.0.43
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: 1.0.7
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 , 21 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 , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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