id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17740 Crash destroying OpenGL context on exit chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202502120650 (2025-02-12 06:50:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001fd910c80 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 440 in quit File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 805 in closeEvent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 302 in event File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 339 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 53) {""app_name"":""ChimeraX"",""timestamp"":""2025-05-20 15:44:39.00 +0200"",""app_version"":""1.10.0"",""slice_uuid"":""18de835b-eddc-3f3a-93bb-285f33da630d"",""build_version"":""1.10.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.4.1 (24E263)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""763EDCDF-55D2-41EC-807D-B1652BB9658F""} { ""uptime"" : 170000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,9"", ""coalitionID"" : 3256, ""osVersion"" : { ""train"" : ""macOS 15.4.1"", ""build"" : ""24E263"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-05-20 15:44:35.9744 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""763EDCDF-55D2-41EC-807D-B1652BB9658F"", ""pid"" : 26629, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-05-19 15:09:49.1121 +0200"", ""procStartAbsTime"" : 3444768901501, ""procExitAbsTime"" : 4198065157128, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.10.0"",""CFBundleVersion"":""1.10.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""04BA6F4D-5EA3-5AB5-898C-B80FEBDB8097"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""ACD98A3C-6377-90CB-9CF4-C997EDDCC893"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""notOptedIn""]}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""D6BE4A58-09BE-4C46-9447-26C65DD5AB47"", ""wakeTime"" : 20649, ""sleepWakeUUID"" : ""75C3B451-3FD7-45D9-9A68-4B882E1FE324"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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""logWritingSignature"" : ""bdd3900510d1dda592befbd59b17f5552050f71b"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000187 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""d5322b03-2bc4-481a-817e-3640bda0eeee"", ""experimentId"" : ""67f4692f84eaf455d73c6090"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202502120650 (2025-02-12) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_00_00279_volume.mrc Opened J935_class_00_00279_volume.mrc as #1, grid size 160,160,160, pixel 2.87, shown at level 0.252, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_01_00279_volume.mrc Opened J935_class_01_00279_volume.mrc as #2, grid size 160,160,160, pixel 2.87, shown at level 0.252, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_02_00279_volume.mrc Opened J935_class_02_00279_volume.mrc as #3, grid size 160,160,160, pixel 2.87, shown at level 0.26, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_03_00279_volume.mrc Opened J935_class_03_00279_volume.mrc as #4, grid size 160,160,160, pixel 2.87, shown at level 0.254, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_04_00279_volume.mrc Opened J935_class_04_00279_volume.mrc as #5, grid size 160,160,160, pixel 2.87, shown at level 0.253, step 1, values float32 > close > open /Users/toni/Downloads/cryosparc_P89_J996_006_volume_map_sharp.mrc Opened cryosparc_P89_J996_006_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 1.53, shown at level 0.149, step 2, values float32 > open /Users/toni/Downloads/cryosparc_P89_J997_007_volume_map_sharp.mrc Opened cryosparc_P89_J997_007_volume_map_sharp.mrc as #2, grid size 300,300,300, pixel 1.53, shown at level 0.144, step 2, values float32 > surface dust #1 size 15.3 > surface dust #2 size 15.3 > hide #!1 models > volume #2 step 1 > volume #1 step 1 > open /Users/toni/Downloads/cryosparc_P89_J998_005_volume_map_sharp.mrc Opened cryosparc_P89_J998_005_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 1.53, shown at level 0.162, step 2, values float32 > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > open /Users/toni/Downloads/cryosparc_P89_J999_005_volume_map_sharp.mrc Opened cryosparc_P89_J999_005_volume_map_sharp.mrc as #4, grid size 300,300,300, pixel 1.53, shown at level 0.142, step 2, values float32 > open /Users/toni/Downloads/cryosparc_P89_J1000_005_volume_map_sharp.mrc Opened cryosparc_P89_J1000_005_volume_map_sharp.mrc as #5, grid size 300,300,300, pixel 1.53, shown at level 0.149, step 2, values float32 > hide #!1 models > volume #1-5 > volume #1-5 step 1 sdLevel 3 > volume #1-5 step 1 sdLevel 5 > surface dust #3 size 15.3 > surface dust #4 size 15.3 > surface dust #5 size 15.3 > hide #!5 models > show #!2 models > hide #!4 models > show #!1 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > hide #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > vop gaussian #1-5 sdlevel 3 > volume gaussian #1-5 sdlevel 3 Expected a keyword > vop gaussian #1-5 sdlevel > volume gaussian #1-5 sdlevel Expected a keyword > vop gaussian #1-5 sDlevel > volume gaussian #1-5 sDlevel Expected a keyword > vop gaussian #1 sdlevel 3 > volume gaussian #1 sdlevel 3 Expected a keyword > vop gaussian #1-5 sDev 3 Opened cryosparc_P89_J996_006_volume_map_sharp.mrc gaussian as #6, grid size 300,300,300, pixel 1.53, shown at step 1, values float32 Opened cryosparc_P89_J997_007_volume_map_sharp.mrc gaussian as #7, grid size 300,300,300, pixel 1.53, shown at step 1, values float32 Opened cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian as #8, grid size 300,300,300, pixel 1.53, shown at step 1, values float32 Opened cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian as #9, grid size 300,300,300, pixel 1.53, shown at step 1, values float32 Opened cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian as #10, grid size 300,300,300, pixel 1.53, shown at step 1, values float32 > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > show #!10 models > volume #1-5 step 1 sdLevel Missing ""sdLevel"" keyword's argument > volume #1-50 step 1 sdLevel 4 > hide #!10 models > show #!9 models > show #!10 models > hide #!9 models > hide #!10 models > show #!6 models > show #!7 models > show #!8 models > hide #!8 models > hide #!7 models > open /Users/toni/Library/CloudStorage/OneDrive- > Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive- Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb --- warnings | Ignored bad PDB record found on line 995 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 1989 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 2983 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 3977 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 4971 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 5965 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 6959 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 