id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19503 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 mate.fulop@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001a671000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001966e000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001866b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700017668000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700016665000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700015662000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001465f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001365c000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700012659000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700011656000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700010653000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00007ff849bee300 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2025-12-09 20:33:59.00 +0100"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.7.6 (23H626)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""7F69D775-4B51-4BE2-91BA-B89BEC8F2B6A""} { ""uptime"" : 300000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,2"", ""coalitionID"" : 671, ""osVersion"" : { ""train"" : ""macOS 14.7.6"", ""build"" : ""23H626"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-12-09 20:33:57.5195 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""7F69D775-4B51-4BE2-91BA-B89BEC8F2B6A"", ""pid"" : 29196, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-12-09 12:11:37.8346 +0100"", ""procStartAbsTime"" : 275581893141567, ""procExitAbsTime"" : 305530336411967, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""C106164E-7566-5C96-B3A4-5FE9467A3D4D"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""EA636F1F-39D3-04C4-577C-66F6B37F5D3D"", ""lowPowerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 5186, ""bridgeVersion"" : {""build"":""22P5072"",""train"":""9.5""}, ""sleepWakeUUID"" : ""61DB531B-E9AC-4CB3-9A12-E3CE44CA18F9"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any 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Bytes before following region: 4445429736\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108f7e000-108f7f000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":29196}, ""ktriageinfo"" : ""VM - (arg = 0x0) Waiting on busy page was interrupted\n"", ""vmregioninfo"" : ""0x18 is not in any region. 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\n=========== ======= ======= \nTOTAL 8.6G 3087 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""a94b4860e94be4d2fd2677eae0d610dc7ee90e17"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""654439cdafbf5b61207873a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1213_006_volume_map.mrc Opened cryosparc_P9_J1213_006_volume_map.mrc as #1, grid size 320,320,320, pixel 1.63, shown at level 0.0923, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1213_006_volume_mask_refine.mrc Opened cryosparc_P9_J1213_006_volume_mask_refine.mrc as #2, grid size 320,320,320, pixel 1.63, shown at level 1, step 2, values float32 > volume #1 step 1 > volume #2 step 1 > volume #1 level 0.3149 > volume #1 level 0.3539 > volume #1 level 0.4057 > volume #1 level 0.4533 > select add #2 2 models selected > hide #!2 models > show #!2 models > view #2 clip false No displayed objects specified. > select subtract #2 Nothing selected > volume #2 level 0.8348 > volume #2 level 0.7648 > volume #2 level 0.93 > ui mousemode right ""map eraser"" Can only have one displayed volume when erasing > select add #1 2 models selected > select subtract #1 Nothing selected > volume #1 level 0.1139 > close #3 > volume #1 level 0.07929 > volume #1 level 0.03606 > volume #1 level 0.05767 > volume #1 level 0.1052 > volume gaussian #1 sDev 2 Opened cryosparc_P9_J1213_006_volume_map.mrc gaussian as #3, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > hide #!3 models > show #!3 models > ui mousemode right ""map eraser"" > volume erase #3 center 169.95,130.54,169.25 radius 49.156 > volume erase #3 center 249.83,132.51,158.68 radius 49.156 > volume erase #3 center 284.37,323.16,497.48 radius 49.156 > volume resample #3 onGrid #1 Opened