id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17475 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x0000000324487000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032347b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003164cb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003154bf000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003144b3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003134a7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031249b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031148f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000310483000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f477000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030e46b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ec748840 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54) 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swapped_out=0K(0%) unallocated=2.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1168K 58 \nColorSync 656K 33 \nCoreAnimation 2848K 156 \nCoreGraphics 48K 3 \nCoreUI image data 5568K 51 \nFoundation 48K 2 \nKernel Alloc Once 1504K 5 \nMALLOC 1.9G 104 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 720K 45 \nStack 367.0M 46 \nStack Guard 56.0M 1 \nVM_ALLOCATE 285.0M 320 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 33.3M 1063 \n__DATA_CONST 34.1M 1080 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 637.4M 154 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1100 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 2 \nmapped file 303.0M 88 \nowned unmapped memory 85.8M 1 \npage table in kernel 1703K 1 \nshared memory 3216K 27 \n=========== ======= ======= \nTOTAL 5.1G 6312 \nTOTAL, minus reserved VM space 5.0G 6312 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""c60400b0e9e1e862b3b8b26f11939280986ec8fb"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Registration file '/Users/au746648/Library/Application Support/ChimeraX/registration' has expired 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: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8S3O Summary of feedback from opening 8S3O fetched from pdb --- notes | Fetching compressed mmCIF 8s3o from http://files.rcsb.org/download/8s3o.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif 8s3o title: Structure of native human CD109 [more info...] Chain information for 8s3o #1 --- Chain | Description | UniProt A | CD109 antigen | CD109_HUMAN 22-1420 Non-standard residues in 8s3o #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open /Users/au746648/Desktop/cryosparc_P1451_J29_class_03_00162_volume.mrc Opened cryosparc_P1451_J29_class_03_00162_volume.mrc as #2, grid size 128,128,128, pixel 2.33, shown at level 0.0434, step 1, values float32 > volume #2 level 0.04338 > volume #2 level 0.04694 > volume #2 level 0.0505 > volume #2 level 0.05406 > volume #2 level 0.05761 > volume #2 level 0.06117 > volume #2 level 0.06473 > volume #2 level 0.06829 > volume #2 level 0.07185 > volume #2 level 0.0754 > volume #2 level 0.07896 > volume #2 level 0.08252 > volume #2 level 0.08608 > volume #2 level 0.08964 > volume #2 level 0.09319 > volume #2 level 0.09675 > volume #2 level 0.1003 > volume #2 level 0.1039 > volume #2 level 0.1074 > volume #2 level 0.111 > volume #2 level 0.1145 > volume #2 level 0.111 > volume #2 level 0.1074 > volume #2 level 0.1039 > volume #2 level 0.1003 > volume #2 level 0.09675 > volume #2 level 0.09319 > volume #2 level 0.09675 > volume #2 level 0.1003 > volume #2 level 0.1039 > volume #2 level 0.1074 > volume #2 level 0.111 > volume #2 level 0.1145 > volume #2 level 0.1181 > volume #2 level 0.1217 > volume #2 level 0.1252 > volume #2 level 0.1288 > volume #2 level 0.1323 > volume #2 level 0.1359 > volume #2 level 0.1394 > volume #2 level 0.143 > volume #2 level 0.1466 > volume #2 level 0.1501 > volume #2 level 0.1537 > volume #2 level 0.1572 > volume #2 level 0.1608 > volume #2 level 0.1644 > volume #2 level 0.1679 > volume #2 level 0.1715 > volume #2 level 0.175 > volume #2 level 0.1786 > volume #2 level 0.1821 > volume #2 level 0.1857 > volume #2 level 0.1893 > volume #2 level 0.1928 > volume #2 level 0.1964 > volume #2 level 0.1999 > volume #2 level 0.2035 > volume #2 level 0.1999 > volume #2 level 0.1964 > volume #2 level 0.1928 > volume #2 level 0.1893 > volume #2 level 0.1857 > volume #2 level 0.1821 > volume #2 level 0.1786 > volume #2 level 0.175 > volume #2 level 0.1715 > volume #2 level 0.1679 > volume #2 level 0.1644 > volume #2 level 0.1608 > volume #2 level 0.1572 > volume #2 level 0.1537 > volume #2 level 0.1501 > volume #2 level 0.1466 > volume #2 level 0.143 > volume #2 level 0.1394 > volume #2 level 0.1359 > volume #2 level 0.1323 > volume #2 level 0.1288 > volume #2 level 0.1252 > volume #2 level 0.1217 > volume #2 level 0.1181 > volume #2 level 0.1145 > volume #2 level 0.111 > volume #2 level 0.1074 > volume #2 level 0.1039 > volume #2 level 0.1003 > volume #2 level 0.09675 > volume #2 level 0.09319 > volume #2 level 0.08964 > volume #2 level 0.08608 > volume #2 level 0.08252 > volume #2 level 0.07896 > volume #2 level 0.0754 > volume #2 level 0.07185 > volume #2 level 0.06829 > volume #2 level 0.06473 > volume #2 level 0.06117 > volume #2 level 0.05761 > volume #2 level 0.05406 > volume #2 level 0.0505 > volume #2 level 0.04338 > volume #2 level 0.03982 > volume #2 level 0.04338 > volume #2 level 0.04694 > volume #2 level 0.0505 > volume #2 level 0.0754 > volume #2 level 0.07896 > volume #2 level 0.08608 > volume #2 level 0.08964 > volume #2 level 0.09319 > volume #2 level 0.09675 > volume #2 level 0.1003 > volume #2 level 0.1039 > volume #2 level 0.1074 > volume #2 level 0.111 > volume #2 level 0.1145 > volume #2 level 0.1181 > volume #2 level 0.1217 > volume #2 level 0.1252 > volume #2 level 0.1288 > volume #2 level 0.1323 > volume #2 level 0.1288 > volume #2 level 0.1252 > volume #2 level 0.1217 > volume #2 level 0.1181 > volume #2 level 0.1217 > volume #2 level 0.1252 > volume #2 level 0.1217 > volume #2 level 0.1181 > volume #2 level 0.1145 > volume #2 level 0.1181 > volume #2 level 0.1217 > volume #2 level 0.1252 > volume #2 level 0.1288 > volume #2 level 0.1323 > volume #2 level 0.1359 > volume #2 level 0.1394 > volume #2 level 0.143 > volume #2 level 0.1466 > volume #2 level 0.1501 > volume #2 level 0.1537 > volume #2 level 0.1572 > volume #2 level 0.1608 > volume #2 level 0.1644 > volume #2 level 0.1679 > volume #2 level 0.1715 > volume #2 level 0.175 > volume #2 level 0.1786 > volume #2 level 0.1821 > volume #2 level 0.1857 > volume #2 level 0.1893 > volume #2 level 0.1928 > volume #2 level 0.1964 > volume #2 level 0.1999 > volume #2 level 0.2035 > volume #2 level 0.207 > volume #2 level 0.2106 > volume #2 level 0.2142 > volume #2 level 0.2177 > volume #2 level 0.2213 > volume #2 level 0.2248 > volume #2 level 0.2284 > volume #2 level 0.232 > volume #2 level 0.2391 > volume #2 level 0.2462 > volume #2 level 0.2497 > volume #2 level 0.2533 > volume #2 level 0.2569 > volume #2 level 0.2604 > volume #2 level 0.264 > volume #2 level 0.2675 > volume #2 level 0.2711 > volume #2 level 0.2747 > volume #2 level 0.2782 > volume #2 level 0.2747 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule 8s3o (#1) to map cryosparc_P1451_J29_class_03_00162_volume.mrc (#2) using 21074 atoms average map value = 0.1784, steps = 168 shifted from previous position = 29.3 rotated from previous position = 29.5 degrees atoms outside contour = 14328, contour level = 0.27465 Position of 8s3o (#1) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc (#2) coordinates: Matrix rotation and translation 0.98673194 -0.06934381 0.14680431 -22.89304410 0.13015026 0.87839106 -0.45988048 48.94802861 -0.09706173 0.47288538 0.87576163 -45.13285333 Axis 0.94741205 0.24769520 0.20262650 Axis point 0.00000000 110.36768063 87.32861469 Rotation angle (degrees) 29.48991961 Shift along axis -18.71006591 > ui tool show ""Map Filter"" > open /Users/au746648/Desktop/cryosparc_P1451_J29_class_03_00162_volume.mrc Opened cryosparc_P1451_J29_class_03_00162_volume.mrc as #3, grid size 128,128,128, pixel 2.33, shown at level 0.0434, step 1, values float32 > select add #2 2 models selected > select add #3 4 models selected > close #3 > close #2.1 > close #2 > open /Users/au746648/Desktop/cryosparc_P1451_J29_class_03_00162_volume.mrc Opened cryosparc_P1451_J29_class_03_00162_volume.mrc as #2, grid size 128,128,128, pixel 2.33, shown at level 0.0434, step 1, values float32 > volume #2 level 0.3955 > flip volume #2 Unknown command: flip volume #2 > flip map #2 Unknown command: flip map #2 > volume flip #2 Opened cryosparc_P1451_J29_class_03_00162_volume.mrc z flip as #3, grid size 128,128,128, pixel 2.33, shown at step 1, values float32 > fitmap #1 inMap #3 Fit molecule 8s3o (#1) to map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) using 21074 atoms average map value = 0.172, steps = 104 shifted from previous position = 16 rotated from previous position = 26 degrees atoms outside contour = 16305, contour level = 0.39554 Position of 8s3o (#1) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation 0.88191360 -0.31330391 0.35223438 4.80890097 0.47054988 0.63020059 -0.61760021 60.07449895 -0.02848175 0.71041387 0.70320759 -82.10067576 Axis 0.83607390 0.23968633 0.49348851 Axis point 0.00000000 115.53665637 36.66651364 Rotation angle (degrees) 52.57943820 Shift along axis -22.09610722 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.38609,-0.92245,-0.0045046,228.06,-0.86413,-0.35997,-0.35171,378.79,0.32281,0.13969,-0.9361,204.35 > view matrix models > #3,-0.97023,0.14089,0.19701,248.08,0.17077,0.97474,0.14395,-42.329,-0.17175,0.17331,-0.96978,278.61 > view matrix models > #3,0.43611,0.46169,0.77243,-91.788,-0.68802,0.72432,-0.04448,150.18,-0.58003,-0.51205,0.63354,214 > view matrix models > #3,0.85495,0.32933,-0.40075,30.205,-0.27916,0.9433,0.17962,24.953,0.43717,-0.041689,0.89841,-45.347 > view matrix models > #3,0.68271,-0.59814,0.41969,76.051,0.30085,0.75353,0.58453,-91.733,-0.66588,-0.2728,0.69439,183.3 > view matrix models > #3,0.81144,-0.37987,0.44414,21.273,-0.53036,-0.15935,0.83266,131.96,-0.24553,-0.91121,-0.33077,358.25 > select add #1 21074 atoms, 21302 bonds, 4 pseudobonds, 1332 residues, 5 models selected > view matrix models > #1,0.12505,-0.85222,0.50802,193.87,0.98961,0.14375,-0.0024616,-42.337,-0.070928,0.50305,0.86134,-65.94,#3,0.93319,0.1443,-0.32914,35.244,0.35739,-0.46876,0.80779,43.166,-0.037724,-0.87146,-0.48902,342.56 > select subtract #3 21074 atoms, 21302 bonds, 4 pseudobonds, 1332 residues, 3 models selected > close #1 > open ""/Users/au746648/Library/CloudStorage/OneDrive-Aarhusuniversitet/GRA > Lab/star-project/_PDB files/GRA pdb files/natc3_from_6ru5.pdb"" Chain information for natc3_from_6ru5.pdb #1 --- Chain | Description A | No description available B | No description available Computing secondary structure > fitmap #1 inMap #3 Fit molecule natc3_from_6ru5.pdb (#1) to map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) using 12913 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 12913, contour level = 0.39554 Position of natc3_from_6ru5.pdb (#1) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation 0.93319167 0.35739365 -0.03772388 -35.39402723 0.14429906 -0.46876443 -0.87145722 313.67343565 -0.32913689 0.80779310 -0.48901863 144.24747792 Axis 0.97766213 0.16966110 -0.12406400 Axis point 0.00000000 117.98814910 160.94269738 Rotation angle (degrees) 120.81686645 Shift along axis 0.71886232 > ui mousemode right select > select #3 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #3,0.93319,0.1443,-0.32914,43.53,0.35739,-0.46876,0.80779,-3.3774,-0.037724,-0.87146,-0.48902,313.57 > view matrix models > #3,0.93319,0.1443,-0.32914,-73.761,0.35739,-0.46876,0.80779,-140.51,-0.037724,-0.87146,-0.48902,245.38 > view matrix models > #3,0.93319,0.1443,-0.32914,-131.02,0.35739,-0.46876,0.80779,-45.132,-0.037724,-0.87146,-0.48902,263.88 > view matrix models > #3,0.93319,0.1443,-0.32914,-148.53,0.35739,-0.46876,0.80779,-34.479,-0.037724,-0.87146,-0.48902,253.51 > view matrix models > #3,0.93319,0.1443,-0.32914,-178.12,0.35739,-0.46876,0.80779,-69.797,-0.037724,-0.87146,-0.48902,236.12 > fitmap #1 inMap #3 Fit molecule natc3_from_6ru5.pdb (#1) to map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) using 12913 atoms average map value = 0.1351, steps = 136 shifted from previous position = 6.5 rotated from previous position = 15.6 degrees atoms outside contour = 10380, contour level = 0.39554 Position of natc3_from_6ru5.pdb (#1) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation 0.97055394 0.22498934 -0.08605143 208.40837663 0.09249783 -0.67793994 -0.72927470 197.76711838 -0.22241674 0.69984086 -0.67878830 135.25199718 Axis 0.99126589 0.09458597 -0.09189902 Axis point 0.00000000 55.69303169 115.43462800 Rotation angle (degrees) 133.87498334 Shift along axis 212.86458283 > view matrix models > #3,0.93319,0.1443,-0.32914,-173.21,0.35739,-0.46876,0.80779,-66.863,-0.037724,-0.87146,-0.48902,234.16 > fitmap #1 inMap #3 Fit molecule natc3_from_6ru5.pdb (#1) to map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) using 12913 atoms average map value = 0.1351, steps = 52 shifted from previous position = 6.05 rotated from previous position = 0.00691 degrees atoms outside contour = 10376, contour level = 0.39554 Position of natc3_from_6ru5.pdb (#1) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation 0.97054185 0.22499904 -0.08616235 208.41722163 0.09241678 -0.67792493 -0.72929893 197.76088130 -0.22250316 0.69985228 -0.67874821 135.24478175 Axis 0.99126218 0.09456627 -0.09195933 Axis point 0.00000000 55.68889574 115.43916999 Rotation angle (degrees) 133.87327385 Shift along axis 212.86059808 > ui mousemode right select > select clear Drag select of 3 cryosparc_P1451_J29_class_03_00162_volume.mrc z flip , 674 residues, 1 pseudobonds > select clear > hide #!3 models > select clear Drag select of 6 residues > select clear > show #!3 models > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.73373,0.52904,-0.42633,35.063,-0.17188,0.46254,0.86978,-132.29,0.65735,0.71146,-0.24844,-136.13 > view matrix models > #3,0.06067,-0.97658,-0.20642,104.86,-0.93424,-0.12837,0.33274,144.77,-0.35144,0.17266,-0.92015,189.41 > view matrix models > #3,0.37505,0.15,-0.91479,-7.3489,0.92693,-0.073211,0.36802,-148.39,-0.011768,-0.98597,-0.1665,201.48 > view matrix models > #3,0.55409,0.42112,-0.71808,-101.76,0.80262,-0.041393,0.59505,-166.39,0.22086,-0.90606,-0.36093,182.23 > hide #!3 models > show #!2 models > volume flip #3 Opened cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip as #4, grid size 128,128,128, pixel 2.33, shown at step 1, values float32 > hide #!2 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > ui mousemode right select > select #4 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.58897,-0.20748,0.78107,-68.722,-0.25297,-0.87058,-0.42201,270.58,0.76754,-0.44614,0.46026,-93.917 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.58897,-0.20748,0.78107,-64.751,-0.25297,-0.87058,-0.42201,265.93,0.76754,-0.44614,0.46026,-96.166 > view matrix models > #4,-0.58897,-0.20748,0.78107,-61.548,-0.25297,-0.87058,-0.42201,269.71,0.76754,-0.44614,0.46026,-97.985 > view matrix models > #4,-0.58897,-0.20748,0.78107,-7.0256,-0.25297,-0.87058,-0.42201,262.46,0.76754,-0.44614,0.46026,-150.07 > lighting soft > graphics silhouettes true > set bgColor black > ui tool show ""Side View"" > lighting soft > lighting simple > view matrix models > #4,-0.58897,-0.20748,0.78107,0.56154,-0.25297,-0.87058,-0.42201,259.58,0.76754,-0.44614,0.46026,-149.05 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.13033,0.7758,-0.61737,3.0909,0.29697,0.62464,0.72224,-218.39,0.94595,-0.08921,-0.3118,-109.18 > view matrix models > #4,0.065805,0.5924,-0.80296,29.018,0.3131,0.7518,0.58031,-217.56,0.94744,-0.28959,-0.13601,-107.15 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.065805,0.5924,-0.80296,27.274,0.3131,0.7518,0.58031,-255.4,0.94744,-0.28959,-0.13601,-142.35 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.81391,0.13317,0.56553,16.017,-0.3812,-0.85697,-0.34682,227.46,0.43845,-0.49786,0.74826,-171.53 > view matrix models > #4,-0.85119,0.16522,0.49817,27.317,-0.41315,-0.79631,-0.44182,238.03,0.3237,-0.58189,0.74607,-141.62 > volume #4 level 0.6234 > view matrix models > #4,-0.54826,-0.28609,0.78585,3.4258,0.19353,-0.95756,-0.21358,135.17,0.81361,0.034993,0.58036,-280.03 > view matrix models > #4,-0.76349,0.015736,0.64563,13.266,-0.44972,-0.73044,-0.51402,245.02,0.4635,-0.6828,0.56476,-119.95 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.76349,0.015736,0.64563,-6.5798,-0.44972,-0.73044,-0.51402,294.33,0.4635,-0.6828,0.56476,-17.141 > view matrix models > #4,-0.76349,0.015736,0.64563,-16.181,-0.44972,-0.73044,-0.51402,284.48,0.4635,-0.6828,0.56476,-24.083 > view matrix models > #4,-0.76349,0.015736,0.64563,-25.022,-0.44972,-0.73044,-0.51402,283.48,0.4635,-0.6828,0.56476,-9.2939 > fitmap #1 inMap #4 Fit molecule natc3_from_6ru5.pdb (#1) to map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) using 12913 atoms average map value = 0.1442, steps = 176 shifted from previous position = 14.3 rotated from previous position = 33.5 degrees atoms outside contour = 11703, contour level = 0.62345 Position of natc3_from_6ru5.pdb (#1) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) coordinates: Matrix rotation and translation -0.81791226 -0.56904358 0.08490568 110.99142220 0.44518169 -0.71942824 -0.53313817 210.21423503 0.36446239 -0.39826178 0.84175695 140.13027054 Axis 0.12716287 -0.26356900 0.95622225 Axis point 10.96369226 139.30729528 0.00000000 Rotation angle (degrees) 147.97229606 Shift along axis 92.70371393 > transparency sel 50 > view matrix models > #4,-0.76349,0.015736,0.64563,-9.6336,-0.44972,-0.73044,-0.51402,277.47,0.4635,-0.6828,0.56476,-17.646 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.68909,-0.092266,0.71877,-16.3,-0.49894,-0.65893,-0.56292,281.95,0.52556,-0.74653,0.40803,6.4912 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.68909,-0.092266,0.71877,-10.833,-0.49894,-0.65893,-0.56292,288.31,0.52556,-0.74653,0.40803,10.145 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.68909,-0.092266,0.71877,-50.909,-0.49894,-0.65893,-0.56292,312.03,0.52556,-0.74653,0.40803,-6.5384 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.76062,-0.22255,0.60985,-4.3038,-0.40716,-0.56814,-0.71515,308.4,0.50564,-0.79227,0.34152,13.398 > view matrix models > #4,-0.80296,-0.26485,0.53396,19.946,-0.27811,-0.62587,-0.72865,299.51,0.52718,-0.73358,0.42889,-11.891 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.69669,-0.37312,0.6127,7.664,-0.31259,-0.61085,-0.72743,302.31,0.64568,-0.69832,0.30894,-16.395 > show #!3 models > hide #!4 models > select subtract #4 Nothing selected > transparency #3.1 50 > ui mousemode right ""rotate selected models"" > select add #3 2 models selected > view matrix models > #3,0.63244,0.40573,-0.65985,-119.52,0.74365,-0.079611,0.66381,-161.63,0.2168,-0.91052,-0.35207,182.24 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.63244,0.40573,-0.65985,-125.84,0.74365,-0.079611,0.66381,-154.62,0.2168,-0.91052,-0.35207,180.79 > view matrix models > #3,0.63244,0.40573,-0.65985,-177.36,0.74365,-0.079611,0.66381,-222.18,0.2168,-0.91052,-0.35207,154.52 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.1668,-0.62281,-0.76439,58.041,-0.18165,-0.78139,0.59702,29.234,-0.96911,0.039268,-0.24347,178.62 > volume #3 level 0.5739 > open /Users/au746648/Desktop/cryosparc_P1451_J29_class_04_00162_volume.mrc Opened cryosparc_P1451_J29_class_04_00162_volume.mrc as #5, grid size 128,128,128, pixel 2.33, shown at level 0.101, step 1, values float32 > color #5 #0096ffff models > select add #5 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.1668,-0.62281,-0.76439,31.113,-0.18165,-0.78139,0.59702,3.9264,-0.96911,0.039268,-0.24347,164.14,#5,1,0,0,-26.928,0,1,0,-25.307,0,0,1,-14.482 > select subtract #3 2 models selected > view matrix models #5,1,0,0,-205.77,0,1,0,-110.35,0,0,1,-103.57 > volume #5 level 0.2077 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.42706,-0.79813,0.42498,-81.911,0.72986,0.026822,-0.68307,9.3556,0.53378,0.60189,0.59398,-199.21 > view matrix models > #5,-0.63029,-0.7741,0.059166,127.24,0.069296,-0.132,-0.98882,174.03,0.77326,-0.61915,0.13684,-8.7573 > view matrix models > #5,-0.80794,-0.57415,-0.13261,156.79,0.15217,0.014112,-0.98825,142.82,0.56927,-0.81863,0.075968,56.405 > view matrix models > #5,-0.39278,-0.90137,-0.18233,144.71,0.31193,0.055927,-0.94846,107.7,0.86511,-0.42941,0.2592,-65.264 > view matrix models > #5,-0.44439,-0.89572,-0.014326,126.34,0.38772,-0.17789,-0.90445,119.9,0.80758,-0.40748,0.42634,-84.718 > view matrix models > #5,-0.30866,-0.94886,0.066271,100.87,0.2686,-0.15379,-0.9509,141.5,0.91246,-0.2757,0.30233,-98.584 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.30866,-0.94886,0.066271,112.26,0.2686,-0.15379,-0.9509,172.79,0.91246,-0.2757,0.30233,-96.966 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.49594,-0.83407,0.24159,98.909,-0.19058,-0.16689,-0.96738,245.2,0.84719,-0.5258,-0.076191,1.9511 > view matrix models > #5,-0.18861,-0.97318,0.13168,87.701,-0.2558,-0.080774,-0.96335,243.2,0.94815,-0.21538,-0.23371,-29.282 > view matrix models > #5,-0.51874,-0.84952,0.095998,126.22,0.011507,-0.11922,-0.9928,212.86,0.85485,-0.5139,0.071618,-22.987 > view matrix models > #5,-0.39465,-0.42933,0.81236,-54.227,-0.20663,-0.82001,-0.53375,266.33,0.8953,-0.3785,0.2349,-71.025 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.39465,-0.42933,0.81236,-61.029,-0.20663,-0.82001,-0.53375,292.65,0.8953,-0.3785,0.2349,-73.828 > view matrix models > #5,-0.39465,-0.42933,0.81236,-62.116,-0.20663,-0.82001,-0.53375,283.6,0.8953,-0.3785,0.2349,-73.735 > volume #5 level 0.1938 > open /Users/au746648/Desktop/cryosparc_P1451_J31_class_04_00182_volume.mrc Opened cryosparc_P1451_J31_class_04_00182_volume.mrc as #6, grid size 128,128,128, pixel 2.33, shown at level 0.0503, step 1, values float32 > volume #6 level 0.1366 > select subtract #5 Nothing selected > select add #6 3 models selected > volume #6 level 0.4293 > view matrix models #6,1,0,0,-21.412,0,1,0,-76.003,0,0,1,-135.01 > view matrix models #6,1,0,0,-10.95,0,1,0,-50.237,0,0,1,-75.777 > view matrix models #6,1,0,0,-134.75,0,1,0,-142.73,0,0,1,-138.65 > view matrix models #6,1,0,0,-172.39,0,1,0,-125.19,0,0,1,-115.35 > hide #!5 models > view matrix models #6,1,0,0,-129.47,0,1,0,-78.462,0,0,1,-106.72 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.26897,0.50156,0.82224,-127.64,0.37643,-0.73106,0.56908,44.919,0.88654,0.46258,0.0078352,-171.67 > view matrix models > #6,0.29362,-0.91589,0.27373,77.86,-0.90261,-0.17134,0.39489,180.24,-0.31477,-0.36302,-0.877,261.19 > view matrix models > #6,0.66586,-0.50076,0.55305,-81.031,-0.72326,-0.61517,0.31378,231.3,0.1831,-0.60893,-0.7718,207.46 > select add #3 5 models selected > view matrix models > #3,0.17781,-0.6548,-0.73458,29.403,-0.16106,-0.75578,0.63471,-4.0508,-0.97079,0.0054535,-0.23985,166.57,#6,0.63217,-0.51366,0.5801,-74.183,-0.75502,-0.57659,0.31224,226.45,0.17409,-0.63537,-0.75233,214.41 > select subtract #6 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.17781,-0.6548,-0.73458,197.96,-0.16106,-0.75578,0.63471,128.43,-0.97079,0.0054535,-0.23985,223.57 > ui tool show ""Fit in Map"" > fitmap #6 inMap #3 Fit map cryosparc_P1451_J31_class_04_00182_volume.mrc in map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip using 5727 points correlation = 0.6238, correlation about mean = 0.02271, overlap = 951.9 steps = 276, shift = 21.8, angle = 62.1 degrees Position of cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation -0.19929433 0.95960251 0.19860713 7.36246138 0.83305112 0.27263528 -0.48134795 48.42049611 -0.51605002 0.06951998 -0.85373261 342.28841856 Axis 0.60458124 0.78434100 -0.13889101 Axis point 37.50177706 0.00000000 173.82533954 