id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19407 Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.1-arm64-arm-64bit ChimeraX Version: 1.11.dev202511122144 (2025-11-12 21:44:22 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000000030704f000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000306043000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000305037000 (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 948 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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030402b000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030301f000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000302013000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000301007000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017fa1b000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017ea0f000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017da03000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017c9f7000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017b9eb000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017a9df000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000001799d3000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000001789c7000 (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 982 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000001eff76080 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 122 in make_current File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 555 in make_current File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 584 in use_shared_context File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 146 in render File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 115 in _redraw File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 169 in update_graphics_now File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 153 in resizeEvent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 61 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 368 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 1064 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 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, PIL._imaging, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54) {""app_name"":""ChimeraX"",""timestamp"":""2025-11-21 13:01:12.00 +0000"",""app_version"":""1.11.0"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.1 (25B78)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""F3B99729-58DA-4B67-BB90-C8ECACDFF3C3""} { ""uptime"" : 130000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac16,8"", ""coalitionID"" : 3860, ""osVersion"" : { ""train"" : ""macOS 26.1"", ""build"" : ""25B78"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-11-21 13:01:04.8056 +0000"", ""codeSigningMonitor"" : 2, ""incident"" : ""F3B99729-58DA-4B67-BB90-C8ECACDFF3C3"", ""pid"" : 92642, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-11-20 10:43:49.0632 +0000"", ""procStartAbsTime"" : 2428120746459, ""procExitAbsTime"" : 3138699170735, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.0"",""CFBundleVersion"":""1.11.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""8330DCBC-A847-5780-B99F-5EE3831D3E46"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""4B8D0552-F25E-3117-5FC1-7C04C199AF25"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""siriAssetIsNotReady"",""assetIsNotReady"",""notOptedIn""]}, ""developerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""5BFC8FC6-F9E6-4AB5-B703-0BDAF9626BAD"", ""wakeTime"" : 4, ""sleepWakeUUID"" : ""2548C9E8-F622-4B11-8C92-0C9BC4A21851"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xb00001d00 is in 0x878000000-0xb69400000; bytes after start: 10871643392 bytes before end: 1765794559 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL MALLOC_LARGE 60e000000-60e294000 [ 2640K] rw-\/rwx SM=PRV GAP OF 0x269d6c000 BYTES ---> commpage (reserved) 878000000-b69400000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated) MALLOC_SMALL b69400000-b69800000 [ 4096K] rw-\/rwx SM=PRV "", ""exception"" : {""codes"":""0x0000000000000002, 0x0000000b00001d00"",""rawCodes"":[2,47244647680],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGBUS"",""subtype"":""KERN_PROTECTION_FAILURE at 0x0000000b00001d00""}, ""termination"" : {""flags"":0,""code"":10,""namespace"":""SIGNAL"",""indicator"":""Bus error: 10"",""byProc"":""ChimeraX"",""byPid"":92642}, ""vmregioninfo"" : ""0xb00001d00 is in 0x878000000-0xb69400000; bytes after start: 10871643392 bytes before end: 1765794559 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL MALLOC_LARGE 60e000000-60e294000 [ 2640K] rw-\/rwx SM=PRV GAP OF 0x269d6c000 BYTES ---> commpage (reserved) 878000000-b69400000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated) MALLOC_SMALL b69400000-b69800000 [ 4096K] rw-\/rwx SM=PRV "", ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0}, ""faultingThread"" : 0, ""threads"" : [{ 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""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : [ ""66d8b2f77cd4b62688efd2cf"" ], ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.dev202511122144 (2025-11-12) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold No sequence chosen for AlphaFold match > open alphafold P11388 'alphafold' has no suffix Fetching compressed P11388 UniProt info from https://www.uniprot.org/uniprot/P11388.xml > alphafold match P11388 Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Fetching compressed AlphaFold P11388 from https://alphafold.ebi.ac.uk/files/AF-P11388-F1-model_v6.cif 1 AlphaFold model found using UniProt identifier: P11388 (UniProt P11388) Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % P11388 | P11388 | 100.0 | 100.0 Opened 1 AlphaFold model > sequence chain #1Alignment identifier is 1/A > select /A:11917 atoms, 6 bonds, 1 residue, 1 model selected > select /A:1-11919625 atoms, 9814 bonds, 1191 residues, 1 model selected > color sel red> background whiteUnknown command: background white > set bgColor white> select up12261 atoms, 12495 bonds, 1531 residues, 1 model > selected > select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected > select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected > select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected > select up12261 atoms, 12495 bonds, 1531 residues, 1 model selected > select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected > select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected > select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected > select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected > select down9625 atoms, 9814 bonds, 1191 residues, 1 model selected > color sel black> select /A:1275-1320376 atoms, 384 bonds, 46 residues, 1 > model selected > select /A:136-13209539 atoms, 9723 bonds, 1185 residues, 1 model selected > select /A:13579 atoms, 8 bonds, 1 residue, 1 model selected > select /A:1357-1402345 atoms, 352 bonds, 46 residues, 1 model selected > open /Users/johnsor2/Downloads/emd_49171.mapOpened emd_49171.map as #2, grid > size 480,480,480, pixel 1.4, shown at level 0.0271, step 2, values float32 > close #1> close> open /Users/johnsor2/Downloads/emd_49171.mapOpened > emd_49171.map as #1, grid size 480,480,480, pixel 1.4, shown at level > 0.0271, step 2, values float32 > volume #1 level 0.02004> volume #1 level 0.01769> volume #1 level 0.009239> volume #1 level 0.01323> volume #1 style image> volume #1 style mesh> volume #1 style image maximumIntensityProjection true> volume #1 maximumIntensityProjection false> volume #1 region 0,0,238,479,479,238 step 1 showOutlineBox true> volume #1 region 0,0,0,479,479,479 step 2> volume #1 region 0,0,0,479,479,479 step 1 colorMode opaque8 orthoplanes xyz positionPlanes 239,239,239 imageMode orthoplanes> volume #1 imageMode ""box faces""> volume #1 region 0,0,0,479,479,479 step 2 colorMode auto8 imageMode ""tilted slab"" tiltedSlabAxis 0.2958,0.05286,-0.9538 tiltedSlabOffset -236.5 tiltedSlabSpacing 1.402 tiltedSlabPlaneCount 48> volume #1 style surface> volume #1 change image level -0.002962,0 level 0.02707,0.8 level 0.1141,1> volume #1 level 0.04139> volume #1 level 0.02755> volume #1 level 0.0259> volume #1 step 1> volume #1 level 0.03061> volume #1 step 4> volume #1 step 2> volume #1 level 0.03038> volume #1 level 0.02709> volume #1 level 0.01582> open 9N9J | Summary of feedback from opening 9N9J fetched from pdb --- warnings | Atom HO5' is not in the residue template for C /L5:1 Atom HO5' is not in the residue template for C /L8:1 notes | Fetching compressed mmCIF 9n9j from http://files.rcsb.org/download/9n9j.cif Fetching CCD BMA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif Fetching CCD ELU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/ELU/ELU.cif Fetching CCD MAN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif Fetching CCD NDG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NDG/NDG.cif 9n9j title: Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon [more info...] Chain information for 9n9j #2 --- Chain | Description | UniProt 5 | Translocon-associated protein subunit alpha | SSRA_HUMAN 1-286 6 | Translocon-associated protein subunit beta | SSRB_HUMAN 1-183 7 | Translocon-associated protein subunit gamma | SSRG_HUMAN 1-185 8 | Translocon-associated protein subunit delta | SSRD_HUMAN 1-173 A | Peptidyl-prolyl cis-trans isomerase FKBP11 | FKB11_HUMAN -26-174 B | Coiled-coil domain-containing protein 134 | CC134_HUMAN 1-229 D | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_HUMAN 1-476 E | Protein transport protein Sec61 subunit beta | SC61B_HUMAN 1-96 F | Protein transport protein Sec61 subunit gamma | SC61G_HUMAN 1-68 G | Stress-associated endoplasmic reticulum protein 1 | SERP1_HUMAN 1-66 I | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A | STT3A_HUMAN 1-705 J | Oligosaccharyltransferase complex subunit OSTC | OSTC_HUMAN 1-149 K2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 | OST4_HUMAN 1-37 L2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258 | TM258_HUMAN 1-79 L5 | 28S ribosomal RNA | L7 | 5S ribosomal RNA | L8 | 5.8S ribosomal RNA | LA | 60S ribosomal protein L8 | RL8_HUMAN 1-257 LB | 60S ribosomal protein L3 | RL3_HUMAN 1-403 LC | Large ribosomal subunit protein uL4 | RL4_HUMAN 1-427 LD | Large ribosomal subunit protein uL18 | RL5_HUMAN 1-297 LE | Large ribosomal subunit protein eL6 | RL6_HUMAN 1-288 LF | 60S ribosomal protein L7 | RL7_HUMAN 1-248 LG | Large ribosomal subunit protein eL8 | RL7A_HUMAN 1-266 LH | Large ribosomal subunit protein uL6 | RL9_HUMAN 1-192 LI | Ribosomal protein uL16-like | RL10L_HUMAN 1-214 LJ | Large ribosomal subunit protein uL5 | RL11_HUMAN 1-178 LL | Large ribosomal subunit protein eL13 | RL13_HUMAN 1-211 LM | Large ribosomal subunit protein eL14 | RL14_HUMAN 1-215 LN | Large ribosomal subunit protein eL15 | RL15_HUMAN 1-204 LO | Large ribosomal subunit protein uL13 | RL13A_HUMAN 1-203 LP | Large ribosomal subunit protein uL22 | RL17_HUMAN 1-184 LQ | Large ribosomal subunit protein eL18 | RL18_HUMAN 1-188 LR | Large ribosomal subunit protein eL19 | RL19_HUMAN 1-196 LS | Large ribosomal subunit protein eL20 | RL18A_HUMAN 1-176 LT | Large ribosomal subunit protein eL21 | RL21_HUMAN 1-160 LU | Large ribosomal subunit protein eL22 | RL22_HUMAN 1-128 LV | Large ribosomal subunit protein uL14 | RL23_HUMAN 1-140 LW | Large ribosomal subunit protein eL24 | RL24_HUMAN 1-157 LX | Large ribosomal subunit protein uL23 | RL23A_HUMAN 1-156 LY | Large ribosomal subunit protein uL24 | RL26_HUMAN 1-145 LZ | Large ribosomal subunit protein eL27 | RL27_HUMAN 1-136 La | 60S ribosomal protein L27a | RL27A_HUMAN 1-148 Lb | 60S ribosomal protein L29 | RL29_HUMAN 1-159 Lc | Large ribosomal subunit protein eL30 | RL30_HUMAN 1-115 Ld | Large ribosomal subunit protein eL31 | RL31_HUMAN 1-125 Le | Large ribosomal subunit protein eL32 | RL32_HUMAN 1-135 Lf | Large ribosomal subunit protein eL33 | RL35A_HUMAN 1-110 Lg | Large ribosomal subunit protein eL34 | RL34_HUMAN 1-117 Lh | Large ribosomal subunit protein uL29 | RL35_HUMAN 1-123 Li | Large ribosomal subunit protein eL36 | RL36_HUMAN 1-105 Lj | Large ribosomal subunit protein eL37 | RL37_HUMAN 1-97 Lk | Large ribosomal subunit protein eL38 | RL38_HUMAN 1-70 Ll | Large ribosomal subunit protein eL39 | RL39_HUMAN 1-51 Lm | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN 1-128 Ln | Small ribosomal subunit protein eS32 | RS32_HUMAN 1-25 Lo | Large ribosomal subunit protein eL42 | RL36A_HUMAN 1-106 Lp | Large ribosomal subunit protein eL43 | RL37A_HUMAN 1-92 Lr | 60S ribosomal protein L28 | RL28_HUMAN 1-137 Ls | 60S acidic ribosomal protein P0 | RLA0_HUMAN 1-317 Lt | 60S ribosomal protein L12 | RL12_HUMAN 1-165 Lz | 60S ribosomal protein L10a | RL10A_HUMAN 1-217 M2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 | DAD1_HUMAN 1-113 N | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 | KTAP2_HUMAN 1-136 N2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit | OST48_HUMAN 1-456 O2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | RPN1_HUMAN 1-607 P2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 | RPN2_HUMAN 1-631 u3 | tRNA | v3 | tRNA | y3 | Endoplasmin | ENPL_HUMAN 1-302 Non-standard residues in 9n9j #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) ELU — phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine; 2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE) ZN — zinc ion > volume #1 level 0.02028 > volume #1 level 0.01582 > show #2 ribbons > hide #2 > select #1 3 models selected > transparency sel 50 > transparency sel 80 > ~select Nothing selected > ui tool show ""Side View"" > select #1 4 models selected > transparency sel 40 > transparency sel 20 > hide #1 > select /LC:69 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 1053 atoms, 1067 bonds, 68 residues, 1 model selected > select up 6031 atoms, 6085 bonds, 368 residues, 1 model selected > select down 1053 atoms, 1067 bonds, 68 residues, 1 model selected > select down 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 1053 atoms, 1067 bonds, 68 residues, 1 model selected > select up 6031 atoms, 6085 bonds, 368 residues, 1 model selected > select down 1053 atoms, 1067 bonds, 68 residues, 1 model selected > select up 6031 atoms, 6085 bonds, 368 residues, 1 model selected > select down 1053 atoms, 1067 bonds, 68 residues, 1 model selected > select up 6031 atoms, 6085 bonds, 368 residues, 1 model selected > select /y3:208 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 142 atoms, 141 bonds, 9 residues, 1 model selected > select up 1413 atoms, 1430 bonds, 89 residues, 1 model selected > invert sel Unknown command: invert sel > select invert Expected an objects specifier or a keyword > select ~sel 324694 atoms, 336815 bonds, 4350 pseudobonds, 16062 residues, 7 models selected > hide sel ribbons > select 326107 atoms, 338245 bonds, 4352 pseudobonds, 16151 residues, 7 models selected Desktop color scheme is dark Desktop color scheme is light ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.dev202511122144 (2025-11-12) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2H3B/A Chip: Apple M4 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 13822.41.1 OS Loader Version: 13822.41.1 Software: System Software Overview: System Version: macOS 26.1 (25B78) Kernel Version: Darwin 25.1.0 Time since boot: 4 days, 16 hours, 8 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: DELL U2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.11.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.11.0 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0.3 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.1 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.dev202511122144 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.2 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.2.6 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.48.4 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.0 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.11.3 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.17 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.60.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.4 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.1 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.20 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals-py: 3.1.0 rpds-py: 0.28.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 sniffio: 1.3.1 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.0.3 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.2 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.2 urllib3: 2.5.0 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX