id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17623 Crash on exit destroying OpenGL contexts chimerax-bug-report@… Tom Goddard "{{{ 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. 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""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4b2e88329e4ae6192672167dc5503cb18f506829"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""654d8c0661e7447155256fcd"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""67fda5a79dc968490af7a32e"" }, ""deploymentId"" : 240000311 } ], ""experiments"" : [ ] } } ===== 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 }}} " defect closed normal Window Toolkit duplicate all ChimeraX