Rotation angle (degrees) 152.89786448 Shift along axis -5.11139590 > fitmap #6 inMap #3 Fit map cryosparc_P1451_J31_class_04_00182_volume.mrc in map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip using 5727 points correlation = 0.6238, correlation about mean = 0.02273, overlap = 951.9 steps = 40, shift = 0.00661, angle = 0.0189 degrees Position of cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation -0.19920731 0.95955532 0.19892218 7.31356276 0.83302519 0.27272461 -0.48134222 48.40497062 -0.51612546 0.06982030 -0.85366249 342.24203829 Axis 0.60458510 0.78435514 -0.13879434 Axis point 37.50664920 0.00000000 173.80416507 Rotation angle (degrees) 152.88237039 Shift along axis -5.11289771 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.14199,-0.558,0.8176,12.712,0.98683,-0.14444,0.072808,-54.322,0.077464,0.81718,0.57116,-167.37 > fitmap #6 inMap #3 Fit map cryosparc_P1451_J31_class_04_00182_volume.mrc in map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip using 5727 points correlation = 0.6814, correlation about mean = 0.06839, overlap = 1103 steps = 124, shift = 10.6, angle = 25.6 degrees Position of cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) relative to cryosparc_P1451_J29_class_03_00162_volume.mrc z flip (#3) coordinates: Matrix rotation and translation -0.70515919 -0.69372884 -0.14659748 382.00739334 0.70127425 -0.65182444 -0.28868552 187.81374797 0.10471364 -0.30637429 0.94613417 31.92288425 Axis -0.01247824 -0.17728309 0.98408079 Axis point 151.79535877 177.43126339 0.00000000 Rotation angle (degrees) 134.86386756 Shift along axis -6.64828230 > hide #!3 models > show #!4 models > fitmap #4 inMap #6 Fit map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip in map cryosparc_P1451_J31_class_04_00182_volume.mrc using 3140 points correlation = 0.1976, correlation about mean = 0.03125, overlap = 6.175 steps = 88, shift = 24.4, angle = 7.46 degrees Position of cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) relative to cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) coordinates: Matrix rotation and translation 0.73817778 0.24758634 0.62753049 -48.99103457 -0.47314843 0.85307023 0.22000386 74.80790175 -0.48085764 -0.45931704 0.74686260 77.91863052 Axis -0.45701655 0.74567369 -0.48487794 Axis point 145.25343067 0.00000000 109.25726151 Rotation angle (degrees) 48.00580375 Shift along axis 40.39097233 > fitmap #4 inMap #6 Fit map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip in map cryosparc_P1451_J31_class_04_00182_volume.mrc using 3140 points correlation = 0.1979, correlation about mean = 0.03124, overlap = 6.179 steps = 40, shift = 0.0318, angle = 0.0133 degrees Position of cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) relative to cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) coordinates: Matrix rotation and translation 0.73828141 0.24752933 0.62743107 -48.99803649 -0.47297743 0.85317886 0.21995030 74.80233469 -0.48086679 -0.45914596 0.74696190 77.87680966 Axis -0.45695166 0.74575370 -0.48481604 Axis point 145.22110355 0.00000000 109.23280752 Rotation angle (degrees) 47.99379315 Shift along axis 40.41792523 > ui mousemode right ""translate selected models"" > select add #4 4 models selected > select subtract #3 2 models selected > view matrix models > #4,-0.71136,-0.30894,0.63129,62.818,-0.27669,-0.70257,-0.65562,336.59,0.64607,-0.64105,0.4143,-5.8717 > fitmap #4 inMap #6 Fit map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip in map cryosparc_P1451_J31_class_04_00182_volume.mrc using 3140 points correlation = 0.74, correlation about mean = 0.04626, overlap = 800.1 steps = 204, shift = 10.1, angle = 61.4 degrees Position of cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) relative to cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) coordinates: Matrix rotation and translation 0.82666406 -0.52370425 0.20581626 75.22577789 0.51014453 0.85187177 0.11860443 -75.71048999 -0.23744271 0.00695002 0.97137666 27.98936244 Axis -0.09877485 0.39212817 0.91459227 Axis point 164.79507905 86.92502533 0.00000000 Rotation angle (degrees) 34.41594191 Shift along axis -11.51977609 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.4118,-0.65812,-0.63032,146.48,-0.74824,-0.63901,0.17835,261.2,-0.52015,0.39819,-0.75557,192.15 > fitmap #4 inMap #6 Fit map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip in map cryosparc_P1451_J31_class_04_00182_volume.mrc using 3140 points correlation = 0.6279, correlation about mean = -0.02295, overlap = 588.9 steps = 120, shift = 4.39, angle = 35.2 degrees Position of cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) relative to cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) coordinates: Matrix rotation and translation 0.66923884 0.60304520 -0.43411499 32.53845806 0.74035303 -0.59088169 0.32052483 66.76472476 -0.06321964 -0.53590603 -0.84190734 358.75043710 Axis -0.90787069 -0.39317245 0.14555495 Axis point 0.00000000 75.93166120 172.96105992 Rotation angle (degrees) 151.85724052 Shift along axis -3.57286002 > view matrix models > #4,-0.042351,-0.77601,-0.62929,229.56,-0.98127,-0.086179,0.17231,218.25,-0.18795,0.6248,-0.75783,110.88 > view matrix models > #4,-0.10998,0.041592,-0.99306,176.2,-0.86694,-0.49268,0.075382,275.44,-0.48612,0.86922,0.090245,-10.697 > fitmap #4 inMap #6 Fit map cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip in map cryosparc_P1451_J31_class_04_00182_volume.mrc using 3140 points correlation = 0.9892, correlation about mean = 0.6918, overlap = 1720 steps = 160, shift = 10.8, angle = 69.6 degrees Position of cryosparc_P1451_J29_class_03_00162_volume.mrc z flip z flip (#4) relative to cryosparc_P1451_J31_class_04_00182_volume.mrc (#6) coordinates: Matrix rotation and translation 0.99935630 -0.01772327 -0.03119011 9.29263904 -0.01918488 -0.99870104 -0.04720313 307.30678154 -0.03031300 0.04777113 -0.99839822 292.35927320 Axis 0.99983898 -0.00923375 -0.01538697 Axis point 0.00000000 150.22203932 149.90287021 Rotation angle (degrees) 177.27772561 Shift along axis 1.95502573 > transparency sel 0 > transparency sel 50 > transparency sel 0 > transparency sel 50 > transparency sel 0 > transparency sel 50 > select add #6 5 models selected > select subtract #4 3 models selected > transparency sel 50 > color #4 #fffb00ff models > color #4 #8efa00ff models > color #4 #008f00ff models > view matrix models > #6,-0.59863,0.32299,0.73302,-45.619,-0.65773,-0.72051,-0.21967,320.21,0.4572,-0.61363,0.64376,-19.417 > view matrix models > #6,-0.36588,0.69549,0.61841,-121.16,-0.75557,-0.60994,0.23893,253.68,0.54337,-0.37983,0.74865,-82.658 > select add #4 5 models selected > select subtract #6 2 models selected > select subtract #4 Nothing selected > select add #6 3 models selected > hide #!4 models > view matrix models > #6,-0.095615,0.84648,0.52376,-171.81,-0.79675,-0.38049,0.46949,192.78,0.5967,-0.37241,0.71081,-86.572 > view matrix models > #6,0.18732,0.54836,0.81499,-211.14,-0.16934,-0.79923,0.57668,145.09,0.96759,-0.24603,-0.056852,-53.815 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.18732,0.54836,0.81499,-252.77,-0.16934,-0.79923,0.57668,106.44,0.96759,-0.24603,-0.056852,-91.939 > view matrix models > #6,0.18732,0.54836,0.81499,-267.07,-0.16934,-0.79923,0.57668,68.549,0.96759,-0.24603,-0.056852,-70.966 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.39455,0.7521,0.52789,-168.48,-0.47254,-0.65878,0.58542,92.389,0.78806,-0.018472,0.61532,-172.84 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.39455,0.7521,0.52789,-161.71,-0.47254,-0.65878,0.58542,108.21,0.78806,-0.018472,0.61532,-163.7 > view matrix models > #6,-0.39455,0.7521,0.52789,-158.03,-0.47254,-0.65878,0.58542,110.17,0.78806,-0.018472,0.61532,-160.91 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.12861,-0.8217,-0.55523,152.58,-0.89633,0.14325,-0.41961,195.77,0.42433,0.55163,-0.71809,-3.1036 > view matrix models > #6,-0.4296,-0.11883,-0.89517,179.72,0.3377,0.89824,-0.2813,-125.99,0.8375,-0.42314,-0.34575,28.343 > view matrix models > #6,-0.83849,-0.46653,-0.28157,207.92,0.01935,-0.54188,0.84023,-18.521,-0.54457,0.69908,0.46339,-44.37 > view matrix models > #6,-0.562,0.82661,-0.029446,-65.003,-0.56084,-0.35465,0.74812,54.772,0.60796,0.43696,0.66291,-208.87 > view matrix models > #6,-0.44627,0.79614,0.40865,-139.94,-0.28991,-0.56064,0.77565,40.623,0.84664,0.22768,0.48101,-188.02 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.44627,0.79614,0.40865,-132.17,-0.28991,-0.56064,0.77565,40.838,0.84664,0.22768,0.48101,-183.16 > view matrix models > #6,-0.44627,0.79614,0.40865,-139.01,-0.28991,-0.56064,0.77565,43.631,0.84664,0.22768,0.48101,-177.52 > view matrix models > #6,-0.44627,0.79614,0.40865,-142.09,-0.28991,-0.56064,0.77565,39.375,0.84664,0.22768,0.48101,-181.96 > view matrix models > #6,-0.44627,0.79614,0.40865,-72.106,-0.28991,-0.56064,0.77565,63.502,0.84664,0.22768,0.48101,-215.23 > ui mousemode right ""contour level"" > volume #6 level 0.6753 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.44627,0.79614,0.40865,-119.04,-0.28991,-0.56064,0.77565,63.861,0.84664,0.22768,0.48101,-189.97 > view matrix models > #6,-0.44627,0.79614,0.40865,-127.71,-0.28991,-0.56064,0.77565,73.894,0.84664,0.22768,0.48101,-178.23 > view matrix models > #6,-0.44627,0.79614,0.40865,-147.26,-0.28991,-0.56064,0.77565,66.323,0.84664,0.22768,0.48101,-164.54 > view matrix models > #6,-0.44627,0.79614,0.40865,-140.67,-0.28991,-0.56064,0.77565,62.128,0.84664,0.22768,0.48101,-170.34 > view matrix models > #6,-0.44627,0.79614,0.40865,-152.05,-0.28991,-0.56064,0.77565,56.907,0.84664,0.22768,0.48101,-168.73 > view matrix models > #6,-0.44627,0.79614,0.40865,-148.02,-0.28991,-0.56064,0.77565,58.391,0.84664,0.22768,0.48101,-170.61 > view matrix models > #6,-0.44627,0.79614,0.40865,-155.17,-0.28991,-0.56064,0.77565,39.8,0.84664,0.22768,0.48101,-171.78 > view matrix models > #6,-0.44627,0.79614,0.40865,-151.66,-0.28991,-0.56064,0.77565,40.126,0.84664,0.22768,0.48101,-172.92 > volume flip #6 Opened cryosparc_P1451_J31_class_04_00182_volume.mrc z flip as #7, grid size 128,128,128, pixel 2.33, shown at step 1, values float32 > select add #7 4 models selected > select subtract #6 2 models selected > view matrix models > #7,-0.44627,0.79614,0.40865,-140.12,-0.28991,-0.56064,0.77565,46.152,0.84664,0.22768,0.48101,-176.37 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.19304,0.97772,-0.082498,-188.68,-0.20971,-0.041024,-0.9769,225.55,-0.95852,0.20588,0.19712,144 > view matrix models > #7,0.38582,0.86184,0.32921,-263.8,0.70898,-0.048644,-0.70355,45.475,-0.59033,0.50484,-0.62979,170.5 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.38582,0.86184,0.32921,-261.46,0.70898,-0.048644,-0.70355,40.536,-0.59033,0.50484,-0.62979,160.27 > view matrix models > #7,0.38582,0.86184,0.32921,-259.2,0.70898,-0.048644,-0.70355,35.852,-0.59033,0.50484,-0.62979,161.6 > view matrix models > #7,0.38582,0.86184,0.32921,-264.32,0.70898,-0.048644,-0.70355,31.468,-0.59033,0.50484,-0.62979,166.22 > show #!6 models > hide #!7 models > select add #6 4 models selected > select subtract #7 2 models selected > select add #7 4 models selected > select subtract #6 2 models selected > select subtract #7 Nothing selected > select add #7 2 models selected > select subtract #7 Nothing selected > select add #6 2 models selected > select add #5 4 models selected > select subtract #6 2 models selected > select subtract #5 Nothing selected > select add #7 2 models selected > select subtract #7 Nothing selected > select add #6 2 models selected > select add #7 4 models selected > select subtract #7 2 models selected > select add #7 4 models selected > select subtract #6 2 models selected > select subtract #7 Nothing selected > select add #6 2 models selected > select subtract #6 Nothing selected > volume #3 level 0.7686 > hide #!6 models > select add #6 2 models selected > show #!6 models > view matrix models > #6,-0.44627,0.79614,0.40865,-158.18,-0.28991,-0.56064,0.77565,64.583,0.84664,0.22768,0.48101,-190.02 > view matrix models > #6,-0.44627,0.79614,0.40865,-165.03,-0.28991,-0.56064,0.77565,46.943,0.84664,0.22768,0.48101,-174.26 > view matrix models > #6,-0.44627,0.79614,0.40865,-148.41,-0.28991,-0.56064,0.77565,47.12,0.84664,0.22768,0.48101,-182.05 > view matrix models > #6,-0.44627,0.79614,0.40865,-146.21,-0.28991,-0.56064,0.77565,41.904,0.84664,0.22768,0.48101,-178.89 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.43087,0.80462,0.40858,-149.81,-0.38043,-0.57252,0.72629,64.375,0.81831,0.1575,0.55278,-174.13 > view matrix models > #6,0.20372,-0.55432,-0.80699,131.08,0.55928,-0.61065,0.56064,-48.762,-0.80356,-0.56554,0.18562,232.55 > view matrix models > #6,0.38282,-0.48722,-0.7849,90.703,0.64541,-0.46685,0.60457,-89.735,-0.66099,-0.73802,0.13574,244.07 > view matrix models > #6,0.19309,-0.84001,-0.50705,133.5,0.65817,-0.27238,0.70187,-134.79,-0.72769,-0.46925,0.50027,162.08 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.19309,-0.84001,-0.50705,135.59,0.65817,-0.27238,0.70187,-128.31,-0.72769,-0.46925,0.50027,170.64 > view matrix models > #6,0.19309,-0.84001,-0.50705,147.35,0.65817,-0.27238,0.70187,-125.98,-0.72769,-0.46925,0.50027,164.33 > view matrix models > #6,0.19309,-0.84001,-0.50705,145.04,0.65817,-0.27238,0.70187,-129.54,-0.72769,-0.46925,0.50027,166.2 > view matrix models > #6,0.19309,-0.84001,-0.50705,146.42,0.65817,-0.27238,0.70187,-129.54,-0.72769,-0.46925,0.50027,164.41 > view matrix models > #6,0.19309,-0.84001,-0.50705,148.14,0.65817,-0.27238,0.70187,-130.52,-0.72769,-0.46925,0.50027,162.26 > view matrix models > #6,0.19309,-0.84001,-0.50705,149.54,0.65817,-0.27238,0.70187,-132.01,-0.72769,-0.46925,0.50027,163.31 > volume #7 level 0.6692 > volume #6 level 0.6008 > view matrix models > #6,0.19309,-0.84001,-0.50705,149.26,0.65817,-0.27238,0.70187,-134.28,-0.72769,-0.46925,0.50027,161.25 > view matrix models > #6,0.19309,-0.84001,-0.50705,148.98,0.65817,-0.27238,0.70187,-135.24,-0.72769,-0.46925,0.50027,161.25 ===== Log before crash end ===== Log: Startup Messages --- warning | Registration file '/Users/au746648/Library/Application Support/ChimeraX/registration' has expired note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S000A0DK/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 28 days, 23 hours, 39 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal SyncMaster: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX