id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20302 Crash in swap_buffers when status line exposed Mac Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x0000000306043000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 948 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017f99b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017e98f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017d983000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017c977000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017b96b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017a95f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000179953000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000001f05ef100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.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-1.11.1.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, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, PIL._imaging, 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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 54) {""app_name"":""ChimeraX"",""timestamp"":""2026-05-11 11:05:13.00 -0400"",""app_version"":""1.11.1"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.3.1 (25D2128)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""BC0019A5-CD75-4BAF-A008-734E1EE042AB""} { ""uptime"" : 2100000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac16,10"", ""coalitionID"" : 205024, ""osVersion"" : { ""train"" : ""macOS 26.3.1"", ""build"" : ""25D2128"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-05-11 11:05:01.8943 -0400"", ""codeSigningMonitor"" : 2, ""incident"" : ""BC0019A5-CD75-4BAF-A008-734E1EE042AB"", ""pid"" : 34348, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procLaunch"" : ""2026-05-10 12:55:15.9415 -0400"", ""procStartAbsTime"" : 50405781391898, ""procExitAbsTime"" : 51036127057896, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.1"",""CFBundleVersion"":""1.11.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""C80F9357-4296-5CBE-996A-5F12375F901E"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""869C4393-65A3-C33E-929F-AE7C6A88BE41"", ""appleIntelligenceStatus"" : {""state"":""available""}, ""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"" : ""6006EEEA-D740-4BCE-8F84-3596A269DBAF"", ""wakeTime"" : 27, ""sleepWakeUUID"" : ""77550541-A12F-460B-8300-5259D28886E3"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x700002ec0 is in 0x468000000-0x728c00000; bytes after start: 11140083392 bytes before end: 683659583 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL MALLOC_LARGE 462c00000-463078000 [ 4576K] rw-\/rwx SM=PRV GAP OF 0x4f88000 BYTES ---> commpage (reserved) 468000000-728c00000 [ 11.0G] ---\/--- SM=NUL reserved VM address space (unallocated) MALLOC_SMALL 728c00000-729000000 [ 4096K] rw-\/rwx SM=PRV "", ""exception"" : {""codes"":""0x0000000000000002, 0x0000000700002ec0"",""rawCodes"":[2,30064783040],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGBUS"",""subtype"":""KERN_PROTECTION_FAILURE at 0x0000000700002ec0""}, ""termination"" : {""flags"":0,""code"":10,""namespace"":""SIGNAL"",""indicator"":""Bus error: 10"",""byProc"":""ChimeraX"",""byPid"":34348}, ""vmregioninfo"" : ""0x700002ec0 is in 0x468000000-0x728c00000; bytes after start: 11140083392 bytes before end: 683659583 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL MALLOC_LARGE 462c00000-463078000 [ 4576K] rw-\/rwx SM=PRV GAP OF 0x4f88000 BYTES ---> commpage (reserved) 468000000-728c00000 [ 11.0G] ---\/--- SM=NUL reserved VM address space (unallocated) MALLOC_SMALL 728c00000-729000000 [ 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"" : [{ ""threadState"":{""x"":[{""value"":0},{""value"":0},{""value"":1},{""value"":31818824344},{""value"":99},{""value"":97},{""value"":0},{""value"":0},{""value"":17362740248728773849},{""value"":17362740242549167577},{""value"":14757395258967641293},{""value"":4294967286},{""value"":31818824274},{""value"":0},{""value"":53},{""value"":4294967280},{""value"":328},{""value"":8350535616},{""value"":0},{""value"":10},{""value"":259},{""value"":8327721440 ,""symbolLocation"":224,""symbol"": ""_main_thread""},{""value"":0},{""value"":1},{""value"":4368500280 ,""symbolLocation"":0,""symbol"": ""faulthandler_handlers""},{""value"":1},{""value"":4349399272},{""value"":4365187896 ,""symbolLocation"":0,""symbol"": 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model panel to edit those fields UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9gbc fromDatabase pdb format mmcif