cryosparc_P9_J1213_006_volume_map.mrc gaussian resampled as #4, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > close #3 > save /Users/fulop/Desktop/cryosparc/GISul2/pre-cleavage/mask.mrc models #4 > ui tool show ""Segment Map"" Segmenting mask.mrc, density threshold 0.095449 Showing 29 region surfaces 469 watershed regions, grouped to 29 regions Showing mask.seg - 29 regions, 29 surfaces > select #3.1 1 model selected Segmenting mask.mrc, density threshold 0.095449 Showing 29 region surfaces 469 watershed regions, grouped to 29 regions Showing mask.seg - 29 regions, 29 surfaces > select #3.1 1 model selected Ungrouped to 4 regions > select #3.31 1 model selected Ungrouped to 4 regions > select #3.34 1 model selected > select add #3.36 2 models selected > hide #!4 models > select #3.35 1 model selected Ungrouped to 8 regions > select #3.37 1 model selected > select add #3.31 2 models selected > select #3.2 1 model selected > select add #3.5 2 models selected > select add #3.18 3 models selected > select add #3.6 4 models selected > select subtract #3.6 3 models selected > select add #3.10 4 models selected > select add #3.43 5 models selected > select add #3.28 6 models selected > select add #3.15 7 models selected > select add #3.3 8 models selected > select add #3.29 9 models selected > select add #3.16 10 models selected > select add #3.27 11 models selected > select add #3.17 12 models selected > select add #3.23 13 models selected > select add #3.21 14 models selected > select add #3.14 15 models selected > select add #3.24 16 models selected > select add #3.40 17 models selected > select add #3.30 18 models selected > select add #3.39 19 models selected > select add #3.42 20 models selected > select add #3.38 21 models selected > select add #3.11 22 models selected > select add #3.32 23 models selected > select add #3.41 24 models selected > select add #3.9 25 models selected > select clear Drag select of 663, 25607 of 30476 triangles, 642, 6928 of 30200 triangles, 658, 3618 of 27300 triangles, 640, 615, 13463 of 16180 triangles, 641, 579, 12378 of 14496 triangles, 583, 8632 of 11356 triangles, 581, 9017 of 9156 triangles, 592 Drag select of 663, 642, 669, 658, 646, 666, 640, 17704 of 17712 triangles, 615, 641, 579, 583, 581, 592, 655, 660, 178, 564 > select clear Drag select of 663, 642, 669, 658, 646, 25028 of 25032 triangles, 666, 640, 615, 641, 579, 583, 581, 592, 655, 660, 178, 564 Saving 17 regions to mrc file... Opened mask_prec_cat+filament.mrc as #5, grid size 93,85,167, pixel 1.63, shown at step 1, values float32 Wrote mask_prec_cat+filament.mrc > volume resample #5 onGrid #1 Opened mask_prec_cat+filament.mrc resampled as #6, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > save /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/mask_prec_cat+filament.mrc models #6 > show #!4 models > hide #!4 models > close #6 > close #5 > select clear > select #3.11 1 model selected > select #3.32 1 model selected > select add #3.41 2 models selected > select add #3.11 3 models selected > select add #3.33 4 models selected > select add #3.1 5 models selected Drag select of 663, 642, 669, 658, 646, 640, 615, 641, 579, 583, 581, 592 Saving 17 regions to mrc file... Opened mask_prec_fil_1.mrc as #5, grid size 93,85,167, pixel 1.63, shown at step 1, values float32 Wrote mask_prec_fil_1.mrc > volume resample #5 onGrid #1 Opened mask_prec_fil_1.mrc resampled as #6, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > select #6 2 models selected > hide #!6 models > show #!6 models > hide #!6 models > select subtract #6 Nothing selected > hide #!3 models > show #!3 models Drag select of 663, 642, 669, 658, 646, 640, 615, 14165 of 16180 triangles, 641, 579, 583, 581, 592 > show #!5 models > hide #!5 models > hide #!3 models > show #!5 models > hide #!5 models > show #!5 models > volume #5 level 0.09476 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!3 models > select clear Drag select of 663, 642, 18656 of 30200 triangles, 669, 20006 of 28376 triangles, 658, 646, 12273 of 25032 triangles, 640, 15799 of 17712 triangles, 615, 13057 of 16180 triangles, 641, 579, 583, 581, 592 Saving 12 regions to mrc file... Opened mask_prec_fil_1.mrc as #7, grid size 93,85,158, pixel 1.63, shown at step 1, values float32 Wrote mask_prec_fil_1.mrc > close #6 > show #!5 models > hide #!5 models > hide #!3 models > close #5 > volume resample #7 onGrid #1 Opened mask_prec_fil_1.mrc resampled as #5, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > volume #5 level 0.09714 > show #!3 models > select #3.9 1 model selected Ungrouped to 7 regions > select #3.48 1 model selected > select add #3.45 2 models selected > select add #3.44 3 models selected > close #5,7 > select #3.22 1 model selected > select up 48 models selected > select up 49 models selected > select down 48 models selected > select down 1 model selected > select up 48 models selected > select down 1 model selected > select clear Drag select of 663, 23767 of 30476 triangles, 642, 23957 of 30200 triangles, 669, 19701 of 28376 triangles, 658, 18583 of 27300 triangles, 640, 9109 of 17712 triangles, 615, 3662 of 16180 triangles, 641, 8973 of 14200 triangles, 579, 583, 7389 of 11356 triangles, 581, 592, 501, 1625 of 7368 triangles, 553, 895 of 3348 triangles, 571, 3472 of 9020 triangles, 637, 3549 of 5904 triangles > show #!4 models > hide #!4 models Saving 15 regions to mrc file... Opened mask_prec_fil_1.mrc as #5, grid size 79,85,158, pixel 1.63, shown at step 1, values float32 Wrote mask_prec_fil_1.mrc > volume resample #5 onGrid #1 Opened mask_prec_fil_1.mrc resampled as #6, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > save /Users/fulop/Desktop/cryosparc/GISul2/pre-cleavage/mask_prec_fil_1.mrc > models #6 > hide #!6 models > show #!6 models > hide #!3 models > volume #6 level 0.09242 > close #5 > select add #3 49 models selected > select subtract #3 Nothing selected > hide #!6 models > show #!3 models > select #3.35 1 model selected > select add #3.47 2 models selected > select add #3.49 3 models selected > select #3.7 1 model selected > select #3.46 1 model selected > select #3.6 1 model selected > select add #3.7 2 models selected > select add #3.8 3 models selected > select add #3.4 4 models selected > select add #3.13 5 models selected > select add #3.20 6 models selected > select add #3.25 7 models selected > select add #3.26 8 models selected > select add #3.19 9 models selected > select add #3.12 10 models selected > select add #3.22 11 models selected Saving 11 regions to mrc file... Opened mask_prec_fil_2.mrc as #5, grid size 79,85,158, pixel 1.63, shown at step 1, values float32 Wrote mask_prec_fil_2.mrc > close #6 > volume resample #5 onGrid #1 Opened mask_prec_fil_2.mrc resampled as #6, grid size 320,320,320, pixel 1.63, shown at step 1, values float32 > hide #!3 models > select add #3 49 models selected > volume #6 level 0.09341 > save /Users/fulop/Desktop/cryosparc/GISul2/pre-cleavage/mask_prec_fil_2.mrc > models #6 > close #5 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1216_map_sharp.mrc Opened cryosparc_P9_J1216_map_sharp.mrc as #5, grid size 320,320,320, pixel 1.63, shown at level 0.0919, step 2, values float32 > volume #5 step 1 > select subtract #3 Nothing selected > close #6 > close #3-4 > close #2 > volume #5 level 0.2925 > volume #5 level 0.4013 > volume #5 level 0.493 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_mask_prec_cat+filament.mrc Opened cryosparc_P9_mask_prec_cat+filament.mrc as #2, grid size 320,320,320, pixel 1.63, shown at level 2.91e-05, step 2, values float32 > open ""/Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_mask_prec_cat+filament (1).mrc"" > /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_mask_prec_fil_2.mrc Opened cryosparc_P9_mask_prec_cat+filament (1).mrc as #3.1, grid size 320,320,320, pixel 1.63, shown at level 2.91e-05, step 2, values float32 Opened cryosparc_P9_mask_prec_fil_2.mrc as #3.2, grid size 320,320,320, pixel 1.63, shown at level 2.91e-05, step 2, values float32 > hide #!2 models > hide #!3 models > show #!1 models > volume #1 level 0.1831 > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.2 models > hide #!5 models > volume #2 step 1 > volume #3.1 step 1 > volume #3.2 step 1 > volume #3.1 level 0.02188 > volume #3.1 level 0.02 > volume #2 level 0.02 > volume #3.2 level 0.02 > show #!3.1 models > hide #!2 models > show #!3.2 models > hide #!3.2 models > hide #!3.1 models > show #!3.2 models > hide #!3.2 models > show #!5 models > hide #!5 models > show #!5 models > volume #5 level 0.02 > volume #5 level 0.141 > hide #!5 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1220_005_volume_mask_refine.mrc Opened cryosparc_P9_J1220_005_volume_mask_refine.mrc as #4, grid size 320,320,320, pixel 1.63, shown at level 1, step 2, values float32 > hide #!3 models > hide #!2 models > hide #!1 models > mmaker #2 to #4 No 'to' model specified > mmaker #4 to #1 No 'to' model specified > volume #4 step 1 > volume #4 level 0.9224 > mmaker #4 to #1 No 'to' model specified > volume #4 level 0.001848 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1227_004_volume_mask_refine.mrc Opened cryosparc_P9_J1227_004_volume_mask_refine.mrc as #6, grid size 320,320,320, pixel 1.63, shown at level 1, step 2, values float32 > hide #!4 models > volume #6 level 0.2551 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1220_005_volume_map.mrc Opened cryosparc_P9_J1220_005_volume_map.mrc as #7, grid size 320,320,320, pixel 1.63, shown at level 0.126, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1220_005_volume_map_sharp.mrc Opened cryosparc_P9_J1220_005_volume_map_sharp.mrc as #8, grid size 320,320,320, pixel 1.63, shown at level 0.127, step 2, values float32 > hide #!6 models > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1228_map_locres.mrc Opened cryosparc_P9_J1228_map_locres.mrc as #9, grid size 320,320,320, pixel 1.63, shown at level 11.2, step 2, values float32 > volume #6 step 1 > volume #9 step 1 > volume #8 step 1 > volume #7 step 1 > hide #!8 models > volume #9 level 4.758 > select add #7 2 models selected > select add #8 4 models selected > ui tool show ""Surface Color"" > color sample #7.1 map #9 palette 3,#ff0000:5,#ffffff:7,#0000ff Map values for surface ""surface"": minimum 0, mean 8.496, maximum 55.21 > color sample #8.1 map #9 palette 3,#ff0000:5,#ffffff:7,#0000ff Map values for surface ""surface"": minimum 0, mean 8.611, maximum 57.79 > hide #!9 models > select subtract #8 2 models selected > select subtract #7 Nothing selected > volume #7 level 0.1942 > volume #7 level 0.3954 > volume #8 level 0.3604 > volume #8 level 0.395 > volume #8 level 0.4225 > volume #7 level 0.4056 > volume #7 level 0.4295 > volume #8 level 0.4431 > volume #8 level 0.3355 > volume #7 level 0.3886 > volume #7 level 0.3306 > hide #!7 models > volume #8 level 0.4339 > movie record > turn y 2 180 > wait 180 > movie encode /Users/fulop/Desktop/movie2.mp4 Movie saved to /Users/fulop/Desktop/movie2.mp4 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1221_005_volume_map.mrc Opened cryosparc_P9_J1221_005_volume_map.mrc as #10, grid size 320,320,320, pixel 1.63, shown at level 0.111, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1230_map_locres.mrc Opened cryosparc_P9_J1230_map_locres.mrc as #11, grid size 320,320,320, pixel 1.63, shown at level 10.1, step 2, values float32 > hide #!8 models > volume #10 step 1 > volume #11 step 1 > show #!11 models > volume #11 level 3.981 Window position QRect(1037,-223 367x188) outside any known screen, using primary screen Window position QRect(1018,-193 367x188) outside any known screen, using primary screen > color sample #10.1 map #11 palette 3,#ff0000:5,#ffffff:7,#0000ff Map values for surface ""surface"": minimum 0, mean 8.098, maximum 52.37 > hide #!11 models > volume #10 level 0.1404 > volume #10 level 0.2203 > volume #10 level 0.2692 > select #10 2 models selected > view clip false > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/fulop/Desktop/movie2.mp4 Movie saved to /Users/fulop/Desktop/movie2.mp4 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1227_004_volume_map.mrc Opened cryosparc_P9_J1227_004_volume_map.mrc as #12, grid size 320,320,320, pixel 1.63, shown at level 0.11, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1229_map_locres.mrc Opened cryosparc_P9_J1229_map_locres.mrc as #13, grid size 320,320,320, pixel 1.63, shown at level 9.45, step 2, values float32 > volume #12 step 1 > volume #13 step 1 > hide #!10 models > volume #13 level 3.649 > color sample #12.1 map #13 palette 3,#ff0000:5,#ffffff:7,#0000ff Map values for surface ""surface"": minimum 0, mean 7.571, maximum 