id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14383 Crash in garbage collection while restoring session chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000324fba000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000323fb7000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000322fb4000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000321fb1000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000320fae000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031ffab000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031efa8000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031dfa5000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031cfa2000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031bf9f000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031af9c000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000319f99000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000318f96000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000317f93000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000316f90000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000204859240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 514 in collated_open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 334 in _qt_safe File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 61) {""app_name"":""ChimeraX"",""timestamp"":""2024-01-15 22:10:58.00 +0000"",""app_version"":""1.7.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.2.1 (23C71)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A9BB8999-FB07-4A6C-8459-4E85AC447408""} { ""uptime"" : 700000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,5"", ""coalitionID"" : 109067, ""osVersion"" : { ""train"" : ""macOS 14.2.1"", ""build"" : ""23C71"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-01-15 22:10:57.7385 +0000"", ""codeSigningMonitor"" : 1, ""incident"" : ""A9BB8999-FB07-4A6C-8459-4E85AC447408"", ""pid"" : 81614, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-01-15 22:08:43.9115 +0000"", ""procStartAbsTime"" : 16952727606138, ""procExitAbsTime"" : 16955938913629, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""13C36163-CC03-5074-9FDF-F7545CEC4403"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""F9070259-436C-FF97-23D6-B37F3ACB6C68"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", 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\nmapped file 7.4G 1533 \nshared memory 3532K 27 \nunshared pmap 15.7M 10 \n=========== ======= ======= \nTOTAL 12.0G 5447 \nTOTAL, minus reserved VM space 11.8G 5447 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f06a03e30220641bd2e560ef258fb6240354f3f7"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63f9578e238e7b23a1f3030a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 } ], ""experiments"" : [ { ""treatmentId"" : ""52e9806b-48cf-4718-ba06-6aaa79468566"", ""experimentId"" : ""6553f184553f07431fda611f"", ""deploymentId"" : 400000004 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF8A913EA78)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-onepf.cxs"" Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level 0.00373, step 1, values float32 Log from Sun Jan 14 15:43:04 2024UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-individuals.cxs"" format session Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level 0.00373, step 1, values float32 Log from Sun Jan 14 14:55:25 2024UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Fit-240114.cxs"" format session Opened postprocess_masked330_onepf.mrc as #6, grid size 274,274,274, pixel 1.51, shown at level 0.0124, step 2, values float32 Log from Sun Jan 14 14:18:05 2024UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Fit14-27.cxs"" format session Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level 0.0195, step 1, values float32 Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at level 0.0174, step 1, values float32 Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at level 0.0209, step 1, values float32 Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown at level 0.0176, step 1, values float32 Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51, shown at level 0.0104, step 2, values float32 Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel 1.51, shown at level 0.00964, step 1, values float32 Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel 1.51, shown at level 0.0121, step 1, values float32 Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size 274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32 Log from Fri Jan 12 07:27:46 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Fit14-20.cxs"" format session Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level 0.0195, step 1, values float32 Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at level 0.0174, step 1, values float32 Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at level 0.0209, step 1, values float32 Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown at level 0.0176, step 1, values float32 Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51, shown at level 0.0104, step 2, values float32 Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel 1.51, shown at level 0.00964, step 1, values float32 Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel 1.51, shown at level 0.014, step 1, values float32 Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size 274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32 Log from Wed Jan 10 14:43:33 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. [deleted to fit within ticket limits] > show cartoons > show atoms > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel > hide atoms > hide cartoons > show cartoons > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > ui tool show Matchmaker > hide #!2 models > matchmaker #2/G to #1/G pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf- alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst- rechained.pdb, chain G (#1) with pointy-1pf-relative-rechained.pdb, chain G (#2), sequence alignment score = 573.4 RMSD between 71 pruned atom pairs is 0.804 angstroms; (across all 111 pairs: 3.894) > show #!2 models > morph Missing or invalid ""structures"" argument: empty atom specifier > morph #1.2 Require at least 2 structures for morph > morph #1 #2 Computed 51 frame morph #3 > coordset #3 1,51 > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > morph #2 #1 Computed 51 frame morph #4 > coordset #4 1,51 > hide #!3 models > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > select #2/A 265 atoms, 264 bonds, 19 residues, 1 model selected > color #2/A corflower blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #2/A bychain corflower blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color > color /A blue > color /A cornflower blue [Repeated 1 time(s)] > color /B medium turquoise > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E peach puff > color /F plum > color /G medium orchid > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E peach puff > color /F plum > color /G slate blue > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E peach puff > color /F plum > color /G slate blue > color /H lavender > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E peach puff > color /F plum > color /G slate blue > color /H lavender > color /I salmon > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E goldenrod > color /F plum > color /G slate blue > color /H lavender > color /I salmon > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E goldenrod > color /F plum > color /G dark cyan > color /H lavender > color /I salmon > color /A cornflower blue > color /B medium turquoise > color /C medium sea green > color /D pale goldenrod > color /E goldenrod > color /F plum > color /G hot pink > color /H lavender > color /I salmon > morph Missing or invalid ""structures"" argument: empty atom specifier > morph #2 #1 wrap true Computed 101 frame morph #5 > coordset #5 1,101 > hide #!4 models > lighting soft > set bgColor white > cartoon style coil width 1.5 thickness 0.8 > cartoon style helix xsection round width 3 thickness 0.8 > cartoon style strand xsection round width 3 thickness 0.8 > cartoon style strand arrowScale 1 > cartoon style helix xsection oval sides 10 > graphics silhouettes true > graphics silhouettes width 1.5 > graphics silhouettes depthJump 0.003 > lighting msDepthBias 0.004 > lighting shadows true intensity 0.06 > lighting depthCueColor #000000 > movie record > movie encode /Users/chaaban/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/chaaban/Desktop/movie.mp4 > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/postprocess_masked330_onepf.mrc"" Opened postprocess_masked330_onepf.mrc as #6, grid size 274,274,274, pixel 1.51, shown at level 9.42e-06, step 2, values float32 > volume #6 level 0.01241 > hide #!6 models > hide #!5 models > show #!6 models > show #!1 models > hide #!1 models > show #!1 models > ui tool show ""Fit in Map"" > fitmap #1 inMap #6 Fit molecule Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf- alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb (#1) to map postprocess_masked330_onepf.mrc (#6) using 6218 atoms average map value = 0.01328, steps = 40 shifted from previous position = 0.162 rotated from previous position = 0.147 degrees atoms outside contour = 3565, contour level = 0.012408 Position of Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf- alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb (#1) relative to postprocess_masked330_onepf.mrc (#6) coordinates: Matrix rotation and translation 0.99999701 -0.00172986 0.00172963 0.05739393 0.00173119 0.99999820 -0.00077010 -0.06466265 -0.00172830 0.00077310 0.99999821 0.15764343 Axis 0.30081486 0.67405099 0.67465968 Axis point 68.53340975 19.14218260 0.00000000 Rotation angle (degrees) 0.14696576 Shift along axis 0.08003468 > transparency #1,6 50 > ui tool show ""Hide Dust"" > surface dust #6 size 9.04 > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Fit-240114.cxs"" ——— End of log from Sun Jan 14 14:18:05 2024 ——— opened ChimeraX session > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Fit-240114-back.png"" width 1600 transparentBackground > true > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/188.cif"" Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive- MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 188.cif #7 --- Chain | Description A0 | No description available A1 | No description available A2 | No description available A3 | No description available A4 | No description available A5 | No description available A6 | No description available A7 | No description available A8 | No description available A9 | No description available Aa | No description available Aaa | No description available Aab | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj | No description available Ak | No description available Al | No description available Am | No description available An | No description available Ao | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Au | No description available Av | No description available Aw | No description available Ax | No description available Ay | No description available Az | No description available > hide #!6 models > hide #!1 models > show #!1 models > close session > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/188.cif"" format mmcif Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive- MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 188.cif #1 --- Chain | Description A0 | No description available A1 | No description available A2 | No description available A3 | No description available A4 | No description available A5 | No description available A6 | No description available A7 | No description available A8 | No description available A9 | No description available Aa | No description available Aaa | No description available Aab | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj | No description available Ak | No description available Al | No description available Am | No description available An | No description available Ao | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Au | No description available Av | No description available Aw | No description available Ax | No description available Ay | No description available Az | No description available > hide atoms > show cartoons > preset custom clean-chain Using preset: Custom / Clean-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain ui windowfill true > ui windowfill toggle > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/188_b250.mrc"" Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level 0.00707, step 1, values float32 > hide cartoons > show atoms > style stick Changed 20272 atom styles > transparency 50 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > ui mousemode right zoom > ui tool show ""Color Zone"" > color zone #2 near #1 distance 4.96 > transparency 50 > select clear > lighting depthCueColor #999999 > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114.csx"" No known data format for file suffix '.csx' > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114.cxs"" > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-fitmap.png"" width 1600 > transparentBackground true > hide #!1 models > transparency #2 0 > view > ui tool show ""Hide Dust"" > surface dust #2 size 4.96 > volume #2 level 0.006833 > volume #2 level 0.006236 > surface dust #2 size 4.96 > transparency #2 50 > select clear > transparency #2 0 > color zone #2 near #1 distance 4.96 > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-map.png"" width 1600 > transparentBackground true > show #!1 models > transparency 50 > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select clear > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-map-withfit.png"" width 1600 > transparentBackground true > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114.cxs"" > color byhetero > hide #!1 models > show #!1 models > hide #!2 models > show cartoons > view sel > show #!2 models > select clear > volume #2 level 0.004206 > transparency 50 > view > color zone #2 near #1 distance 4.96 > select clear > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > color zone #2 near #1 distance 4.96 > volume splitbyzone #2 Opened 188_b250.mrc 0 as #3.1, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 1 as #3.2, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 2 as #3.3, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 3 as #3.4, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 4 as #3.5, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 5 as #3.6, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 6 as #3.7, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 7 as #3.8, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 8 as #3.9, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 9 as #3.10, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 10 as #3.11, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 11 as #3.12, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 12 as #3.13, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 13 as #3.14, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 14 as #3.15, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 15 as #3.16, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 16 as #3.17, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 17 as #3.18, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 18 as #3.19, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 19 as #3.20, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 20 as #3.21, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 21 as #3.22, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 22 as #3.23, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 23 as #3.24, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 24 as #3.25, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 25 as #3.26, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 26 as #3.27, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 27 as #3.28, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 28 as #3.29, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 29 as #3.30, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 30 as #3.31, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 31 as #3.32, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 32 as #3.33, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 33 as #3.34, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 34 as #3.35, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 35 as #3.36, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 36 as #3.37, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 37 as #3.38, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 Opened 188_b250.mrc 38 as #3.39, grid size 250,250,250, pixel 0.826, shown at level 0.00421, step 1, values float32 > hide #!3.1-36 target m > hide #!1 models > hide #!3.37 models > hide #!3.38 models > hide #!3.39 models > show #!3.37 models > hide #!3.37 models > show #!3.36 models > hide #!3.36 models > show #!3.35 models > hide #!3.35 models > show #!3.34 models > hide #!3.34 models > show #!3.33 models > hide #!3.33 models > show #!3.32 models > hide #!3.32 models > show #!3.31 models > hide #!3.31 models > show #!3.30 models > hide #!3.30 models > show #!3.29 models > hide #!3.29 models > show #!3.28 models > hide #!3.28 models > show #!3.27 models > hide #!3.27 models > show #!3.26 models > hide #!3.26 models > show #!3.25 models > hide #!3.25 models > show #!3.24 models > hide #!3.24 models > show #!3.23 models > hide #!3.23 models > show #!3.22 models > hide #!3.22 models > show #!3.21 models > hide #!3.21 models > show #!3.20 models > hide #!3.20 models > show #!3.19 models > hide #!3.19 models > show #!3.18 models > hide #!3.18 models > show #!3.17 models > hide #!3.17 models > show #!3.16 models > hide #!3.16 models > show #!3.15 models > hide #!3.15 models > show #!3.14 models > hide #!3.14 models > show #!3.13 models > hide #!3.13 models > show #!3.12 models > hide #!3.12 models > show #!3.11 models > hide #!3.11 models > show #!3.10 models > hide #!3.10 models > show #!3.9 models > hide #!3.9 models > show #!3.8 models > hide #!3.8 models > show #!3.7 models > hide #!3.7 models > show #!3.7 models > hide #!3.7 models > show #!3.6 models > hide #!3.6 models > show #!3.5 models > hide #!3.5 models > show #!3.4 models > hide #!3.4 models > show #!3.3 models > hide #!3.3 models > show #!3.2 models > hide #!3.2 models > show #!3.1 models > hide #!3.1 models > show #!3.2 models > hide #!3.2 models > show #!3.3 models > hide #!3.3 models > show #!3.4 models > hide #!3.4 models > show #!3.5 models > hide #!3.5 models > show #!1 models > close #3 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.003848 > volume #2 level 0.003729 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select add #1 20272 atoms, 20308 bonds, 2600 residues, 1 model selected > color sel bypolymer > select subtract #1 Nothing selected > color bychain > hide atoms > show cartoons > color sel light sea green > ui tool show ""Color Actions"" > color sel lavender > color sel pale goldenrod > color sel alice blue > color sel azure > color sel light steel blue > color sel aquamarine > color sel sky blue > select ~sel 10240 atoms, 10261 bonds, 1314 residues, 3 models selected > color sel violet > select clear > undo > select clear [Repeated 2 time(s)] > color sel pale turquoise > color sel light sky blue > select ~sel 9985 atoms, 10001 bonds, 1278 residues, 3 models selected > color sel violet > color sel plum > color sel violet > color sel cornsilk > color sel lemon chiffon > color sel navajo white > color sel peach puff [Repeated 1 time(s)] > color sel pink > color sel misty rose > color sel bisque > color sel light pink > color sel light coral > color sel magenta > color sel pale violet red > color sel light coral > color sel wheat > color sel honeydew > color sel pale goldenrod > color sel violet > color sel pale goldenrod > select clear > color sel light blue > color sel light sky blue > select clear > show cartoons > redo > undo > combine sel > select ~sel 30573 atoms, 30625 bonds, 3924 residues, 2 models selected > select subtract #3 10301 atoms, 10317 bonds, 1324 residues, 1 model selected > combine sel > hide #!1 models > select add #1 20272 atoms, 20308 bonds, 2600 residues, 1 model selected > select subtract #1 Nothing selected > select add #4 20272 atoms, 20308 bonds, 2600 residues, 1 model selected > hide #!4 models > show #!4 models > hide sel cartoons > hide #!4 models > hide #!3 models > color sel wheat > color sel khaki > color sel pale goldenrod > color sel light goldenrod yellow > color sel yellow > color sel khaki > color sel antique white > color sel old lace > color sel light pink > color sel lemon chiffon > color sel ivory > color sel white > select clear > undo > color sel light yellow > select clear > select ~sel 50845 atoms, 50933 bonds, 6524 residues, 5 models selected > select subtract #4 30573 atoms, 30625 bonds, 3924 residues, 4 models selected > select subtract #3 10301 atoms, 10317 bonds, 1324 residues, 3 models selected > select subtract #2 10301 atoms, 10317 bonds, 1324 residues, 1 model selected > show sel cartoons > select ~sel 50515 atoms, 50605 bonds, 6476 residues, 5 models selected > hide sel & #!1 cartoons > select clear > color sel cornflower blue > select clear > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-individuals.cxs"" ——— End of log from Sun Jan 14 14:55:25 2024 ——— opened ChimeraX session > close #3-4 > select clear > show cartoons > combine #1 > select #3/Ad 985 atoms, 990 bonds, 126 residues, 1 model selected > select ~sel 39559 atoms, 39626 bonds, 5074 residues, 4 models selected > select subtract #1 19287 atoms, 19318 bonds, 2474 residues, 3 models selected > select subtract #2 19287 atoms, 19318 bonds, 2474 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/Aj 482 atoms, 483 bonds, 63 residues, 1 model selected > select ~sel 20775 atoms, 20815 bonds, 2663 residues, 4 models selected > select subtract #3 19790 atoms, 19825 bonds, 2537 residues, 3 models selected > select subtract #2 19790 atoms, 19825 bonds, 2537 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show Matchmaker > matchmaker #1/Aj to #3/Ad pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker copy of 188.cif, chain Ad (#3) with 188.cif, chain Aj (#1), sequence alignment score = 122 RMSD between 25 pruned atom pairs is 0.122 angstroms; (across all 25 pairs: 0.122) > select clear > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel > color sel cornflower blue > select clear > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-onesubunit.cxs"" > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/188.cif"" Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive- MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 188.cif #4 --- Chain | Description A0 | No description available A1 | No description available A2 | No description available A3 | No description available A4 | No description available A5 | No description available A6 | No description available A7 | No description available A8 | No description available A9 | No description available Aa | No description available Aaa | No description available Aab | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj | No description available Ak | No description available Al | No description available Am | No description available An | No description available Ao | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Au | No description available Av | No description available Aw | No description available Ax | No description available Ay | No description available Az | No description available > hide atoms > show cartoons > combine #1,3 [Repeated 5 time(s)] > hide #!5-10 target m > hide #!1 models > hide #!4 models > hide #!3 models > show #!4 models > show #!5 models > hide #!4 models > mmaker #5/Ad to #4/A[ No 'to' model specified > mmaker #5/Ad to #4/Ap Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ap (#4) with combination, chain Ad (#5), sequence alignment score = 65.8 RMSD between 15 pruned atom pairs is 0.182 angstroms; (across all 15 pairs: 0.182) > show #!4 models > mmaker #6/Ad to #4/Af Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Af (#4) with combination, chain Ad (#6), sequence alignment score = 168.3 RMSD between 35 pruned atom pairs is 0.095 angstroms; (across all 35 pairs: 0.095) > show #!6 models > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > mmaker #7/Ad to #4/Ae Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ae (#4) with combination, chain Ad (#7), sequence alignment score = 601.3 RMSD between 115 pruned atom pairs is 0.134 angstroms; (across all 121 pairs: 1.198) > show #!7 models > mmaker #7/Ad to #4/At Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain At (#4) with combination, chain Ad (#7), sequence alignment score = 283.5 RMSD between 57 pruned atom pairs is 0.084 angstroms; (across all 57 pairs: 0.084) > mmaker #8/Ad to #4/Ae Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ae (#4) with combination, chain Ad (#8), sequence alignment score = 601.3 RMSD between 115 pruned atom pairs is 0.134 angstroms; (across all 121 pairs: 1.198) > show #!8 models > mmaker #9/Ad to #4/Ad Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ad (#4) with combination, chain Ad (#9), sequence alignment score = 646.7 RMSD between 126 pruned atom pairs is 0.000 angstroms; (across all 126 pairs: 0.000) > show #!9 models > mmaker #10/Ad to #4/Ab Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ab (#4) with combination, chain Ad (#10), sequence alignment score = 505.8 RMSD between 100 pruned atom pairs is 0.246 angstroms; (across all 103 pairs: 0.930) > show #!10 models > hide #!4 models > lighting soft > set bgColor white > cartoon style coil width 1.5 thickness 0.8 > cartoon style helix xsection round width 3 thickness 0.8 > cartoon style strand xsection round width 3 thickness 0.8 > cartoon style strand arrowScale 1 > cartoon style helix xsection oval sides 10 > graphics silhouettes true > graphics silhouettes width 1.5 > graphics silhouettes depthJump 0.003 > lighting msDepthBias 0.004 > lighting shadows true intensity 0.06 > lighting depthCueColor #000000 > color sel bychain > color #5 #8efa00ff > color #5 #0096ffff > color #6 #d783ffff > color #7 #ff2f92ff > color #8 #942193ff > color #9 #00fa92ff > color #9 #009193ff > color #9 #8efa00ff > color #9 #008f00ff > color #9 #4f8f00ff > color #9 #009051ff > color #9 #009193ff > color #10 #00f900ff > color #10 #008f00ff > color #10 #929000ff > color #10 #4f8f00ff > color #10 #008f00ff > color #10 #009051ff > select clear > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-onepf.cxs"" > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-onepf.png"" width 1600 > transparentBackground true > show #!4 models > hide #!4 models > combine #1,3 > show #!4 models > mmaker #11/Ad to #4/Ao Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ao (#4) with combination, chain Ad (#11), sequence alignment score = 287.7 RMSD between 60 pruned atom pairs is 0.275 angstroms; (across all 63 pairs: 1.143) > hide #!4 models > color #11 #73fcd6ff > color #11 #73fa79ff > mmaker #11/Ad to #4/Ao Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 188.cif, chain Ao (#4) with combination, chain Ad (#11), sequence alignment score = 287.7 RMSD between 60 pruned atom pairs is 0.275 angstroms; (across all 63 pairs: 1.143) > lighting soft > set bgColor white > cartoon style coil width 1.5 thickness 0.8 > cartoon style helix xsection round width 3 thickness 0.8 > cartoon style strand xsection round width 3 thickness 0.8 > cartoon style strand arrowScale 1 > cartoon style helix xsection oval sides 10 > graphics silhouettes true > graphics silhouettes width 1.5 > graphics silhouettes depthJump 0.003 > lighting msDepthBias 0.004 > lighting shadows true intensity 0.06 > lighting depthCueColor #000000 > select clear > save ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-onepf.cxs"" ——— End of log from Sun Jan 14 15:43:04 2024 ——— opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #1/Aj #4/Aj #5/Aj #6/Aj #7/Aj #8/Aj #9/Aj #10/Aj #11/Aj Alignment identifier is 1 > select #7/Aj:147 8 atoms, 7 bonds, 1 residue, 1 model selected > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/Diorge/Membranes/Filament-240114-individuals.cxs"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,5 Model Number: Z17J0018AB/A Chip: Unknown Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 10 days, 14 hours, 40 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.3 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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-ISOLDE: 1.7 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard Greg Couch all ChimeraX