Summary of feedback from opening 9gbc fetched from pdb --- note | Fetching compressed mmCIF 9gbc from http://files.rcsb.org/download/9gbc.cif 9gbc title: Bacteroides thetaiotaomicron siderophore transporter XusA in complex with surface-exposed lipoprotein XusB [more info...] Chain information for 9gbc #1 --- Chain | Description | UniProt A | TonB-linked outer membrane receptor | Q8A621_BACTN 1-796 B | DUF4374 domain-containing protein | Q8A622_BACTN 1-464 > close session > open 9bgc fromDatabase pdb format mmcif Summary of feedback from opening 9bgc fetched from pdb --- notes | Fetching compressed mmCIF 9bgc from http://files.rcsb.org/download/9bgc.cif Fetching CCD A1AHB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/A1AHB/A1AHB.cif Fetching CCD GNP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 9bgc title: Tri-complex of Daraxonrasib (RMC-6236), KRAS G12R, and CypA [more info...] Chain information for 9bgc #1 --- Chain | Description | UniProt A B | GTPase KRas | RASK_HUMAN 1-169 C D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165 Non-standard residues in 9bgc #1 --- A1AHB — (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide GNP — phosphoaminophosphonic acid-guanylate ester MG — magnesium ion 9bgc mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 9 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select /B 1467 atoms, 1409 bonds, 6 pseudobonds, 251 residues, 2 models selected > hide sel cartoons > style sel ball Changed 1467 atom styles > style sel ball Changed 1467 atom styles > style sel stick Changed 1467 atom styles > hide sel atoms > select /C 1403 atoms, 1351 bonds, 252 residues, 1 model selected > hide sel cartoons > hide sel atoms > select /A:395@O 1 atom, 1 residue, 1 model selected > select clear > select /A:395@O 1 atom, 1 residue, 1 model selected > hide sel cartoons > hide sel atoms > select /A:355@O 1 atom, 1 residue, 1 model selected > hide sel atoms > select ::name=""HOH"" 418 atoms, 418 residues, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 58 atoms, 65 bonds, 1 residue, 1 model selected > view sel > set bgColor white > select clear > view > select /A 1498 atoms, 1409 bonds, 6 pseudobonds, 282 residues, 2 models selected > color (#!1 & sel) cornflower blue > select clear > surface > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 58 atoms, 65 bonds, 1 residue, 1 model selected > surface sel > color (#!1 & sel) magenta > select clear > hide #1.5 models > show #1.5 models > hide #1.4 models > show #1.4 models > hide #1.5 models > show #1.5 models > hide #1.3 models > hide #1.4 models > view > save /Users/mrdc/Documents/Structures/daraxonrasib_kras.cxs > select add #1.5 1248 atoms, 163 residues, 1 model selected > transparency (#!1 & sel) 70 > hide sel cartoons > hide sel atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 32 atoms, 34 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > lighting full > lighting soft > lighting simple > lighting full > select add #1.3 1354 atoms, 169 residues, 1 model selected > select subtract #1.3 1 model selected > select add #1.5 1248 atoms, 163 residues, 1 model selected > transparency (#!1 & sel) 60 > select clear > save /Users/mrdc/Documents/Structures/daraxonrasib_kras.cxs > lighting full > save /Users/mrdc/Documents/Structures/daraxonrasib_kras.png width 734 height > 1073 supersample 4 transparentBackground true > close session > open 6ud7 fromDatabase pdb format mmcif 6ud7 title: Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam [more info...] Chain information for 6ud7 #1 --- Chain | Description | UniProt A | DDB1- and CUL4-associated factor 15 | DCA15_HUMAN 2-600 B | DNA damage-binding protein 1,DNA damage-binding protein 1 | DDB1_HUMAN 1-395 706-1140 C | RNA-binding motif protein 39 | Q7Z3L0_HUMAN 248-328 D | DET1- and DDB1-associated protein 1 | DDA1_HUMAN 2-102 Non-standard residues in 6ud7 #1 --- EF6 — N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide (Indisulam) GOL — glycerol (glycerin; propane-1,2,3-triol) 47 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 10844 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > select /C 674 atoms, 638 bonds, 129 residues, 1 model selected > select /C,A 4279 atoms, 4127 bonds, 3 pseudobonds, 756 residues, 2 models selected > select ~sel & ##selected 7309 atoms, 6938 bonds, 3 pseudobonds, 1377 residues, 2 models selected > hide sel cartoons > hide sel atoms > select ::name=""HOH"" 744 atoms, 744 residues, 1 model selected > hide sel atoms > ~label /missing > hide #!1.1 models > hide #1.1.1 models > select /C 674 atoms, 638 bonds, 129 residues, 1 model selected > show sel surfaces > color (#!1 & sel) cornflower blue > select clear > select /A 3605 atoms, 3489 bonds, 3 pseudobonds, 627 residues, 2 models selected > show sel surfaces > select clear\ Expected an objects specifier or a keyword > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 24 atoms, 26 bonds, 1 residue, 1 model selected > show sel surfaces > color (#!1 & sel) magenta > select clear > view > select add #1.3 3376 atoms, 426 residues, 1 model selected > transparency (#!1 & sel) 60 > select /C 674 atoms, 638 bonds, 129 residues, 1 model selected > select clear > select /A 3605 atoms, 3489 bonds, 3 pseudobonds, 627 residues, 2 models selected > hide sel cartoons > hide sel atoms > select clear > save /Users/mrdc/Documents/Projects/RIPTAC/indisulam_mg.png width 734 height > 1073 supersample 4 transparentBackground true > save /Users/mrdc/Documents/Projects/RIPTAC/indisulam_mg.cxs > close session > open 7s5g fromDatabase pdb format mmcif Summary of feedback from opening 7s5g fetched from pdb --- notes | Fetching compressed mmCIF 7s5g from http://files.rcsb.org/download/7s5g.cif Fetching CCD 0A1 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/0A1/0A1.cif Fetching CCD 3WX from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/3WX/3WX.cif Fetching CCD 89N from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/89N/89N.cif Fetching CCD DAL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DAL/DAL.cif Fetching CCD FTR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/FTR/FTR.cif Fetching CCD Z9J from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/Z9J/Z9J.cif 7s5g title: PCSK9 in complex with compound 19 [more info...] Chain information for 7s5g #1 --- Chain | Description | UniProt A | Propeptide of Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN 31-152 B | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN 153-452 C | Z9J-ALA-DAL-PHE-FTR-PRO-THR-0A1-3WX | Non-standard residues in 7s5g #1 --- 89N — (2E)-but-2-ene-1,4-diol GOL — glycerol (glycerin; propane-1,2,3-triol) Z9J — 3-{[(3-{[(2-aminoethyl)sulfanyl]methyl}phenyl)methyl]sulfanyl}propanoic acid (3-[[3-(2-azanylethylsulfanylmethyl)phenyl]methylsulfanyl]propanoic acid) > ~label /missing > select ::name=""GOL"" 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select ::name=""HOH"" 126 atoms, 126 residues, 1 model selected > hide sel atoms > hide #!1.1 models > select /C 98 atoms, 101 bonds, 15 residues, 1 model selected > show sel atoms > surface sel > color (#!1 & sel) magenta > select /B 2178 atoms, 2146 bonds, 1 pseudobond, 360 residues, 2 models selected > surface (#!1 & sel) > color (#!1 & sel) cornflower blue > select /A 790 atoms, 758 bonds, 141 residues, 1 model selected > hide sel cartoons > hide sel atoms > select /C 98 atoms, 101 bonds, 15 residues, 1 model selected > hide sel atoms > select clear > hide cartoons > lighting full > view > lighting full > lighting simple > lighting soft > lighting full > save /Users/mrdc/Documents/Structures/pcsk9_7s5g.cxs > save /Users/mrdc/Documents/Structures/pcsk9_7s5g.png width 734 height 1073 > supersample 3 > close session > open 7uwi fromDatabase pdb format mmcif Summary of feedback from opening 7uwi fetched from pdb --- notes | Fetching compressed mmCIF 7uwi from http://files.rcsb.org/download/7uwi.cif Fetching CCD PO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif Fetching CCD WHL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/WHL/WHL.cif 7uwi title: Structure of beta-catenin in complex with FP01567, a Helicon Polypeptide [more info...] Chain information for 7uwi #1 --- Chain | Description | UniProt A | Catenin beta-1 | CTNB1_HUMAN 143-663 F | Helicon Polypeptide FP01567 | Non-standard residues in 7uwi #1 --- GOL — glycerol (glycerin; propane-1,2,3-triol) NH2 — amino group PO4 — phosphate ion WHL — N,N'-(1,4-phenylene)diacetamide 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3952 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > select ::name=""HOH"" 60 atoms, 60 residues, 1 model selected > hide sel atoms > select ::name=""GOL"" 36 atoms, 30 bonds, 6 residues, 1 model selected > hide sel atoms > select ::name=""PO4"" 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > select ::name=""NH2"" 1 atom, 1 residue, 1 model selected > hide sel atoms > select /A 3944 atoms, 3931 bonds, 1 pseudobond, 571 residues, 2 models selected > show sel surfaces > color (#!1 & sel) cornflower blue > select /F 124 atoms, 128 bonds, 16 residues, 1 model selected > show sel surfaces > hide sel surfaces > select /F:101@CB 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 123 atoms, 128 bonds, 15 residues, 1 model selected > show sel surfaces > hide sel surfaces > select ::name=""WHL"" 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel surfaces > select /F 124 atoms, 128 bonds, 16 residues, 1 model selected > show sel surfaces > hide sel surfaces > select /F 124 atoms, 128 bonds, 16 residues, 1 model selected > select /F,FWHL 124 atoms, 128 bonds, 16 residues, 1 model selected > show sel surfaces > color (#!1 & sel) magenta > select clear > view > ~label /missing > hide cartoons > save /Users/mrdc/Documents/Structures/bcat_7uwi.png width 734 height 1073 > supersample 4 transparentBackground true > save /Users/mrdc/Documents/Structures/bcat_7uwi.cxs > close session > open /Users/mrdc/Documents/Projects/TernaryComplex/protacModelAll.pdb Summary of feedback from opening /Users/mrdc/Documents/Projects/TernaryComplex/protacModelAll.pdb --- warnings | Ignored bad PDB record found on line 74 SITE 1 AC10 5 ILE A 100 ILE A 101 LYS A 102 THR A 103 Ignored bad PDB record found on line 75 SITE 2 AC10 5 ASN A 135 Ignored bad PDB record found on line 76 SITE 1 AC11 3 PRO A 142 VAL A 147 GLU A 151 Ignored bad PDB record found on line 77 SITE 1 AC12 5 TYR A 137 ASN A 140 LYS A 141 PRO A 142 Ignored bad PDB record found on line 78 SITE 2 AC12 5 LYS A 160 2 messages similar to the above omitted Cannot find LINK/SSBOND atom VT1 in residue SER /A:42 Chain information for protacModelAll.pdb #1 --- Chain | Description A | No description available B | No description available > select /B 6021 atoms, 6095 bonds, 1 pseudobond, 370 residues, 2 models selected > show sel surfaces > color (#!1 & sel) cornflower blue > select /A 2121 atoms, 2151 bonds, 127 residues, 1 model selected > show sel surfaces > hide sel cartoons > select /P 107 atoms, 113 bonds, 1 residue, 1 model selected > show sel surfaces > color (#!1 & sel) magenta > select clear > hide cartoons > view > lighting full > transparency 60 > select /A,B 8142 atoms, 8246 bonds, 1 pseudobond, 497 residues, 2 models selected > hide sel atoms > select clear > hide #1.2 models > hide #1.3 models > hide atoms > show #1.2 models > show #1.3 models > view > ui tool show ""Side View"" > transparency 100 > transparency 0 > select add #1.2 6021 atoms, 370 residues, 2 models selected > select add #1.3 8142 atoms, 497 residues, 4 models selected > transparency (#!1 & sel) 60 > select clear > save /Users/mrdc/Documents/Projects/RIPTAC/brd4_riptac_concept.cxs > save /Users/mrdc/Documents/Projects/RIPTAC/brd4_riptac_concept.png width 734 > height 1073 supersample 4 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 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 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: Mac mini Model Identifier: Mac16,10 Model Number: MU9D3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 Performance and 6 Efficiency) Memory: 16 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (25D2128) Kernel Version: Darwin 25.3.0 Time since boot: 51 days, 16 hours, 39 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: KDP2R6KQTD Display Firmware Version: Version 26.2 (Build 23C8051) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 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: 3.1.1 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: 1.61.4 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: 1.11.1 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: 1.7.3 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: 2.17.2 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: 2.7.12 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: 1.4.2 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: 0.3.1 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 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: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 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: 4.26.0 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: 1.10.1 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: 4.5.1 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: 2.12.5 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: 3.3.2 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: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 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: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 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: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Graphics duplicate all ChimeraX