45.45 > hide #!13 models > volume #12 level 0.1314 > color sample #12.1 map #13 palette 3,#ff0000:5,#ffffff:7,#0000ff:9,#808080 Map values for surface ""surface"": minimum 0, mean 7.181, maximum 47.02 > volume #12 level 0.1454 > volume #12 level 0.1873 > volume #12 level 0.5273 > volume #12 level 0.2083 > movie record > turn y 2 180 > wait 180 > movie encode /Users/fulop/Desktop/movie2.mp4 Movie saved to /Users/fulop/Desktop/movie2.mp4 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1218_004_volume_map.mrc Opened cryosparc_P9_J1218_004_volume_map.mrc as #14, grid size 320,320,320, pixel 1.63, shown at level 0.076, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1231_map_locres.mrc Opened cryosparc_P9_J1231_map_locres.mrc as #15, grid size 320,320,320, pixel 1.63, shown at level 10, step 2, values float32 > hide #!12 models > volume #15 step 1 > volume #14 step 1 > volume #15 level 4.346 > volume #14 level 0.0871 > volume #14 level 0.1111 > show #!15 models > color sample #14.1 map #15 palette 3,#ff0000:5,#ffffff:7,#0000ff:9,#808080 Map values for surface ""surface"": minimum 0, mean 8.897, maximum 71.82 > color sample #14.1 map #15 palette 3,#ff0000:5,#ffffff:7,#0000ff:9,#808080 Map values for surface ""surface"": minimum 0, mean 8.897, maximum 71.82 > hide #!15 models > volume #14 level 0.2809 > movie record > turn y 2 180 > wait 180 > movie encode /Users/fulop/Desktop/movie2.mp4 Movie saved to /Users/fulop/Desktop/movie2.mp4 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1239_map_locres.mrc Opened cryosparc_P9_J1239_map_locres.mrc as #16, grid size 320,320,320, pixel 1.63, shown at level 13.6, step 2, values float32 > hide #!16 models > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1239_map_locres.mrc Opened cryosparc_P9_J1239_map_locres.mrc as #17, grid size 320,320,320, pixel 1.63, shown at level 13.6, step 2, values float32 > close #17 > hide #!14 models > show #!15 models > hide #!15 models > close #16 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1236_004_volume_map.mrc Opened cryosparc_P9_J1236_004_volume_map.mrc as #16, grid size 320,320,320, pixel 1.63, shown at level 0.125, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1239_map_locres.mrc Opened cryosparc_P9_J1239_map_locres.mrc as #17, grid size 320,320,320, pixel 1.63, shown at level 13.6, step 2, values float32 > hide #!17 models > volume #16 step 1 > volume #17 step 1 > volume #16 level 0.1614 > hide #18 models > show #!17 models > volume #17 level 4.941 > hide #!17 models > color sample #16.1 map #17 palette 3,#ff0000:5,#ffffff:7,#0000ff:9,#808080 Map values for surface ""surface"": minimum 0, mean 4.999, maximum 50.44 > volume #16 level 0.1598 > volume #16 level 0.1778 > volume #16 level 0.1876 > volume #16 level 0.2938 > save /Users/fulop/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/fulop/Desktop/movie2.mp4 Movie saved to /Users/fulop/Desktop/movie2.mp4 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1213_006_volume_map.mrc Opened cryosparc_P9_J1213_006_volume_map.mrc as #19, grid size 320,320,320, pixel 1.63, shown at level 0.0923, step 2, values float32 > volume #19 step 1 > volume #19 level 0.0838 > volume #19 level 0.1 Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1254_flex_map.mrc Opened cryosparc_P9_J1254_flex_map.mrc as #1, grid size 320,320,320, pixel 1.63, shown at level 0.00316, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1254_flex_map.mrc Opened cryosparc_P9_J1254_flex_map.mrc as #2, grid size 320,320,320, pixel 1.63, shown at level 0.00316, step 2, values float32 > open /Users/fulop/Desktop/cryosparc/GISul2/pre- > cleavage/cryosparc_P9_J1254_flex_map.mrc Opened cryosparc_P9_J1254_flex_map.mrc as #3, grid size 320,320,320, pixel 1.63, shown at level 0.00316, step 2, values float32 > close #2-3 > volume #1 step 1 > volume #1 level 0.004578 > volume #1 level 0.005924 > hide #!1 models OpenGL version: 4.1 INTEL-22.5.12 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0) OS Loader Version: 580.140.1~51 Software: System Software Overview: System Version: macOS 14.7.6 (23H626) Kernel Version: Darwin 23.6.0 Time since boot: 9 days, 16 hours, 16 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Eric Pettersen all ChimeraX