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Opened 6 months ago
Closed 6 months ago
#17623 closed defect (duplicate)
Crash on exit destroying OpenGL contexts
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503250235 (2025-03-25 02:35:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000037ffef000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000037efe3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000037dfd7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000037cfcb000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000037bfbf000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000037afb3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000379fa7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000378f9b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000377f8f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000376f83000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000375f77000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000361767000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000036075b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035f74f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035e743000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035d737000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035c72b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000035b71f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000357487000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003526d3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000346113000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033d26f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f4ccc840 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 440 in quit
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 805 in closeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PIL._imaging, PIL._imagingmath, chimerax.dssp._dssp (total: 54)
{"app_name":"ChimeraX","timestamp":"2025-05-12 00:56:41.00 -0700","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"AF3A31ED-6AC5-44D8-8D2F-8A5625488EE9"}
{
"uptime" : 150000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,13",
"coalitionID" : 5525,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-05-12 00:56:40.7359 -0700",
"codeSigningMonitor" : 1,
"incident" : "AF3A31ED-6AC5-44D8-8D2F-8A5625488EE9",
"pid" : 97233,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-12 00:30:00.9229 -0700",
"procStartAbsTime" : 3695206291132,
"procExitAbsTime" : 3733601468441,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"22F9E1B8-787A-5306-A000-9EB72D5EB01F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AD4C3A18-F6B3-7AC1-A36D-02975FF11634",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "67B75783-CA15-43B5-9C15-551A23213E12",
"wakeTime" : 28459,
"sleepWakeUUID" : "53E10330-F9EA-4F19-93EF-EF4C692F4CC3",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4339712000\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102aac000-102ab0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":97233},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4339712000\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102aac000-102ab0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202503250235 (2025-03-25)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/audreykishishita/pymol_scripts/closed_integrin.pdb
Chain information for closed_integrin.pdb #1
---
Chain | Description
A | No description available
B | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> select /B:55-690
4182 atoms, 4272 bonds, 1 pseudobond, 539 residues, 2 models selected
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> alphafold match #1/B
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold P05106 from
https://alphafold.ebi.ac.uk/files/AF-P05106-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: P05106 (chain B)
AlphaFold prediction matching closed_integrin.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
B | P05106 | ITB3_HUMAN | 2.51 | 692 | 539 | 99
Opened 1 AlphaFold model
> sequence chain /B
Chains must have same sequence
> sequence chain /B
Chains must have same sequence
> sequence chain #1 /B
Alignment identifier is 1/B
> sequence chain #2 /B
Alignment identifier is 2.1/B
> ui tool show "Modeller Comparative"
Populating font family aliases took 114 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> modeller comparative 2.1/B:1 numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: UOTX0S29372VG8IM
Webservices job finished: UOTX0S29372VG8IM
> select clear
Webservices job finished: UOTX0S29372VG8IM
> ui tool show "Modeller Comparative"
Webservices job finished: UOTX0S29372VG8IM
Modeller job (ID UOTX0S29372VG8IM) finished
Computing secondary structure
Parameters
---
Chain pairing | ss
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 AlphaFold ITB3_HUMAN chain B, chain B (#2.1) with chain_B, chain B
(#), sequence alignment score = 3955
RMSD between 690 pruned atom pairs is 0.373 angstroms; (across all 692 pairs:
0.482)
Computing secondary structure
Parameters
---
Chain pairing | ss
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 AlphaFold ITB3_HUMAN chain B, chain B (#2.1) with chain_B, chain B
(#), sequence alignment score = 3982
RMSD between 686 pruned atom pairs is 0.724 angstroms; (across all 692 pairs:
0.815)
Computing secondary structure
Parameters
---
Chain pairing | ss
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 AlphaFold ITB3_HUMAN chain B, chain B (#2.1) with chain_B, chain B
(#), sequence alignment score = 3991
RMSD between 690 pruned atom pairs is 0.496 angstroms; (across all 692 pairs:
0.589)
Associated chain_B chain B to chain B with 0 mismatches
Chain information for chain_B
---
Chain | Description
3.1/B 3.2/B 3.3/B | No description available
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #2.1 models
> hide #!2 models
> show #3.1 models
> hide #3.1 models
> show #3.2 models
> hide #3.2 models
> show #3.3 models
> hide #3.3 models
> show #3.2 models
> select #3.1/B:1 #3.2/B:1 #3.3/B:1
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #3.1/B:1-26 #3.2/B:1-26 #3.3/B:1-26
564 atoms, 576 bonds, 78 residues, 3 models selected
Integrin Beta-3 (AlphaFold ITB3_HUMAN Chain B (#2.1) Chain B) [ID: 2.1/B]
region chain B [1-26] RMSD: 19.480
> select
> #2.1/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
> #3.1/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
> #3.2/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
> #3.3/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
5360 atoms, 5339 bonds, 700 residues, 4 models selected
> select #3.1/B:1-2 #3.2/B:1-2 #3.3/B:1-2
57 atoms, 54 bonds, 6 residues, 3 models selected
> select #3.1/B:1-24 #3.2/B:1-24 #3.3/B:1-24
531 atoms, 543 bonds, 72 residues, 3 models selected
Integrin Beta-3 (AlphaFold ITB3_HUMAN Chain B (#2.1) Chain B) [ID: 2.1/B]
region chain B [1-24] RMSD: 20.222
> select #3.1/B:1-26 #3.2/B:1-26 #3.3/B:1-26
564 atoms, 576 bonds, 78 residues, 3 models selected
> delete #3.1/B:1-26 #3.2/B:1-26 #3.3/B:1-26
> show #3.1 models
> show #3.3 models
> hide #3.3 models
> hide #3.2 models
> show #3.2 models
> show #3.3 models
> hide #3.3 models
> hide #3.2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2.1/B:631 #3.1/B:631 #3.2/B:631 #3.3/B:631
28 atoms, 28 bonds, 4 residues, 4 models selected
> select #2.1/B:631-718 #3.1/B:631-788 #3.2/B:631-788 #3.3/B:631-788
4509 atoms, 4602 bonds, 562 residues, 4 models selected
Integrin Beta-3 (AlphaFold ITB3_HUMAN Chain B (#2.1) Chain B) [ID: 2.1/B]
region chain B [631-788] RMSD: 11.946
> select
> #2.1/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
> #3.1/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
> #3.2/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
> #3.3/B:27-28,30-33,39-45,67-72,77-79,93-96,151-168,197-200,204-206,211-213,226-233,248-257,259-262,285-289,294-295,308-311,314-327,341-350,366-378,462-466,489,519-523,535-536,562-564,591-593,601-603,631-646,650-653,657-660,713-717
5360 atoms, 5339 bonds, 700 residues, 4 models selected
> select add #1
19541 atoms, 19813 bonds, 39 pseudobonds, 2342 residues, 7 models selected
> select subtract #1
5360 atoms, 5339 bonds, 700 residues, 4 models selected
> select add #2
9329 atoms, 9411 bonds, 1217 residues, 5 models selected
> select subtract #2
4020 atoms, 4005 bonds, 525 residues, 3 models selected
> select add #3
17616 atoms, 18024 bonds, 2286 residues, 4 models selected
> select subtract #3
Nothing selected
> select #2.1/B:631-718 #3.1/B:631-788 #3.2/B:631-788 #3.3/B:631-788
4509 atoms, 4602 bonds, 562 residues, 4 models selected
> show #!2 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> select add #3.1
9113 atoms, 9315 bonds, 1166 residues, 4 models selected
> select add #3.3
13717 atoms, 14028 bonds, 1770 residues, 4 models selected
> select subtract #3.3
7845 atoms, 8020 bonds, 1008 residues, 3 models selected
> select add #3.2
12449 atoms, 12733 bonds, 1612 residues, 3 models selected
> select subtract #3.2
6577 atoms, 6725 bonds, 850 residues, 2 models selected
> show #3.3 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> save /Users/audreykishishita/Desktop/beta_extracellular.pdb models #3.1
> hide #!3 models
> hide #3.1 models
> hide #1.1 models
> hide #1.2 models
> select add #2
11181 atoms, 11414 bonds, 1454 residues, 3 models selected
> select subtract #2
5872 atoms, 6008 bonds, 762 residues, 1 model selected
> select add #2.1
11181 atoms, 11414 bonds, 1454 residues, 2 models selected
> select add #3
22925 atoms, 23430 bonds, 2978 residues, 5 models selected
> select subtract #3
5309 atoms, 5406 bonds, 692 residues, 1 model selected
> select add #2
5309 atoms, 5406 bonds, 692 residues, 2 models selected
> select subtract #2
Nothing selected
> show #!1 models
> select #1/A
7249 atoms, 7411 bonds, 33 pseudobonds, 934 residues, 3 models selected
> show #1.2 models
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 3 fast true
> adjacentFlexible 1 protocol standard
Webservices job id: LQJTQ6QMFOAKWD9E
Webservices job finished: LQJTQ6QMFOAKWD9E
Modeller job (ID LQJTQ6QMFOAKWD9E) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 97, in
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and
pdb files are different: 1466 1642 For alignment entry: 1
closed_integrin.pdb_1
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
4.18.0-553.51.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/05/12 00:48:11
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 775109 756.942
0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775137 756.970 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775165 756.997 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 781025 762.720 0.745
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 784845 766.450 0.748
Read the alignment from file : alignment.ali
Total number of alignment positions: 1495
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 closed_in 1466 2 closed_inte
2 chain_A 956 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./closed_integrin.pdb_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1226370 1197.627
1.170
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1226370 1197.627
1.170
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1226541 1197.794
1.170
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1227391 1198.624
1.171
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1228649 1199.853
1.172
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1230553 1201.712
1.174
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1230553 1201.712
1.174
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1230643 1201.800
1.174
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1233499 1204.589
1.176
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1233499 1204.589
1.176
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1233634 1204.721
1.176
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1237918 1208.904
1.181
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1237918 1208.904
1.181
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1238116 1209.098
1.181
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1244542 1215.373
1.187
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1244542 1215.373
1.187
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1244839 1215.663
1.187
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1254461 1225.060
1.196
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1254461 1225.060
1.196
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1254911 1225.499
1.197
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1269361 1239.610
1.211
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1269361 1239.610
1.211
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1270036 1240.270
1.211
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1291694 1261.420
1.232
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1291694 1261.420
1.232
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1292702 1262.404
1.233
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1325206 1294.146
1.264
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1325206 1294.146
1.264
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1326718 1295.623
1.265
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1375474 1343.236
1.312
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1375474 1343.236
1.312
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1377742 1345.451
1.314
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1450876 1416.871
1.384
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1450876 1416.871
1.384
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1454278 1420.193
1.387
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1563962 1527.307
1.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1563962 1527.307
1.492
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1563962 1527.307
1.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1563962 1527.307
1.492
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1569065 1532.290
1.496
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1733591 1692.960
1.653
read_pd_459W> Residue type NAG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1733591 1692.960
1.653
read_pd_459W> Residue type NDG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1733591 1692.960
1.653
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1786555 1744.683
1.704
read_te_290E> Number of residues in the alignment and pdb files are different:
1466 1642
For alignment entry: 1 closed_integrin.pdb_1
x (mismatch at alignment position 1467)
Alignment EDSSGKSILYVVEEPECPKG/ - - - - - - - - -
PDB EDSSGKSILYVVEEPECPKG/../../../../../../../..33333/..3/GALEER
Match *********************
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 closed_integrin.pdb_1
No output models from Modeller; see log for Modeller text output.
> select clear
> select add #1.2
2 pseudobonds, 1 model selected
> hide #!1 atoms
> show #!1 cartoons
> alphafold match #1/A
Fetching compressed AlphaFold L7RXH0 from
https://alphafold.ebi.ac.uk/files/AF-L7RXH0-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: L7RXH0 (chain A)
AlphaFold prediction matching closed_integrin.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | L7RXH0 | L7RXH0_HUMAN | 2.85 | 957 | 927 | 100
Opened 1 AlphaFold model
> sequence chain #4 /B
Chains must have same sequence
> sequence chain /B
Chains must have same sequence
> sequence chain #4 /B
Chains must have same sequence
> sequence chain #4.1
Alignment identifier is 4.1/A
> sequence chain #1 /A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select clear
> select add #1.2
2 pseudobonds, 1 model selected
> select clear
> select
> #4.1/A:33,39-42,52-56,65-70,84-90,97-99,109-111,114-115,117-118,124,127-131,134-139,143-144,153,157-162,165-169,190-193,198-203,211-217,238-239,252,255-259,268-273,282-286,293-298,309-313,322-327,331-333,339-341,344-350,356-362,373-378,387-392,402-406,419-422,434-442,451-456,461-465,467,470-480,483-484,491-492,499-500,502-512,520-528,541-543,550-558,564-572,585-593,607-608,615-622,636-642,646-648,652-663,668,671-676,681-686,697-703,706-714,717,722-732,740-748,756,760-767,772-779,782-785,798,805-814,820,822-833,836-837,839-847,850-854,864,899-902,908-916,919,924-933,947-960,971-983
3432 atoms, 3418 bonds, 436 residues, 1 model selected
> select clear
> select #4.1/A:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.1/A:34-38
36 atoms, 36 bonds, 5 residues, 1 model selected
> select
> #4.1/A:33,39-42,52-56,65-70,84-90,97-99,109-111,114-115,117-118,124,127-131,134-139,143-144,153,157-162,165-169,190-193,198-203,211-217,238-239,252,255-259,268-273,282-286,293-298,309-313,322-327,331-333,339-341,344-350,356-362,373-378,387-392,402-406,419-422,434-442,451-456,461-465,467,470-480,483-484,491-492,499-500,502-512,520-528,541-543,550-558,564-572,585-593,607-608,615-622,636-642,646-648,652-663,668,671-676,681-686,697-703,706-714,717,722-732,740-748,756,760-767,772-779,782-785,798,805-814,820,822-833,836-837,839-847,850-854,864,899-902,908-916,919,924-933,947-960,971-983
3432 atoms, 3418 bonds, 436 residues, 1 model selected
> select #4.1/A:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.1/A:74-76
22 atoms, 21 bonds, 3 residues, 1 model selected
> select clear
> select #1/A:868-876
62 atoms, 62 bonds, 9 residues, 1 model selected
> select #1/A:829
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:829-873
124 atoms, 124 bonds, 1 pseudobond, 16 residues, 2 models selected
> select
> #4.1/A:33,39-42,52-56,65-70,84-90,97-99,109-111,114-115,117-118,124,127-131,134-139,143-144,153,157-162,165-169,190-193,198-203,211-217,238-239,252,255-259,268-273,282-286,293-298,309-313,322-327,331-333,339-341,344-350,356-362,373-378,387-392,402-406,419-422,434-442,451-456,461-465,467,470-480,483-484,491-492,499-500,502-512,520-528,541-543,550-558,564-572,585-593,607-608,615-622,636-642,646-648,652-663,668,671-676,681-686,697-703,706-714,717,722-732,740-748,756,760-767,772-779,782-785,798,805-814,820,822-833,836-837,839-847,850-854,864,899-902,908-916,919,924-933,947-960,971-983
3432 atoms, 3418 bonds, 436 residues, 1 model selected
> select #4.1/A:834
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.1/A:834-924
698 atoms, 704 bonds, 91 residues, 1 model selected
> select add #4
7445 atoms, 7604 bonds, 957 residues, 2 models selected
> select subtract #4
Nothing selected
> ui tool show "Modeller Comparative"
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 347, in _update_sequence_menus
row_info.fieldItem.widget().destroy()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/widgets.py", line 104, in destroy
self.alignment.remove_observer(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 780, in remove_observer
self.observers.remove(observer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 780, in remove_observer
self.observers.remove(observer)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 334, in _list_selection_cb
mb = self.seq_menu[sel_aln]
~~~~~~~~~~~~~^^^^^^^^^
KeyError:
KeyError:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 334, in _list_selection_cb
mb = self.seq_menu[sel_aln]
~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 334, in _list_selection_cb
mb = self.seq_menu[sel_aln]
~~~~~~~~~~~~~^^^^^^^^^
KeyError:
KeyError:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 334, in _list_selection_cb
mb = self.seq_menu[sel_aln]
~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202503250235 (2025-03-25)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,13
Model Number: Z1GF000HXLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 7 days, 11 hours, 41 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202503250235
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.3
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
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: 1.1.2
ChimeraX-ProfileGrids: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.44
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.7.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.13
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.7
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.3.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2025.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on exit destroying OpenGL contexts |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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From before the code was fixed