7953 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 8947 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 9941 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 10935 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 11929 Ignored bad PDB record found on line 11930 Chain information for biological_assembly_e3BP_A.pdb #11 --- Chain | Description A B C D E F G H I J K L | No description available > select add #11 11904 atoms, 12096 bonds, 12 pseudobonds, 1512 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #11,1,0,0,13.017,0,1,0,2.0623,0,0,1,45.548 > view matrix models #11,1,0,0,14.038,0,1,0,31.209,0,0,1,32.738 > ui tool show ""Fit in Map"" > fitmap #11 inMap #6 Fit molecule biological_assembly_e3BP_A.pdb (#11) to map cryosparc_P89_J996_006_volume_map_sharp.mrc gaussian (#6) using 11904 atoms average map value = 0.1231, steps = 100 shifted from previous position = 14.8 rotated from previous position = 0.422 degrees atoms outside contour = 3067, contour level = 0.088286 Position of biological_assembly_e3BP_A.pdb (#11) relative to cryosparc_P89_J996_006_volume_map_sharp.mrc gaussian (#6) coordinates: Matrix rotation and translation 0.99999184 0.00334560 -0.00226314 25.32757196 -0.00335949 0.99997535 -0.00616553 27.54298177 0.00224245 0.00617309 0.99997843 23.69083973 Axis 0.83663654 -0.30550765 -0.45464753 Axis point 0.00000000 -3969.37531503 4582.43915000 Rotation angle (degrees) 0.42249970 Shift along axis 2.00439896 > show #!7 models > hide #!6 models > fitmap #11 inMap #7 Fit molecule biological_assembly_e3BP_A.pdb (#11) to map cryosparc_P89_J997_007_volume_map_sharp.mrc gaussian (#7) using 11904 atoms average map value = 0.07373, steps = 48 shifted from previous position = 0.106 rotated from previous position = 1.31 degrees atoms outside contour = 7000, contour level = 0.08561 Position of biological_assembly_e3BP_A.pdb (#11) relative to cryosparc_P89_J997_007_volume_map_sharp.mrc gaussian (#7) coordinates: Matrix rotation and translation 0.99982467 -0.01872422 -0.00016475 29.47648205 0.01872413 0.99982452 -0.00057362 22.02535374 0.00017547 0.00057044 0.99999982 25.24774376 Axis 0.03053484 -0.00908048 0.99949246 Axis point -1174.42621402 1542.94618641 0.00000000 Rotation angle (degrees) 1.07342380 Shift along axis 25.93498838 > show #!8 models > hide #!7 models > fitmap #11 inMap #8 Fit molecule biological_assembly_e3BP_A.pdb (#11) to map cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) using 11904 atoms average map value = 0.1178, steps = 52 shifted from previous position = 0.254 rotated from previous position = 0.863 degrees atoms outside contour = 3807, contour level = 0.093453 Position of biological_assembly_e3BP_A.pdb (#11) relative to cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) coordinates: Matrix rotation and translation 0.99998600 -0.00455613 -0.00268979 27.19678492 0.00454270 0.99997729 -0.00497884 25.65353023 0.00271241 0.00496655 0.99998399 23.66181293 Axis 0.68485808 -0.37200560 0.62656305 Axis point 0.00000000 -1725.64990633 6946.75093443 Rotation angle (degrees) 0.41602320 Shift along axis 23.90829861 > show #!9 models > hide #!8 models > fitmap #11 inMap #8 Fit molecule biological_assembly_e3BP_A.pdb (#11) to map cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) using 11904 atoms average map value = 0.1178, steps = 28 shifted from previous position = 0.0182 rotated from previous position = 0.00833 degrees atoms outside contour = 3803, contour level = 0.093453 Position of biological_assembly_e3BP_A.pdb (#11) relative to cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) coordinates: Matrix rotation and translation 0.99998538 -0.00469848 -0.00267582 27.23274020 0.00468519 0.99997676 -0.00495308 25.61342002 0.00269903 0.00494047 0.99998415 23.68413135 Axis 0.67500972 -0.36671089 0.64022262 Axis point -0.00000000 -1641.66283141 6967.11501166 Rotation angle (degrees) 0.41989279 Shift along axis 24.15276096 > fitmap #11 inMap #9 Fit molecule biological_assembly_e3BP_A.pdb (#11) to map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) using 11904 atoms average map value = 0.07397, steps = 2000 shifted from previous position = 0.459 rotated from previous position = 3.99 degrees atoms outside contour = 6668, contour level = 0.086114 Position of biological_assembly_e3BP_A.pdb (#11) relative to cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99883925 -0.03813402 0.02942714 27.86300108 0.03974892 0.99761678 -0.05639844 29.01802933 -0.02720631 0.05750267 0.99797458 19.61146856 Axis 0.76365377 0.37970086 0.52216873 Axis point 0.00000000 53.16658883 225.89690202 Rotation angle (degrees) 4.27688395 Shift along axis 42.53635207 > show #!10 models > hide #!9 models > select subtract #11 Nothing selected > hide #!11 models > show #!9 models > fitmap #9 inMap #10 Fit map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian in map cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian using 436516 points correlation = 0.969, correlation about mean = 0.6195, overlap = 6695 steps = 48, shift = 0.0813, angle = 0.182 degrees Position of cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) relative to cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian (#10) coordinates: Matrix rotation and translation 0.99999516 -0.00078211 0.00301125 -0.55059297 0.00078025 0.99999951 0.00061733 -0.26306370 -0.00301174 -0.00061498 0.99999528 0.79046249 Axis -0.19427246 0.94952193 0.24630532 Axis point 257.93610444 0.00000000 179.91285577 Rotation angle (degrees) 0.18171906 Shift along axis 0.05187542 > select add #10 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.78611,0.49308,-0.37269,21.419,-0.46658,0.86888,0.1654,99.287,0.40537,0.043868,0.9131,-83.21 > view matrix models > #10,0.68932,0.66307,0.29183,-148.34,-0.70669,0.5268,0.4723,162.54,0.15943,-0.5318,0.83173,124.45 > view matrix models > #10,0.54594,0.8177,0.18251,-125.84,-0.73106,0.35852,0.58053,181.95,0.40927,-0.45036,0.79352,57.119 > fitmap #9 inMap #10 Fit map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian in map cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian using 436516 points correlation = 0.9644, correlation about mean = 0.513, overlap = 6581 steps = 76, shift = 0.477, angle = 5.48 degrees Position of cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) relative to cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian (#10) coordinates: Matrix rotation and translation 0.55885039 -0.71956560 0.41220333 171.83919178 0.79085423 0.31292324 -0.52595498 97.09428588 0.24947110 0.61992289 0.74394877 -140.95108443 Axis 0.60218635 0.08551970 0.79376191 Axis point 55.30522761 204.98600276 0.00000000 Rotation angle (degrees) 72.06961606 Shift along axis -0.09891203 > fitmap #9 inMap #10 Fit map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian in map cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian using 436516 points correlation = 0.9644, correlation about mean = 0.513, overlap = 6581 steps = 28, shift = 0.0342, angle = 0.0163 degrees Position of cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) relative to cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian (#10) coordinates: Matrix rotation and translation 0.55908073 -0.71945589 0.41208247 171.81762357 0.79068794 0.31310053 -0.52609946 97.14411975 0.24948211 0.61996071 0.74391357 -140.95545735 Axis 0.60232031 0.08545581 0.79366715 Axis point 55.24521293 205.02674211 0.00000000 Rotation angle (degrees) 72.05840218 Shift along axis -0.08094137 > close #7-11 > close #6 > close #4-5 > open /Users/toni/Downloads/cryosparc_P89_J1024_006_volume_map_sharp.mrc Opened cryosparc_P89_J1024_006_volume_map_sharp.mrc as #4, grid size 300,300,300, pixel 1.53, shown at level 0.154, step 2, values float32 > open /Users/toni/Downloads/cryosparc_P89_J1025_009_volume_map_sharp.mrc Opened cryosparc_P89_J1025_009_volume_map_sharp.mrc as #5, grid size 300,300,300, pixel 1.53, shown at level 0.157, step 2, values float32 > select add #5 2 models selected > view matrix models > #5,0.88194,0.22402,-0.41472,72.157,-0.30249,0.94376,-0.13349,114.75,0.36149,0.24317,0.90011,-117.55 > view matrix models > #5,0.5114,-0.70734,-0.48799,393.32,0.34881,0.68985,-0.63439,139.97,0.78537,0.15421,0.59951,-124.93 > view matrix models > #5,0.48196,-0.70241,-0.52377,407.39,0.3334,0.69982,-0.63174,140.6,0.81029,0.12985,0.57147,-118.46 > view matrix models > #5,0.86888,0.14802,-0.47238,106.47,-0.23737,0.96197,-0.13518,95.742,0.43441,0.22958,0.87097,-124.5 > view matrix models > #5,0.91252,0.12209,-0.3904,83.194,-0.21356,0.95621,-0.20014,106.77,0.34886,0.26601,0.89863,-119.61 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.91252,0.12209,-0.3904,83.236,-0.21356,0.95621,-0.20014,109.16,0.34886,0.26601,0.89863,-118.15 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.68391,0.72544,-0.077413,-78.012,-0.72777,0.68582,-0.0026576,245.73,0.051163,0.058156,0.997,-23.341 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 33730 points correlation = 0.9534, correlation about mean = 0.8017, overlap = 3176 steps = 108, shift = 6.36, angle = 4.95 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.71349516 -0.70066012 0.00022501 226.50878547 0.70066013 0.71349518 0.00001571 -95.05114281 -0.00017155 0.00014645 0.99999997 0.01819651 Axis 0.00009330 0.00028299 0.99999996 Axis point 229.48027169 229.44302407 0.00000000 Rotation angle (degrees) 44.47999254 Shift along axis 0.01243091 > select subtract #5 Nothing selected > hide #!5 models > show #!5 models > hide #!5 models > volume #5 step 1 > volume #4 step 1 > surface dust #4 size 15.3 > show #!5 models > select add #5 2 models selected > surface dust #5 size 15.3 > select subtract #5 Nothing selected > select add #5 2 models selected > view matrix models > #5,0.53513,0.81805,0.21078,-131.18,-0.6753,0.56416,-0.47508,369.93,-0.50755,0.11189,0.85433,125.34 > undo > select add #4 4 models selected > select subtract #5 2 models selected > view matrix models > #4,0.99516,0.08185,-0.054337,-7.0502,-0.083506,0.99609,-0.028921,32.691,0.051757,0.033319,0.9981,-18.033 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99516,0.08185,-0.054337,-8.634,-0.083506,0.99609,-0.028921,59.369,0.051757,0.033319,0.9981,27.739 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99498,0.081588,-0.058003,-7.6905,-0.083138,0.99623,-0.024829,58.313,0.055758,0.029526,0.99801,27.715 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99498,0.081588,-0.058003,4.11,-0.083138,0.99623,-0.024829,43.267,0.055758,0.029526,0.99801,-18.62 > view matrix models > #4,0.99498,0.081588,-0.058003,-1.465,-0.083138,0.99623,-0.024829,37.762,0.055758,0.029526,0.99801,-17.989 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.9537, correlation about mean = 0.8017, overlap = 2.544e+04 steps = 80, shift = 7.68, angle = 3.07 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.71356884 -0.70058511 0.00002445 226.52748083 0.70058511 0.71356884 0.00001489 -95.05882293 -0.00002788 0.00000650 1.00000000 0.01344891 Axis -0.00000599 0.00003735 1.00000000 Axis point 229.51645154 229.50361780 0.00000000 Rotation angle (degrees) 44.47396677 Shift along axis 0.00854215 > view matrix models > #4,0.99626,0.038512,-0.077385,8.2149,-0.038835,0.99924,-0.0026652,15.004,0.077224,0.0056605,0.997,-17.232 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.96702,0.013469,-0.25435,61.27,0.097074,0.90374,0.41692,-90.443,0.23548,-0.42786,0.87263,74.696 > view matrix models > #4,0.95215,0.088024,-0.29268,56.319,0.043762,0.90849,0.4156,-78.996,0.30248,-0.40853,0.86117,57.498 > undo > view matrix models > #4,0.1139,0.13661,-0.98406,396.1,-0.54012,0.83985,0.054072,153.73,0.83384,0.52535,0.16945,-120.69 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03602, overlap = 2715 steps = 104, shift = 0.606, angle = 4.96 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46910610 -0.50234789 -0.72635120 404.06939087 -0.30656844 0.67869035 -0.66737935 297.17688095 0.82822416 0.53574808 0.16437377 -121.18401198 Axis 0.60902820 -0.78693263 0.09910439 Axis point 407.16804487 0.00000000 258.51323205 Rotation angle (degrees) 81.02026571 Shift along axis 0.22160299 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03604, overlap = 2715 steps = 28, shift = 0.0336, angle = 0.00872 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46922285 -0.50234384 -0.72627859 404.00627956 -0.30658423 0.67861445 -0.66744927 297.19405691 0.82815217 0.53584801 0.16441071 -121.21846022 Axis 0.60911798 -0.78686433 0.09909496 Axis point 407.20728121 -0.00000000 258.48696922 Rotation angle (degrees) 81.01800926 Shift along axis 0.22394546 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715 steps = 36, shift = 0.00883, angle = 0.00471 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46918078 -0.50240920 -0.72626055 404.03134786 -0.30654745 0.67860320 -0.66747761 297.19843690 0.82818962 0.53580098 0.16437532 -121.20156407 Axis 0.60910419 -0.78686858 0.09914596 Axis point 407.20117868 0.00000000 258.50837340 Rotation angle (degrees) 81.02058226 Shift along axis 0.22442988 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715 steps = 40, shift = 0.00466, angle = 0.00225 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46920504 -0.50239001 -0.72625815 404.01841108 -0.30656937 0.67859222 -0.66747870 297.20389845 0.82816777 0.53583288 0.16438150 -121.20850433 Axis 0.60912183 -0.78685752 0.09912531 Axis point 407.20910017 0.00000000 258.49917684 Rotation angle (degrees) 81.02001800 Shift along axis 0.22448202 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03602, overlap = 2715 steps = 28, shift = 0.0209, angle = 0.00521 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46915424 -0.50236111 -0.72631096 404.04699215 -0.30656486 0.67865191 -0.66742009 