id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17174 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000700028c8d000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700027c8a000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700026c87000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700025c84000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700024c81000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700023c7e000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700022c7b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700021c78000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700020c75000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001fc72000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001ec6f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001dc6c000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001cc69000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001bc66000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001ac63000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700019c60000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700018c5d000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700017c5a000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700016c57000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff8481e7b00 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PIL._webp (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-24 14:09:29.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""03FAF53B-157D-4242-84D7-56F7A490C0A3""} { ""uptime"" : 250000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 1003, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-24 14:08:52.5349 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""03FAF53B-157D-4242-84D7-56F7A490C0A3"", ""pid"" : 34762, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-24 09:43:10.9461 +0100"", ""procStartAbsTime"" : 241693401052098, ""procExitAbsTime"" : 255450736333536, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""C4027B15-248B-5659-BACC-6FB29543A4B7"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8D528D7E-5C72-169F-357F-E09EC31F9564"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bootSessionUUID"" : ""ECAC3F3E-CD7E-4414-A068-42C10232CC05"", ""wakeTime"" : 39, ""bridgeVersion"" : {""build"":""22P3060"",""train"":""9.3""}, ""sleepWakeUUID"" : ""DB7CFAF6-970D-4FED-ADE4-16B7E49EF866"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. Bytes before following region: 4507873280\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10cb0b000-10cb0f000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.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"":34762}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0 is not in any region. Bytes before following region: 4507873280\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10cb0b000-10cb0f000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""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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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.09, step 1, values float32 opened ChimeraX session > volume #4 level 0.08 > hide #13/J,L atoms > hide #13/K:6-46 atoms > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_zoom_out.tif"" width 1984 height > 1210 supersample 3 > lighting soft > lighting simple > lighting soft > lighting simple > lighting full > lighting simple > lighting full > lighting simple > lighting full > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > volume #4 level 0.06 > show #13/A:83,85 atoms > show #13/K:39-40 atoms > show #13/L:6-7 atoms > select clear > show #13/L,J #13/K:7-46 atoms > color #13/L light gray > color #13/K dim gray > color #13/J dark red > color #13/I rebecca purple > color #13/B forest green > color #13/C,D,E,F,G,H khaki > color #13/A steel blue > color #13/A:232-350 dark turquoise > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoom_out.tif"" width 1984 height > 1210 supersample 3 > color #13/A. byhet Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #13/A byhetero > ui tool show ""Side View"" > hide #13/K:7-46 #13/L cartoons > hide #13/K:7-46 #13/L atoms > show #13/K:39-40 #13/L:6-7 atoms > ui tool show Distances > show #!11 models Exactly two atoms must be selected! > hide #!4 models > show #13/K:39-41 #13/L:6-7 atoms > select #13/A:83@OD1 1 atom, 1 residue, 1 model selected > select add #13/K:40@N2 2 atoms, 2 residues, 1 model selected > distance #13/A:83@OD1 #13/K:40@N2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1 and /K DG 40 N2: 3.013Å > distance style color black > ui tool show ""Color Actions"" > distance style color dimgrey > select #13/A:85@NZ 1 atom, 1 residue, 1 model selected > select add #13/K:41@O2 2 atoms, 2 residues, 1 model selected > distance #13/A:85@NZ #13/K:41@O2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ and /K DC 41 O2: 3.020Å > select #13/A:85@NZ 1 atom, 1 residue, 1 model selected > select add #13/L:6@N2 2 atoms, 2 residues, 1 model selected > distance #13/A:85@NZ #13/L:6@N2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ and /L DG 6 N2: 3.258Å > select #13/A:83@OD1 1 atom, 1 residue, 1 model selected > select add #13/A:85@NZ 2 atoms, 2 residues, 1 model selected > distance #13/A:83@OD1 #13/A:85@NZ Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1 and LYS 85 NZ: 2.939Å > select add #11 2 atoms, 12 pseudobonds, 2 residues, 3 models selected > color sel dim gray > select clear > select add #13/A:85 9 atoms, 9 bonds, 1 residue, 1 model selected > select add #13/A:83 17 atoms, 15 bonds, 2 residues, 1 model selected > color sel steel blue > color sel byhetero > color sel dim gray > select clear > show #!4 models > volume #4 level 0.08 > volume #4 level 0.07 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif"" width 1984 height > 1210 supersample 3 > hide #!4 models > hide #13/K:39 atoms > show #!4 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif"" width 1984 height > 1210 supersample 3 > show #11.1 models > distance style decimalPlaces 1 > hide #11.1 models > view #13/L > volume #4 level 0.06 > show #13/k,l cartoons > show #13/k:7-46 #13/l atoms > hide #!4 models > select #13/A:178 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #13/A:193 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > hide #!11 models > hide #13/A:83,85 atoms > select clear > surface dust #4 size 7.25 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif"" width > 1984 height 1210 supersample 3 > show #13/A:191 atoms > select #13/A:193@OD1 1 atom, 1 residue, 1 model selected > select add #13/L:9@N2 2 atoms, 2 residues, 1 model selected > distance #13/A:193@OD1 #13/L:9@N2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASN 193 OD1 and /L DG 9 N2: 2.6Å > show #!11 models > select #13/K:39 19 atoms, 20 bonds, 1 residue, 1 model selected > hide sel cartoons > hide #!4 models > select #13/K:39@OP1 1 atom, 1 residue, 1 model selected > select add #13/A:191@OG 2 atoms, 2 residues, 1 model selected > distance #13/K:39@OP1 #13/A:191@OG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DC 39 OP1 and /A SER 191 OG: 2.9Å > show sel cartoons > show #!4 models > color sel dim gray > select clear > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif"" width > 1984 height 1210 supersample 3 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!13 models > show #!13 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.09 > volume #4 level 0.05 > volume #4 level 0.06 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif"" width > 1984 height 1210 supersample 3 > hide #!4 models > show #!4 models > hide #!11 models > select #13/K:4 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #13/K:3 25 atoms, 26 bonds, 2 residues, 1 model selected > select add #13/K:2 45 atoms, 47 bonds, 3 residues, 1 model selected > select up 886 atoms, 986 bonds, 45 residues, 1 model selected > select down 45 atoms, 47 bonds, 3 residues, 1 model selected > hide #!4 models > select add #13/K:1 54 atoms, 56 bonds, 4 residues, 1 model selected > hide sel cartoons > select clear > select #13/K:3@P 1 atom, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > select up 886 atoms, 986 bonds, 45 residues, 1 model selected > select down 21 atoms, 23 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #13/K:2@O3' 22 atoms, 23 bonds, 2 residues, 1 model selected > select up 41 atoms, 45 bonds, 2 residues, 1 model selected > color sel byhetero > select clear > select #13/K:6 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #13/A:295 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #13/I:140 12 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > show #!4 models > hide #!4 models > select #13/K:6 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #13/K:7 42 atoms, 45 bonds, 2 residues, 1 model selected > hide sel cartoons > show #!4 models > volume #4 level 0.09 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 22 atoms, 24 bonds, 1 residue, 1 model selected > hide #!4 models > select subtract #13/K:6@O3' 21 atoms, 23 bonds, 1 residue, 1 model selected > hide sel atoms > show #!4 models > hide #!4 models > select #13/K:7@OP1 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel cartoons > select #13/K:6@O3' 1 atom, 1 residue, 1 model selected > hide sel atoms > show #!4 models > hide #!4 models > select #13/I:50 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #13/I:51 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > show #!4 models > volume #4 level 0.06 > volume #4 level 0.08 > select #13/I:51@CD 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 11 atoms, 9 bonds, 2 residues, 1 model selected > select up 18 atoms, 17 bonds, 2 residues, 1 model selected > hide sel atoms > select clear > volume #4 level 0.1 > color #13/i byhetero > select clear > select #13/K:7 20 atoms, 21 bonds, 1 residue, 1 model selected > volume #4 level 0.07 > select clear > volume #4 level 0.09 > show #!2 models > hide #!2 models > hide #!4 models > select #13/A:295@SG 1 atom, 1 residue, 1 model selected > select add #13/I:140@SG 2 atoms, 2 residues, 1 model selected > distance #13/A:295@SG #13/I:140@SG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A CYS 295 SG and /I CYS 140 SG: 3.9Å > show #!11 models > color sel dim gray > select clear > hide #13/A:230-350 atoms > hide #13/o atoms > select #13/A:295 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!4 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/cas8_cas6_cys_pair_0p09.tif"" width > 1984 height 1210 supersample 3 > hide #!4 models > show #11.1 models > hide #11.1 models > show #!2 models > select #2/E:706@CG 1 atom, 1 residue, 1 model selected > hide sel atoms > select #2/E:706@CD 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #2/E:706@CG 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/E:707@CD1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #13/I:140@SG 1 atom, 1 residue, 1 model selected > select add #13/A:295@SG 2 atoms, 2 residues, 1 model selected > select up 12 atoms, 10 bonds, 2 residues, 1 model selected > hide sel atoms > select clear > show #13/A:305,304,280,328 > select #2/E:718 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #13/A:319 16 atoms, 14 bonds, 2 residues, 2 models selected > show sel atoms > show #13/O > select clear > hide #!11 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj_2.tif"" width 1984 > height 1210 supersample 3 > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/chimera_session.cxs"" > hide #!2 models > hide #!13 models ===== Log before crash end ===== OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0) OS Loader Version: 582~3311 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 7 days, 53 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Thunderbolt Display: Display Type: LCD Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: C02QM2AXF2GC Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 biopython: 1.84 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 DiffFit: 0.2 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 fsspec: 2024.6.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 joblib: 1.4.2 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.1 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scikit-learn: 1.5.1 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.13.0 tables: 3.8.0 tcia-utils: 1.5.1 threadpoolctl: 3.5.0 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.2.2 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX