id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18663 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-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 0x00000004041bf000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 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 0x0000000327c83000 (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 0x0000000326c77000 (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 0x0000000325c6b000 (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 0x0000000324c5f000 (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 0x0000000323c53000 (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 0x0000000322c47000 (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 0x0000000321c3b000 (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 0x0000000315b0f000 (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 0x0000000314b03000 (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 0x0000000313af7000 (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 0x0000000312aeb000 (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 0x00000002022720c0 (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.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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.mlp._mlp (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2025-08-29 14:01:28.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""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 15.6.1 (24G90)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""9E941E2F-646B-4A59-816F-BB7EB4732C87""} { ""uptime"" : 170000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,12"", ""coalitionID"" : 1161, ""osVersion"" : { ""train"" : ""macOS 15.6.1"", ""build"" : ""24G90"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-08-29 14:00:57.4761 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""9E941E2F-646B-4A59-816F-BB7EB4732C87"", ""pid"" : 1387, ""translated"" : false, ""cpuType"" : 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""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=5.1G written=149.4M(3%) resident=3084K(0%) swapped_out=146.4M(3%) unallocated=5.0G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 768K 6 \nActivity Tracing 256K 1 \nCG backing stores 2304K 1 \nCG image 1152K 52 \nColorSync 624K 33 \nCoreAnimation 2144K 128 \nCoreGraphics 208K 13 \nCoreUI image data 5728K 58 \nFoundation 32K 2 \nKernel Alloc Once 1456K 5 \nMALLOC 4.3G 130 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 57.0M 61 \nStack 368.1M 61 \nVM_ALLOCATE 366.8M 275 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 5515K 694 \n__AUTH_CONST 77.3M 941 \n__CTF 824 1 \n__DATA 34.3M 1091 \n__DATA_CONST 37.0M 1107 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 648.7M 160 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1116 \n__TEXT (graphics) 8192K 11 \n__TPRO_CONST 128K 2 \ndyld private memory 2336K 20 \nmapped file 286.5M 67 \npage table in kernel 3084K 1 \nshared memory 3200K 24 \n=========== ======= ======= \nTOTAL 7.6G 6433 \nTOTAL, minus reserved VM space 7.5G 6433 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4d42cb9bb44b74b54a19c40cb043acbe707ae991"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : { }, ""deploymentId"" : 240000013 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kosipik/Desktop/working.cxs format session Opened cryosparc_P117_J1678_006_volume_map.mrc as #1, grid size 350,350,350, pixel 0.851, shown at level 0.05, step 1, values float32 > set bgColor #ffffff00 opened ChimeraX session > open /Users/kosipik/Downloads/cryosparc_P117_J2018_006_volume_map.mrc Opened cryosparc_P117_J2018_006_volume_map.mrc as #3, grid size 416,416,416, pixel 0.851, shown at level 0.00694, step 2, values float32 > volume #3 step 1 > volume #3 level 0.02014 > volume #3 level 0.06304 > show #!1 models > tile 3 models tiled > fitmap #2 inMap #3 search 20 Found 18 unique fits from 20 random placements having fraction of points inside contour >= 0.100 (18 of 20). Average map values and times found: 0.1289 (1), 0.05663 (1), 0.05473 (1), 0.03555 (1), 0.03492 (1), 0.03341 (1), 0.03301 (1), 0.03153 (1), 0.03112 (1), 0.0263 (1), 0.02612 (1), 0.02416 (1), 0.02375 (1), 0.02252 (1), 0.02194 (1), 0.02169 (1), 0.01708 (1), 0.01589 (1) Best fit found: Fit molecule coot-1-6-coot-21.pdb (#2) to map cryosparc_P117_J2018_006_volume_map.mrc (#3) using 8412 atoms average map value = 0.1289, steps = 656 shifted from previous position = 46.1 rotated from previous position = 83.6 degrees atoms outside contour = 2169, contour level = 0.063037 Position of coot-1-6-coot-21.pdb (#2) relative to cryosparc_P117_J2018_006_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.99511406 0.00673306 -0.09850226 339.64673899 -0.02957252 -0.97219423 0.23230135 290.63253338 -0.09419926 0.23407934 0.96764324 3.18002672 Axis 0.04857502 -0.11755909 -0.99187717 Axis point 171.23069563 143.55628498 0.00000000 Rotation angle (degrees) 178.95134565 Shift along axis -20.82234663 Found 18 fits. Populating font family aliases took 88 ms. Replace uses of missing font family ""Courier"" with one that exists to avoid this cost. > fitmap #2 inMap #1 search 20 Found 15 unique fits from 20 random placements having fraction of points inside contour >= 0.100 (16 of 20). Average map values and times found: 0.06996 (2), 0.02938 (1), 0.0201 (1), 0.01759 (1), 0.01744 (1), 0.01697 (1), 0.01655 (1), 0.01652 (1), 0.01643 (1), 0.01521 (1), 0.01422 (1), 0.01304 (1), 0.01247 (1), 0.01221 (1), 0.0102 (1) Best fit found: Fit molecule coot-1-6-coot-21.pdb (#2) to map cryosparc_P117_J1678_006_volume_map.mrc (#1) using 8412 atoms average map value = 0.06996, steps = 604 shifted from previous position = 46.1 rotated from previous position = 72.4 degrees atoms outside contour = 3058, contour level = 0.049956 Position of coot-1-6-coot-21.pdb (#2) relative to cryosparc_P117_J1678_006_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99999926 0.00090724 0.00085519 -0.27216066 -0.00090691 0.99999951 -0.00042200 0.19916832 -0.00085562 0.00042126 0.99999955 0.06469603 Axis 0.32034982 0.64992470 -0.68918349 Axis point 221.12033416 299.34956771 0.00000000 Rotation angle (degrees) 0.07541030 Shift along axis -0.00232964 Found 15 fits. > fitmap #2 inMap #1 search 20 Found 15 unique fits from 20 random placements having fraction of points inside contour >= 0.100 (16 of 20). Average map values and times found: 0.06996 (2), 0.02938 (1), 0.0201 (1), 0.01759 (1), 0.01744 (1), 0.01697 (1), 0.01655 (1), 0.01652 (1), 0.01643 (1), 0.01521 (1), 0.01422 (1), 0.01304 (1), 0.01248 (1), 0.01221 (1), 0.0102 (1) Best fit found: Fit molecule coot-1-6-coot-21.pdb (#2) to map cryosparc_P117_J1678_006_volume_map.mrc (#1) using 8412 atoms average map value = 0.06996, steps = 604 shifted from previous position = 46.1 rotated from previous position = 72.4 degrees atoms outside contour = 3058, contour level = 0.049956 Position of coot-1-6-coot-21.pdb (#2) relative to cryosparc_P117_J1678_006_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99999927 0.00090736 0.00085591 -0.27226593 -0.00090701 0.99999946 -0.00042141 0.19909599 -0.00085626 0.00042062 0.99999957 0.06489530 Axis 0.31980335 0.65028283 -0.68909945 Axis point 221.00883937 299.43280649 0.00000000 Rotation angle (degrees) 0.07542880 Shift along axis -0.00232217 Found 15 fits. > tile 3 models tiled > select add #3 2 models selected > select subtract #3 Nothing selected > select add #1 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.97681,0.054311,-0.2071,26.178,-0.087026,0.9845,-0.15229,38.076,0.19562,0.16678,0.96639,-49.399 > ui mousemode right translate > select subtract #1 Nothing selected > tile 3 models tiled > hide #!2 models > tile 2 models tiled > volume #3 level 0.05974 > volume #3 level 0.06 > volume #1 level 0.06 > volume #1 level 0.03492 > transparency 0 > transparency 50 > lighting full > lighting shadows false > graphics silhouettes true > lighting shadows true > graphics silhouettes false > lighting full > lighting flat > lighting full > lighting soft > lighting simple > graphics silhouettes false > set bgColor black > set bgColor transparent > volume #3 level 0.0204 > volume #3 level 0.0468 > show #!2 models > hide #!2 models > show #!2 models > volume #3 level 0.07815 > volume #3 level 0.1095 > open /Users/kosipik/Downloads/cryosparc_P117_J2028_006_volume_map.mrc Opened cryosparc_P117_J2028_006_volume_map.mrc as #4, grid size 416,416,416, pixel 0.851, shown at level 0.00666, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 step 1 > volume #4 level 0.07272 > volume #4 level 0.07594 > volume #4 level 0.07916 > volume #4 level 0.08239 > volume #4 level 0.08561 > volume #4 level 0.08722 > volume #4 level 0.08883 > volume #4 level 0.09044 > volume #4 level 0.09205 > volume #4 level 0.09528 > volume #4 level 0.09366 > volume #4 level 0.09205 > volume #4 level 0.09044 > volume #4 level 0.08883 > volume #4 level 0.07755 > volume #4 level 0.05661 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 level 0.05016 > tile 2 models tiled > transparency #3.1#4.1 0 > transparency #3.1#4.1 50 > ui mousemode right ""rotate selected models"" > hide #!2 models > select add #4 2 models selected > view matrix models > #4,-0.99157,0.096527,0.086434,224.48,0.11981,0.93704,0.32802,-93.822,-0.049329,0.33561,-0.94071,539.05 > view matrix models > #4,-0.99777,-0.058948,-0.031404,274.35,-0.062941,0.98717,0.14674,-38.908,0.022351,0.14838,-0.98868,568.69 > select subtract #4 Nothing selected > ui mousemode right translate > volume flip #4 Opened cryosparc_P117_J2028_006_volume_map.mrc z flip as #5, grid size 416,416,416, pixel 0.851, shown at step 1, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #4 > volume #5 level 0.07111 > tile 2 models tiled > show #!1 models > tile 3 models tiled > volume #3 level 0.05505 > open /Users/kosipik/Downloads/cryosparc_P117_J2031_class_01_00162_volume.mrc Opened cryosparc_P117_J2031_class_01_00162_volume.mrc as #4, grid size 128,128,128, pixel 2.66, shown at level 0.054, step 1, values float32 > hide #!1 models > hide #!3 models > hide #!5 models > volume #4 level 0.1773 > volume #4 level 0.1332 > hide #!4 models > show #!5 models > volume #5 level 0.06447 > hide #!5 models > show #!3 models > show #!5 models > show #!2 models > hide #!2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!3 models > show #!2 models > hide #!2 models > volume #3 level 0.1213 > volume #3 level 0.05675 > show #!2 models > select #2/C 122 atoms, 122 bonds, 15 residues, 1 model selected > show sel atoms > volume #3 level 0.04486 > volume #3 level 0.05505 > volume #3 level 0.08223 > volume #3 level 0.1468 > open /Users/kosipik/Downloads/cryosparc_P117_J2041_007_volume_map.mrc Opened cryosparc_P117_J2041_007_volume_map.mrc as #6, grid size 416,416,416, pixel 0.851, shown at level 0.00745, step 2, values float32 > volume #6 step 1 > volume #6 level 0.04884 > volume #6 level 0.1216 > volume #6 level 0.05009 > open /Users/kosipik/Downloads/cryosparc_P117_J2034_005_volume_map.mrc Opened cryosparc_P117_J2034_005_volume_map.mrc as #7, grid size 416,416,416, pixel 0.851, shown at level 0.00298, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #7 step 1 > volume #7 level 0.0207 > volume #7 level 0.02492 > volume #7 level 0.03758 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/kosipik/Downloads/cryosparc_P117_J2056_004_volume_map.mrc Opened cryosparc_P117_J2056_004_volume_map.mrc as #8, grid size 416,416,416, pixel 0.851, shown at level 0.00279, step 2, values float32 > open /Users/kosipik/Downloads/cryosparc_P117_J2057_004_volume_map.mrc Opened cryosparc_P117_J2057_004_volume_map.mrc as #9, grid size 416,416,416, pixel 0.851, shown at level 0.00432, step 2, values float32 > open /Users/kosipik/Downloads/cryosparc_P117_J2058_003_volume_map.mrc Opened cryosparc_P117_J2058_003_volume_map.mrc as #10, grid size 416,416,416, pixel 0.851, shown at level 0.00375, step 2, values float32 > hide #!2 models > hide #!3 models > hide #!5 models > hide #!7 models > tile 3 models tiled > volume #8 level 0.01295 > volume #9 level 0.01758 > volume #10 level 0.03066 > tile 3 models tiled The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #10 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #9 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #8 step 1 > volume #10 level 0.0492 > volume #10 level 0.03159 > volume #8 level 0.0176 > volume #9 level 0.01906 > volume #9 level 0.02569 > volume #9 level 0.03011 > open /Users/kosipik/Downloads/cryosparc_P117_J2041_007_volume_map.mrc Opened cryosparc_P117_J2041_007_volume_map.mrc as #11, grid size 416,416,416, pixel 0.851, shown at level 0.00745, step 2, values float32 > open /Users/kosipik/Downloads/cryosparc_P117_J2042_007_volume_map.mrc Opened cryosparc_P117_J2042_007_volume_map.mrc as #12, grid size 416,416,416, pixel 0.851, shown at level 0.00627, step 2, values float32 > hide #!8 models > hide #!9 models > hide #!10 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #11 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #12 step 1 > tile 2 models tiled > volume #11 level 0.02124 > volume #12 level 0.01471 > volume #12 level 0.02502 > tile 2 models tiled > volume #12 level 0.04002 > volume #11 level 0.04758 > volume #12 level 0.05314 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #12 > volume #11 level 0.05386 > volume #11 level 0.08271 > volume #11 level 0.07643 > volume #11 level 0.0526 > open /Users/kosipik/Downloads/cryosparc_P117_J2053_008_volume_map.mrc Opened cryosparc_P117_J2053_008_volume_map.mrc as #12, grid size 350,350,350, pixel 0.851, shown at level 0.00938, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #12 step 1 > volume #11 level 0.07392 > volume #12 level 0.08006 > volume #12 level 0.04586 > volume #12 color #ff9300 > volume #12 level 0.1029 > open /Users/kosipik/Downloads/cryosparc_P117_J2158_003_volume_map.mrc Opened cryosparc_P117_J2158_003_volume_map.mrc as #13, grid size 100,100,100, pixel 3.4, shown at level 0.00486, step 1, values float32 > volume #13 level 0.3665 > volume #13 level 0.1712 > hide #!13 models > show #!2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #2/B:61 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select down 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 89 atoms, 92 bonds, 10 residues, 1 model selected > select up 3811 atoms, 3898 bonds, 469 residues, 1 model selected > select down 89 atoms, 92 bonds, 10 residues, 1 model selected > select up 3811 atoms, 3898 bonds, 469 residues, 1 model selected > show sel atoms > mlp sel Map values for surface ""coot-1-6-coot-21.pdb_B SES surface"": minimum -30.33, mean -4.233, maximum 23.82 To also show corresponding color key, enter the above mlp command and add key true > select down 89 atoms, 92 bonds, 10 residues, 2 models selected > select down 14 atoms, 15 bonds, 1 residue, 2 models selected > hide sel surfaces > select up 89 atoms, 92 bonds, 10 residues, 2 models selected > select up 3811 atoms, 3898 bonds, 469 residues, 2 models selected > hide sel surfaces > color sel byhetero > select clear > select #2/B:61 14 atoms, 15 bonds, 1 residue, 1 model selected > view sel > select #2/B:1 Nothing selected > ui tool show ""Side View"" > show #!7 models > select #2/B 3811 atoms, 3898 bonds, 469 residues, 1 model selected > select clear > fitmap #2 inMap #7 search 20 Found 19 unique fits from 20 random placements having fraction of points inside contour >= 0.100 (19 of 20). Average map values and times found: 0.01851 (1), 0.01851 (1), 0.01824 (1), 0.01822 (1), 0.01801 (1), 0.01657 (1), 0.01624 (1), 0.01475 (1), 0.01438 (1), 0.01331 (1), 0.01125 (1), 0.0105 (1), 0.01032 (1), 0.008612 (1), 0.008313 (1), 0.008234 (1), 0.008012 (1), 0.007515 (1), 0.006677 (1) Best fit found: Fit molecule coot-1-6-coot-21.pdb (#2) to map cryosparc_P117_J2034_005_volume_map.mrc (#7) using 8412 atoms average map value = 0.01851, steps = 348 shifted from previous position = 17.6 rotated from previous position = 34.2 degrees atoms outside contour = 6593, contour level = 0.037576 Position of coot-1-6-coot-21.pdb (#2) relative to cryosparc_P117_J2034_005_volume_map.mrc (#7) coordinates: Matrix rotation and translation -0.19473748 0.89488230 -0.40157561 123.53206348 -0.98060749 -0.16841839 0.10022115 319.06443431 0.02205342 0.41330472 0.91032563 -37.04496212 Axis 0.16071542 -0.21746180 -0.96274655 Axis point 189.03504971 111.84345660 0.00000000 Rotation angle (degrees) 103.08610644 Shift along axis -13.86591046 Found 19 fits. > fitmap #2 inMap #7 search 20 Found 20 unique fits from 20 random placements having fraction of points inside contour >= 0.100 (20 of 20). Average map values and times found: 0.03729 (1), 0.02466 (1), 0.02235 (1), 0.02169 (1), 0.01886 (1), 0.01881 (1), 0.01869 (1), 0.01828 (1), 0.01817 (1), 0.01708 (1), 0.01622 (1), 0.0159 (1), 0.01537 (1), 0.0146 (1), 0.01397 (1), 0.01008 (1), 0.009435 (1), 0.008637 (1), 0.008158 (1), 0.007754 (1) Best fit found: Fit molecule coot-1-6-coot-21.pdb (#2) to map cryosparc_P117_J2034_005_volume_map.mrc (#7) using 8412 atoms average map value = 0.03729, steps = 544 shifted from previous position = 13.6 rotated from previous position = 79.5 degrees atoms outside contour = 4824, contour level = 0.037576 Position of coot-1-6-coot-21.pdb (#2) relative to cryosparc_P117_J2034_005_volume_map.mrc (#7) coordinates: Matrix rotation and translation 0.94595639 0.32359291 0.02130649 -13.31021491 0.32364970 -0.94617671 0.00082209 268.76297489 0.02042564 0.00611817 -0.99977275 313.20005442 Axis 0.98639405 0.16405762 0.01057689 Axis point 0.00000000 135.27551408 156.85042872 Rotation angle (degrees) 179.84618560 Shift along axis 34.27617964 Found 20 fits. > volume flip #7 Opened cryosparc_P117_J2034_005_volume_map.mrc z flip as #14, grid size 416,416,416, pixel 0.851, shown at step 1, values float32 > fitmap #2 inMap #14 search 20 Found 20 unique fits from 20 random placements having fraction of points inside contour >= 0.100 (20 of 20). Average map values and times found: 0.02666 (1), 0.02073 (1), 0.02034 (1), 0.01962 (1), 0.01958 (1), 0.01949 (1), 0.01889 (1), 0.01787 (1), 0.01752 (1), 0.01654 (1), 0.01528 (1), 0.01216 (1), 0.01012 (1), 0.009728 (1), 0.00934 (1), 0.009324 (1), 0.0089 (1), 0.008884 (1), 0.008663 (1), 0.006932 (1) Best fit found: Fit molecule coot-1-6-coot-21.pdb (#2) to map cryosparc_P117_J2034_005_volume_map.mrc z flip (#14) using 8412 atoms average map value = 0.02666, steps = 480 shifted from previous position = 42.3 rotated from previous position = 53.2 degrees atoms outside contour = 5721, contour level = 0.037576 Position of coot-1-6-coot-21.pdb (#2) relative to cryosparc_P117_J2034_005_volume_map.mrc z flip (#14) coordinates: Matrix rotation and translation 0.97563713 0.00866155 -0.21921922 65.14743647 0.08624634 -0.93391346 0.34694005 255.86527913 -0.20172673 -0.35739450 -0.91190775 408.07527573 Axis -0.99368505 -0.02467866 0.10945770 Axis point 0.00000000 164.99604562 184.10642830 Rotation angle (degrees) 159.24300006 Shift along axis -26.38346541 Found 20 fits. ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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 Air Model Identifier: Mac15,12 Model Number: MRXN3D/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 3 days, 14 hours, 42 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Thunderbolt Display: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes 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 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 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 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 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 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 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 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 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