297.18851608 0.82819822 0.53578438 0.16438616 -121.19359359 Axis 0.60906827 -0.78690053 0.09911307 Axis point 407.18550124 0.00000000 258.51014715 Rotation angle (degrees) 81.01962501 Shift along axis 0.22253602 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715 steps = 28, shift = 0.0238, angle = 0.00428 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46920618 -0.50234859 -0.72628606 404.01279300 -0.30659147 0.67861531 -0.66744508 297.19507315 0.82815894 0.53584247 0.16439471 -121.21371388 Axis 0.60911149 -0.78686954 0.09909345 Axis point 407.20332297 0.00000000 258.48711411 Rotation angle (degrees) 81.01893209 Shift along axis 0.22359975 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715 steps = 40, shift = 0.00387, angle = 0.00484 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.46919264 -0.50241766 -0.72624703 404.02547405 -0.30653776 0.67859463 -0.66749077 297.19943029 0.82818649 0.53580390 0.16438162 -121.20581101 Axis 0.60911280 -0.78686075 0.09915522 Axis point 407.20588933 0.00000000 258.50838860 Rotation angle (degrees) 81.02030407 Shift along axis 0.22433087 > view matrix models > #4,0.18721,-0.17448,-0.9667,446.84,-0.66178,0.70486,-0.25538,284,0.72595,0.68755,0.016484,-97.648 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.2534, correlation about mean = 0.02864, overlap = 3128 steps = 120, shift = 2.53, angle = 7.74 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.62201886 -0.68445581 -0.38027988 331.78991508 -0.18038784 0.34733971 -0.92022570 404.73524920 0.76194013 0.64099561 0.09258435 -114.62169703 Axis 0.78098532 -0.57138412 0.25215495 Axis point 0.00000000 399.25849403 156.00695193 Rotation angle (degrees) 88.22518230 Shift along axis -1.03866855 > view matrix models > #4,0.20308,-0.32042,-0.92525,469.23,-0.52147,0.7644,-0.37917,267.86,0.82875,0.55949,-0.011855,-86.019 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.20308,-0.32042,-0.92525,465.56,-0.52147,0.7644,-0.37917,258.22,0.82875,0.55949,-0.011855,-81.989 > fitmap #4 inMap #5 Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points correlation = 0.9771, correlation about mean = 0.8599, overlap = 2.584e+04 steps = 324, shift = 9.27, angle = 27.8 degrees Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.50002418 -0.86601144 -0.00000887 313.49107673 0.28867002 0.16668412 -0.94280752 341.36539270 0.81648358 0.47142400 0.33333763 -142.56599548 Axis 0.70711576 -0.40824623 0.57734073 Axis point 0.00000000 361.99029665 42.12401708 Rotation angle (degrees) 89.99868439 Shift along axis 0.00419116 > select subtract #4 Nothing selected > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > close #5 > close > open ""/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series > 2/J1471_class_00_02315_volume.mrc"" Opened J1471_class_00_02315_volume.mrc as #1, grid size 240,240,240, pixel 1.91, shown at level 0.0875, step 1, values float32 > open ""/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series > 2/J1471_class_01_02315_volume.mrc"" Opened J1471_class_01_02315_volume.mrc as #2, grid size 240,240,240, pixel 1.91, shown at level 0.0877, step 1, values float32 > open ""/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series > 2/J1471_class_02_02315_volume.mrc"" Opened J1471_class_02_02315_volume.mrc as #3, grid size 240,240,240, pixel 1.91, shown at level 0.0897, step 1, values float32 > open ""/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series > 2/J1471_class_03_02315_volume.mrc"" Opened J1471_class_03_02315_volume.mrc as #4, grid size 240,240,240, pixel 1.91, shown at level 0.0894, step 1, values float32 > open ""/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series > 2/J1471_class_04_02315_volume.mrc"" Opened J1471_class_04_02315_volume.mrc as #5, grid size 240,240,240, pixel 1.91, shown at level 0.0894, step 1, values float32 > open /Users/toni/Downloads/cryosparc_P89_J1471__mask_focus.mrc Opened cryosparc_P89_J1471__mask_focus.mrc as #6, grid size 240,240,240, pixel 1.91, shown at level 5e-05, step 1, values float32 > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > hide #!1 models > show #!1 models > volume #1-50 step 1 sdLevel 4 > volume #1-50 step 1 sdLevel 3 > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!5 models > hide #!4 models > show #!6 models > hide #!5 models > hide #!6 models > show #!5 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!4 models > volume #1-50 step 1 sdLevel 4 > volume #1-50 step 1 sdLevel 5 > show #!3 models > hide #!4 models > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > surface dust #1 size 19.1 > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > close #6 > hide #!1 models > show #!1 models > volume #1-50 step 1 sdLevel 4 > volume #1-50 step 1 sdLevel 3 > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > volume #1-50 step 1 sdLevel 4 > volume #1-50 step 1 sdLevel 5 > volume #1-50 step 1 sdLevel 6 > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > open /Users/toni/Downloads/cryosparc_P89_J1471__mask_focus.mrc Opened cryosparc_P89_J1471__mask_focus.mrc as #6, grid size 240,240,240, pixel 1.91, shown at level 5e-05, step 1, values float32 > hide #!6 models > show #!5 models > hide #!4 models > view #5 clip false > show #!6 models > hide #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!2 models > volume #2 level 0.07446 > hide #!2 models > show #!1 models > volume #1 level 0.0805 > close #5 > close > open > /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_00_01013_volume.mrc Opened J1473_class_00_01013_volume.mrc as #1, grid size 240,240,240, pixel 1.91, shown at level 0.0891, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_01_01013_volume.mrc Opened J1473_class_01_01013_volume.mrc as #2, grid size 240,240,240, pixel 1.91, shown at level 0.0819, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_02_01013_volume.mrc Opened J1473_class_02_01013_volume.mrc as #3, grid size 240,240,240, pixel 1.91, shown at level 0.0888, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_03_01013_volume.mrc Opened J1473_class_03_01013_volume.mrc as #4, grid size 240,240,240, pixel 1.91, shown at level 0.0899, step 1, values float32 > open > /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_04_01013_volume.mrc Opened J1473_class_04_01013_volume.mrc as #5, grid size 240,240,240, pixel 1.91, shown at level 0.09, step 1, values float32 > open /Users/toni/Downloads/cryosparc_P89_J1473__mask_focus.mrc Opened cryosparc_P89_J1473__mask_focus.mrc as #6, grid size 240,240,240, pixel 1.91, shown at level 5e-05, step 1, values float32 > volume #6 level 0.8163 > hide #!6 models > volume #1-50 step 1 sdLevel 6 > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > open /Users/toni/Downloads/cryosparc_P89_J1470_mask.mrc Opened cryosparc_P89_J1470_mask.mrc as #7, grid size 600,600,600, pixel 0.765, shown at level 5e-05, step 4, values float32 > hide #!7 models > show #!7 models > hide #!7 models > hide #!5 models > hide #!4 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!7 models > show #!1 models > open /Users/toni/Downloads/cryosparc_P89_P89_J1334_onlye3bp.mrc Opened cryosparc_P89_P89_J1334_onlye3bp.mrc as #8, grid size 600,600,600, pixel 0.765, shown at level 2.66e-05, step 4, values float32 > hide #!7 models > hide #!8 models > show #!8 models > open /Users/toni/Library/CloudStorage/OneDrive- > Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive- Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb --- warnings | Ignored bad PDB record found on line 995 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 1989 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 2983 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 3977 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 4971 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 5965 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 6959 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 7953 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 8947 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 9941 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 10935 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 11929 Ignored bad PDB record found on line 11930 Chain information for biological_assembly_e3BP_A.pdb #9 --- Chain | Description A B C D E F G H I J K L | No description available > close #9 > open /Users/toni/Library/CloudStorage/OneDrive- > Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive- Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 252 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""1"" on line 130 Bad residue range for struct_conf ""2"" on line 131 Bad residue range for struct_conf ""3"" on line 132 Bad residue range for struct_conf ""4"" on line 133 Bad residue range for struct_conf ""5"" on line 134 2 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""A 1"" on line 232 Invalid sheet range for struct_sheet_range ""A 2"" on line 234 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for E3BP_3_1_monomer_real_space_refined_037.cif #9 --- Chain | Description A | No description available Computing secondary structure > hide #!8 models > select add #9 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.94097,-0.013942,0.33821,-54.481,-0.15444,-0.90677,0.39231,356.81,0.30121,-0.42139,-0.8554,409.48 > view matrix models > #9,0.70952,-0.2054,0.67409,-28.306,-0.61737,-0.6424,0.45408,402.61,0.33976,-0.73833,-0.5826,408.66 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.70952,-0.2054,0.67409,-13.745,-0.61737,-0.6424,0.45408,411.2,0.33976,-0.73833,-0.5826,418.32 > view matrix models > #9,0.70952,-0.2054,0.67409,-14.2,-0.61737,-0.6424,0.45408,411.21,0.33976,-0.73833,-0.5826,418.55 > view matrix models > #9,0.70952,-0.2054,0.67409,-15.874,-0.61737,-0.6424,0.45408,408.77,0.33976,-0.73833,-0.5826,417.86 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.74292,-0.010994,0.66929,-64.126,-0.58096,-0.50725,0.63654,332.38,0.3325,-0.86173,-0.38323,403.21 > view matrix models > #9,0.49608,0.16787,0.8519,-79.581,-0.53488,-0.71378,0.45212,403.8,0.68397,-0.67995,-0.2643,252.45 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.49608,0.16787,0.8519,-69.079,-0.53488,-0.71378,0.45212,397.54,0.68397,-0.67995,-0.2643,266.48 > ui tool show ""Fit in Map"" > fitmap #9 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#9) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.1065, steps = 176 shifted from previous position = 8.91 rotated from previous position = 29 degrees atoms outside contour = 651, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#9) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.74405201 -0.02881021 0.66750025 -52.18022232 -0.61404554 -0.42323302 0.66619958 305.46963556 0.26331479 -0.90556269 -0.33259816 427.31867377 Axis -0.91106276 0.23428372 -0.33922822 Axis point 0.00000000 277.60361246 125.44013394 Rotation angle (degrees) 120.39042292 Shift along axis -25.85253200 > show #!8 models > select add #7 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected > select subtract #7 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > select add #8 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected > select subtract #8 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > select add #8 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected > view matrix models > #8,1,0,0,-4.5027,0,1,0,-13.415,0,0,1,-27.193,#9,0.74405,-0.02881,0.6675,-56.683,-0.61405,-0.42323,0.6662,292.05,0.26331,-0.90556,-0.3326,400.13 > view matrix models > #8,1,0,0,-7.8697,0,1,0,-27.038,0,0,1,-42.023,#9,0.74405,-0.02881,0.6675,-60.05,-0.61405,-0.42323,0.6662,278.43,0.26331,-0.90556,-0.3326,385.3 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.95568,0.17905,0.2337,-99.181,0.08132,0.60237,-0.79407,250.24,-0.28295,0.77788,0.56111,-45.869,#9,0.66267,-0.31494,0.67948,5.5094,-0.51846,0.46179,0.71968,90.678,-0.54044,-0.82919,0.14273,446.29 > view matrix models > #8,0.94584,0.28524,0.15499,-103.5,0.098914,0.2015,-0.97448,389.63,-0.3092,0.93703,0.16238,19.932,#9,0.56941,-0.28833,0.76983,0.50744,-0.30673,0.79432,0.52438,29.607,-0.76268,-0.53472,0.36386,391.69 > view matrix models > #8,0.93527,0.34869,0.060769,-92.39,0.1451,-0.22113,-0.96439,477.59,-0.32283,0.91078,-0.25741,134.97,#9,0.49778,-0.22955,0.83638,-8.7109,-0.010189,0.96272,0.27029,-9.6359,-0.86724,-0.14307,0.47688,320.03 > view matrix models > #8,0.94798,0.20983,-0.23937,13.637,0.10109,-0.91151,-0.39865,523.95,-0.30184,0.35372,-0.88531,425.64,#9,0.51348,0.10065,0.85218,-74.021,0.52996,0.74388,-0.40718,69.887,-0.6749,0.6607,0.32862,171.13 > view matrix models > #8,0.98133,-0.06555,-0.18081,56.652,-0.10149,-0.97506,-0.19735,544.88,-0.16337,0.21202,-0.96351,441.38,#9,0.7228,0.16321,0.67151,-91.843,0.47125,0.59432,-0.6517,167.99,-0.50545,0.78749,0.35266,102.95 > fitmap #8 inMap #1 Fit map cryosparc_P89_P89_J1334_onlye3bp.mrc in map J1473_class_00_01013_volume.mrc using 7049 points correlation = 0.781, correlation about mean = 0.6826, overlap = 56.66 steps = 104, shift = 19.6, angle = 32.8 degrees Position of cryosparc_P89_P89_J1334_onlye3bp.mrc (#8) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.90747772 0.34103784 -0.24531077 -0.21948162 0.12755608 -0.78004945 -0.61257841 519.38463105 -0.40026695 0.52461038 -0.75137895 373.00034346 Axis 0.97413472 0.13273802 -0.18287201 Axis point 0.00000000 198.01914799 272.34413332 Rotation angle (degrees) 144.28937859 Shift along axis 0.51696245 > hide #!8 models > select subtract #8 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > select add #8 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected > select subtract #8 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > show #!8 models > hide #!8 models > hide #!9 models > select subtract #9 Nothing selected > show #!9 models > select add #9 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > view matrix models > #9,0.30418,-0.42358,-0.85326,460.45,0.91757,-0.11044,0.38193,-14.169,-0.25601,-0.8991,0.35508,396.3 > view matrix models > #9,-0.49038,0.72261,-0.4872,337.64,0.50482,0.69121,0.51709,-109.75,0.71041,0.0076224,-0.70375,191.18 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.49038,0.72261,-0.4872,322.7,0.50482,0.69121,0.51709,-104.36,0.71041,0.0076224,-0.70375,202.61 > open /Users/toni/Downloads/cryosparc_P89_J1338_011_volume_map_sharp.mrc Opened cryosparc_P89_J1338_011_volume_map_sharp.mrc as #10, grid size 600,600,600, pixel 0.765, shown at level 0.0448, step 4, values float32 > volume #10 step 1 > volume #10 level 0.05954 > surface dust #1 size 19.1 > surface dust #10 size 7.65 > hide #!1 models > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.49038,0.72261,-0.4872,326.28,0.50482,0.69121,0.51709,-171.8,0.71041,0.0076224,-0.70375,202.25 > view matrix models > #9,-0.49038,0.72261,-0.4872,329.38,0.50482,0.69121,0.51709,-171.89,0.71041,0.0076224,-0.70375,200.5 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.39533,0.71488,-0.57677,130.62,-0.75289,0.6119,0.24237,215,0.52619,0.33843,0.78012,-139.73 > view matrix models > #9,0.87114,0.43749,-0.22296,-4.1559,-0.48145,0.67172,-0.56303,306.7,-0.096551,0.59782,0.79579,-43.457 > view matrix models > #9,0.96863,0.23495,0.080963,-50.345,-0.15614,0.82884,-0.53726,187.47,-0.19334,0.50776,0.83952,-9.7976 > view matrix models > #9,0.83774,0.49998,-0.21959,-9.7757,0.38021,-0.82268,-0.42266,378.44,-0.39197,0.27059,-0.87928,455.6 > view matrix models > #9,0.97204,0.1072,-0.20894,37.512,0.23475,-0.46779,0.85209,68.082,-0.0063987,-0.87731,-0.47988,517.05 > view matrix models > #9,0.56856,0.079117,0.81883,-75.534,-0.73864,-0.38909,0.55047,356.93,0.36215,-0.91779,-0.16278,366.71 > volume #10 level 0.07539 > fitmap #9 inMap #10 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#9) to map cryosparc_P89_J1338_011_volume_map_sharp.mrc (#10) using 992 atoms average map value = 0.02353, steps = 140 shifted from previous position = 4.21 rotated from previous position = 7.39 degrees atoms outside contour = 926, contour level = 0.075394 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#9) relative to cryosparc_P89_J1338_011_volume_map_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.46052523 0.10935370 0.88088494 -65.13837139 -0.79689697 -0.38618778 0.46455809 387.89791415 0.39098814 -0.91591526 -0.09070559 346.99675159 Axis -0.80143732 0.28441083 -0.52612613 Axis point 0.00000000 302.25831154 54.65413271 Rotation angle (degrees) 120.54294694 Shift along axis -20.03736834 > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!1 models > hide #!9 models > show #!9 models > select subtract #9 Nothing selected > hide #!10 models > fitmap #9 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#9) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.1065, steps = 80 shifted from previous position = 10.4 rotated from previous position = 22.1 degrees atoms outside contour = 649, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#9) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.74407238 -0.02758108 0.66752945 -52.43283439 -0.61374840 -0.42295679 0.66664867 305.24018121 0.26394922 -0.90573000 -0.33163831 426.96504474 Axis -0.91103126 0.23383312 -0.33962350 Axis point 0.00000000 277.46906048 125.31099316 Rotation angle (degrees) 120.34870348 Shift along axis -25.86414757 > close #10 > open /Users/toni/Library/CloudStorage/OneDrive- > Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive- Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 252 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""1"" on line 130 Bad residue range for struct_conf ""2"" on line 131 Bad residue range for struct_conf ""3"" on line 132 Bad residue range for struct_conf ""4"" on line 133 Bad residue range for struct_conf ""5"" on line 134 2 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""A 1"" on line 232 Invalid sheet range for struct_sheet_range ""A 2"" on line 234 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for E3BP_3_1_monomer_real_space_refined_037.cif #10 --- Chain | Description A | No description available Computing secondary structure > select add #10 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > view matrix models > #10,-0.25543,-0.83776,-0.48261,590.57,0.39744,0.36406,-0.84232,215.07,0.88136,-0.40696,0.23997,29.339 > view matrix models > #10,-0.80113,-0.58323,0.1343,540.69,-0.39439,0.34567,-0.85145,417.1,0.45017,-0.73509,-0.50695,364.5 > view matrix models > #10,-0.66796,-0.4155,0.61741,369.4,-0.71705,0.58137,-0.38451,347.87,-0.19918,-0.69955,-0.68626,556.1 > view matrix models > #10,0.14765,0.040409,0.98821,-7.8353,0.76662,0.62662,-0.14016,-81.36,-0.62489,0.77828,0.06154,190.63 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.14765,0.040409,0.98821,8.1246,0.76662,0.62662,-0.14016,-66.481,-0.62489,0.77828,0.06154,195.81 > view matrix models > #10,0.14765,0.040409,0.98821,13.773,0.76662,0.62662,-0.14016,-72.51,-0.62489,0.77828,0.06154,199.05 > fitmap #10 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.08083, steps = 140 shifted from previous position = 12.3 rotated from previous position = 43.5 degrees atoms outside contour = 799, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28329892 0.56251511 0.77673578 53.73033503 0.87996380 0.47449881 -0.02268461 -104.25674533 -0.38132064 0.67707284 -0.62941793 309.82382815 Axis 0.50349706 0.83325729 0.22841412 Axis point 132.90618760 0.00000000 157.50603715 Rotation angle (degrees) 135.98096887 Shift along axis 10.94850925 > view matrix models > #10,-0.2833,0.56252,0.77674,67.315,0.87996,0.4745,-0.022685,-106.96,-0.38132,0.67707,-0.62942,305.2 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.25354,0.39472,0.88313,72.662,0.90842,0.41089,0.07715,-121.87,-0.33241,0.82181,-0.46274,227.05 > view matrix models > #10,0.75531,0.42376,0.49992,-101.81,0.37749,0.34225,-0.86045,223.9,-0.53572,0.83862,0.098534,154.31 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.75531,0.42376,0.49992,-109.38,0.37749,0.34225,-0.86045,238.05,-0.53572,0.83862,0.098534,151.52 > fitmap #10 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.07891, steps = 104 shifted from previous position = 6.53 rotated from previous position = 44.4 degrees atoms outside contour = 764, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.89241176 0.41876133 -0.16804818 -2.65854356 -0.05553114 -0.26767125 -0.96190872 492.34295104 -0.44779184 0.86775057 -0.21561868 184.57739511 Axis 0.95757425 0.14640722 -0.24822668 Axis point 0.00000000 173.03079056 280.19711101 Rotation angle (degrees) 107.18386873 Shift along axis 23.71977587 > view matrix models > #10,0.89241,0.41876,-0.16805,-1.8841,-0.055531,-0.26767,-0.96191,495.03,-0.44779,0.86775,-0.21562,186.32 > fitmap #10 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.07893, steps = 56 shifted from previous position = 3.3 rotated from previous position = 0.0554 degrees atoms outside contour = 764, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.89249000 0.41850331 -0.16827532 -2.57263341 -0.05618702 -0.26700805 -0.96205494 492.38609970 -0.44755405 0.86807930 -0.21478757 184.28094744 Axis 0.95757946 0.14612675 -0.24837178 Axis point 0.00000000 173.09580830 280.24034989 Rotation angle (degrees) 107.13671967 Shift along axis 23.71709286 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.6602,0.71576,-0.22765,4.9474,-0.124,-0.19507,-0.97292,496.33,-0.74078,0.67055,-0.040033,261.37 > view matrix models > #10,0.71814,-0.59604,-0.35917,295.25,-0.62259,-0.78088,0.051034,525.29,-0.31089,0.18697,-0.93188,446.82 > view matrix models > #10,0.87295,0.44502,-0.19978,3.3888,-0.12,-0.20106,-0.9722,496.45,-0.47282,0.87266,-0.12211,169.83 > view matrix models > #10,0.75808,0.65214,-0.0054976,-53.214,0.46129,-0.54215,-0.70234,366.86,-0.461,0.52989,-0.71182,364.82 > fitmap #10 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.1089, steps = 92 shifted from previous position = 5.23 rotated from previous position = 23.6 degrees atoms outside contour = 623, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.90148490 0.35685504 -0.24490703 22.91886922 0.13736913 -0.77250423 -0.61997333 484.42737943 -0.41043232 0.52525393 -0.74542177 358.25267936 Axis 0.97237761 0.14054249 -0.18635880 Axis point 0.00000000 179.82785253 261.88910419 Rotation angle (degrees) 143.92243695 Shift along axis 23.60488578 > open /Users/toni/Library/CloudStorage/OneDrive- > Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive- Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 252 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""1"" on line 130 Bad residue range for struct_conf ""2"" on line 131 Bad residue range for struct_conf ""3"" on line 132 Bad residue range for struct_conf ""4"" on line 133 Bad residue range for struct_conf ""5"" on line 134 2 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""A 1"" on line 232 Invalid sheet range for struct_sheet_range ""A 2"" on line 234 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for E3BP_3_1_monomer_real_space_refined_037.cif #11 --- Chain | Description A | No description available Computing secondary structure > select add #11 1984 atoms, 2016 bonds, 92 pseudobonds, 252 residues, 6 models selected > select subtract #10 992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected > view matrix models > #11,0.01914,-0.89621,0.44322,337.63,0.85245,-0.21702,-0.47564,146.75,0.52246,0.38692,0.75982,-159.89 > view matrix models > #11,-0.51092,-0.61235,0.60331,375.01,0.52025,-0.77897,-0.35006,320.82,0.68432,0.13502,0.71657,-137.66 > view matrix models > #11,-0.87184,-0.20112,0.4466,411.1,-0.17044,-0.73025,-0.66158,548.06,0.45918,-0.65291,0.60238,108.61 > view matrix models > #11,-0.78005,0.37807,0.49858,255.14,-0.572,-0.10786,-0.81313,548.59,-0.25364,-0.91947,0.30039,405.79 > view matrix models > #11,-0.58137,0.53872,0.60975,148.35,-0.57258,0.26154,-0.77701,463.14,-0.57806,-0.80086,0.15641,491.84 > view matrix models > #11,-0.17579,0.71849,0.67296,-3.5315,-0.14711,0.65675,-0.73962,266.4,-0.97337,-0.22901,-0.009751,504.6 > view matrix models > #11,-0.12104,0.47493,0.87166,-8.0612,-0.076511,0.87104,-0.48521,149.52,-0.98969,-0.12542,-0.069097,499.44 > view matrix models > #11,0.08568,0.2685,0.95946,-34.456,0.29656,0.91248,-0.28183,5.0106,-0.95116,0.30868,-0.0014431,383.93 > view matrix models > #11,0.12213,0.88893,0.44145,-63.981,-0.095124,0.45322,-0.88631,327.69,-0.98794,0.066255,0.13991,414.05 > view matrix models > #11,0.52491,0.78051,0.33953,-119.21,-0.35544,0.56346,-0.74577,339.01,-0.77339,0.27078,0.57319,225.46 > view matrix models > #11,0.25048,0.86657,0.43164,-88.977,-0.18284,0.48017,-0.85791,337.69,-0.9507,0.13597,0.27872,360.55 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.25048,0.86657,0.43164,-80.114,-0.18284,0.48017,-0.85791,329.76,-0.9507,0.13597,0.27872,350.89 > fitmap #11 inMap #1 Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#11) to map J1473_class_00_01013_volume.mrc (#1) using 992 atoms average map value = 0.1047, steps = 104 shifted from previous position = 7.21 rotated from previous position = 34.3 degrees atoms outside contour = 671, contour level = 0.1237 Position of E3BP_3_1_monomer_real_space_refined_037.cif (#11) relative to J1473_class_00_01013_volume.mrc (#1) coordinates: Matrix rotation and translation 0.33325705 0.84798050 0.41215144 -94.43626399 -0.66702743 0.52099541 -0.53257694 368.09366017 -0.66634387 -0.09743130 0.73925164 235.07951891 Axis 0.22783578 0.56468410 -0.79323561 Axis point 301.67135835 348.52601768 0.00000000 Rotation angle (degrees) 72.73737232 Shift along axis -0.13276833 > select subtract #11 Nothing selected > combine #9-11 Remapping chain ID 'A' in E3BP_3_1_monomer_real_space_refined_037.cif #10 to 'B' Remapping chain ID 'A' in E3BP_3_1_monomer_real_space_refined_037.cif #11 to 'C' > hide #!11 models > hide #!10 models > hide #!9 models > save /Users/toni/Desktop/testtrimer_e3bp_B.pdb models #12 relModel #1 > close #11 > close #2-10,12 > open /Users/toni/Desktop/test_combination.pdb Chain information for test_combination.pdb #2 --- Chain | Description A | No description available > close #2 > open /Users/toni/Desktop/testtrimer_e3bp_B.pdb Chain information for testtrimer_e3bp_B.pdb #2 --- Chain | Description A B C | No description available > molmap #2 20 Opened testtrimer_e3bp_B.pdb map 20 as #3, grid size 28,29,28, pixel 6.67, shown at level 0.0197, step 1, values float32 > open /Users/toni/Downloads/cryosparc_P89_P89_J1334_onlye3bp.mrc Opened cryosparc_P89_P89_J1334_onlye3bp.mrc as #4, grid size 600,600,600, pixel 0.765, shown at level 2.66e-05, step 4, values float32 > fitmap #4 inMap #3 Fit map cryosparc_P89_P89_J1334_onlye3bp.mrc in map testtrimer_e3bp_B.pdb map 20 using 7049 points correlation = 0.6488, correlation about mean = 0.4047, overlap = 81.14 steps = 108, shift = 59.1, angle = 65.2 degrees Position of cryosparc_P89_P89_J1334_onlye3bp.mrc (#4) relative to testtrimer_e3bp_B.pdb map 20 (#3) coordinates: Matrix rotation and translation 0.88600142 -0.28343672 0.36696744 13.81257916 0.45991734 0.43653956 -0.77324592 162.61267531 0.05897049 0.85387167 0.51713214 -149.85647360 Axis 0.89638502 0.16967664 0.40951646 Axis point 0.00000000 203.11936015 66.98167563 Rotation angle (degrees) 65.17573068 Shift along axis -21.39573114 > select add #4 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.65944,0.68458,-0.31063,-3.4316,0.18073,-0.54546,-0.81842,500.68,-0.72971,0.48355,-0.48342,408.03 > view matrix models > #4,0.098254,0.94795,0.30288,-71.887,-0.53984,0.30645,-0.784,469.3,-0.83601,-0.086478,0.54186,326.88 > fitmap #4 inMap #3 Fit map cryosparc_P89_P89_J1334_onlye3bp.mrc in map testtrimer_e3bp_B.pdb map 20 using 7049 points correlation = 0.8988, correlation about mean = 0.8699, overlap = 120.1 steps = 56, shift = 2.88, angle = 21.6 degrees Position of cryosparc_P89_P89_J1334_onlye3bp.mrc (#4) relative to testtrimer_e3bp_B.pdb map 20 (#3) coordinates: Matrix rotation and translation 0.34389382 0.84487784 0.40977859 -136.76376659 -0.66369315 0.52740963 -0.53042482 382.13340810 -0.66426534 -0.08955742 0.74211254 232.14552109 Axis 0.23159577 0.56421506 -0.79248013 Axis point 296.55843400 392.16144316 0.00000000 Rotation angle (degrees) 72.13904959 Shift along axis -0.03919735 > select subtract #4 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > vop resample #4 onGrid #1 Opened cryosparc_P89_P89_J1334_onlye3bp.mrc resampled as #5, grid size 240,240,240, pixel 1.91, shown at step 1, values float32 > save /Users/toni/Desktop/fixed_maskE3BP_config_B.mrc models #5 > close #2-5 > open /Users/toni/Desktop/fixed_maskE3BP_config_B.mrc Opened fixed_maskE3BP_config_B.mrc as #2, grid size 240,240,240, pixel 1.91, shown at level 2.62e-05, step 1, values float32 > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select add #2 2 models selected > select subtract #2 Nothing selected > select add #2 2 models selected > transparency sel 50 > open /Users/toni/Downloads/cryosparc_P89_P89_J1334_onlye3bp.mrc Opened cryosparc_P89_P89_J1334_onlye3bp.mrc as #3, grid size 600,600,600, pixel 0.765, shown at level 2.66e-05, step 4, values float32 > hide #!3 models > volume #2 level 0.04 > open /Users/toni/Downloads/cryosparc_P89_J2846_mask.mrc Opened cryosparc_P89_J2846_mask.mrc as #4, grid size 240,240,240, pixel 1.91, shown at level 5e-05, step 1, values float32 > volume #4 level 0.9029 > open /Users/toni/Downloads/cryosparc_P89_J1470_mask(1).mrc Opened cryosparc_P89_J1470_mask(1).mrc as #5, grid size 600,600,600, pixel 0.765, shown at level 5e-05, step 4, values float32 > volume #5 level 0.8133 > open /Users/toni/Documents/Phenix/ApplyNCS_55/Kastritis_Lab_apply_ncs_55.pdb Summary of feedback from opening /Users/toni/Documents/Phenix/ApplyNCS_55/Kastritis_Lab_apply_ncs_55.pdb --- warnings | Ignored bad PDB record found on line 995 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 1989 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 2983 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 3977 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 4971 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 5965 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 6959 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 7953 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 8947 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 9941 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 10935 Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 987 messages similar to the above omitted Ignored bad PDB record found on line 11929 Ignored bad PDB record found on line 11930 Chain information for Kastritis_Lab_apply_ncs_55.pdb #6 --- Chain | Description A B C D E F G H I J K L | No description available > close > open /Users/toni/Downloads/cryosparc_P89_J1792_map_locres.mrc Opened cryosparc_P89_J1792_map_locres.mrc as #1, grid size 600,600,600, pixel 0.68, shown at level 3.64, step 4, values float32 > open /Users/toni/Library/CloudStorage/OneDrive- > Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E2_core/cryosparc_P89_J1787_015_volume_map_sharp.mrc Opened cryosparc_P89_J1787_015_volume_map_sharp.mrc as #2, grid size 600,600,600, pixel 0.68, shown at level 0.0518, step 4, values float32 > hide #!1 models > volume #2 step 1 > volume #2 level 0.05473 > surface dust #2 size 6.8 > ui tool show ""Surface Color"" > color sample #2.1 map #1 palette #ff0000:#ffffff:#0000ff outsideColor > #808080 Map values for surface ""surface"": minimum 0, mean 2.454, maximum 3.801 > color sample #2.1 map #1 palette 4,#ff0000:3.5,#fffb00:3,#0000ff:2.5,#00fa92 > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 2.454, maximum 3.801 > color single #2.1 > color sample #2.1 map #1 palette 4,#ff0000:3.5,#fffb00:3,#0000ff:2.5,#00fa92 > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 2.454, maximum 3.801 > volume #2 level 0.0727 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00:2.5,#ff0000 > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 2.438, maximum 3.572 > volume #2 level 0.07569 > surface dust #2 size 6.8 > volume #2 level 0.08318 > volume #2 level 0.197 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00 > outsideColor #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00 > outsideColor #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00 > outsideColor #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00 > outsideColor #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00 > outsideColor #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 > color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00 > outsideColor #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 > color sample #2.1 map #1 palette 10,#00fa92:5,#0000ff:3,#fffb00 outsideColor > #808080 Map values for surface ""surface"": minimum 1.777, mean 2.411, maximum 2.661 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202502120650 (2025-02-12) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,9 Model Number: MUW63D/A Chip: Apple M3 Max Total Number of Cores: 16 (12 performance and 4 efficiency) Memory: 48 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 7 days, 7 hours, 16 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal VA24DQLB: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: 180 BenQ BL2381T: Resolution: 1200 x 1920 UI Looks like: 1200 x 1920 @ 60.00Hz Mirror: Off Online: Yes Rotation: 90 Installed Packages: alabaster: 1.0.0 anyio: 4.8.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 babel: 2.17.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.19.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.0.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202502120650 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.7 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-ProfileGrids: 1.0.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.43 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 coverage: 7.6.12 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.12 decorator: 5.1.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.15.4 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.5 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.6 pluggy: 1.5.0 prompt_toolkit: 3.0.50 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.4 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2025.1 pyzmq: 26.2.1 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.1.3 sphinx-autodoc-typehints: 3.0.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2025.1 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX