id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9868 Failed to lock QIOSurfaceGraphicsBuffer chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4.dev202203190100 (2022-03-19 01:00:21 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Illegal instruction Thread 0x00000003228ed000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003218ea000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003208e7000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File 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Thread 0x000000031e8e1000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031d8de000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031c8db000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File 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""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031a8d5000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003198d2000 (most recent call first): File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File 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""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.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"":""2023-09-27 14:36:50.00 -0700"",""app_version"":""1.4.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.4.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.2.1 (22D68)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A73703E4-FF31-45FD-91B6-49A5751966EE""} { ""uptime"" : 34000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 3191, ""osVersion"" : { ""train"" : ""macOS 13.2.1"", ""build"" : ""22D68"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-09-27 14:36:44.8108 -0700"", ""incident"" : ""A73703E4-FF31-45FD-91B6-49A5751966EE"", ""pid"" : 3791, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-09-26 17:45:11.0108 -0700"", ""procStartAbsTime"" : 282702051697, ""procExitAbsTime"" : 825450088057, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.4.0"",""CFBundleVersion"":""1.4.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""2A554CB2-D81E-5AB0-8057-FC287B0A43CC"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, 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""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/holoenzyme hCaW196R_RIa R333K/flipback_hetdimer.mrc"" Opened flipback_hetdimer.mrc as #1, grid size 38,41,46, pixel 3.33,3.33,3.33, shown at level 0.36, step 1, values float32 > volume #1 level 0.2196 > volume #1 level 0.334 > volume #1 level 0.3577 > volume #1 level 0.3883 > volume #1 level 0.3566 > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/holoenzyme hCaW196R_RIa R333K/flipback_hetdimer > (1).pdb"" Chain information for flipback_hetdimer (1).pdb #2 --- Chain | Description A | No description available X | No description available > hide #!1 models > set bgColor white > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 2/A > select /A:13-14 11 atoms, 10 bonds, 2 residues, 1 model selected > select /A:13-204 1587 atoms, 1623 bonds, 192 residues, 1 model selected > select /A:303 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:302-303 22 atoms, 23 bonds, 2 residues, 1 model selected > ui tool show ""Blast Protein"" > blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name > bp1 Webservices job id: KDLD59KE9GFXB08R > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel sphere Changed 14 atom styles > style sel ball Changed 14 atom styles > style sel stick Changed 14 atom styles > show sel atoms > show sel surfaces > show sel cartoons > show sel atoms > hide sel surfaces > ui mousemode right zoom > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/cryosparc_P2_J139_001_volume_map.mrc"" Opened cryosparc_P2_J139_001_volume_map.mrc as #3, grid size 128,128,128, pixel 1.9, shown at level 0.0121, step 1, values float32 > select add #3 14 atoms, 15 bonds, 1 residue, 4 models selected > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 5 models selected > select subtract #2 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-52.688,0,1,0,-80.094,0,0,1,-145.26 > view matrix models #3,1,0,0,-56.654,0,1,0,-100.93,0,0,1,-174.49 > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 4 models selected > select subtract #3 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 3 models selected > view matrix models #2,1,0,0,24.085,0,1,0,-10.985,0,0,1,64.645 > select subtract #2 1 model selected > select add #3 2 models selected > volume #3 level 0.02462 > view matrix models #3,1,0,0,-44.352,0,1,0,-130.58,0,0,1,-161.21 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.79002,-0.056233,-0.6105,63.359,-0.48137,0.55978,-0.67448,66.238,0.37967,0.82673,0.41517,-239.28 > view matrix models > #3,0.75092,-0.18044,-0.63526,86.581,-0.47648,0.51802,-0.71037,75.15,0.45725,0.83612,0.30301,-236.47 > view matrix models > #3,0.1022,-0.78041,-0.61686,239.52,-0.67992,0.39784,-0.61597,103.92,0.72612,0.48237,-0.48996,-129.82 > view matrix models > #3,-0.98071,-0.19545,-0.0009505,227.94,-0.17272,0.86892,-0.46383,-36.21,0.091484,-0.45472,-0.88592,113.44 > view matrix models > #3,-0.81508,-0.57388,0.079479,244.01,-0.56085,0.7472,-0.35656,14.316,0.14524,-0.3352,-0.93088,97.466 > view matrix models > #3,-0.72894,-0.51442,-0.45169,290.7,-0.037919,0.68913,-0.72364,0.75346,0.68353,-0.51037,-0.52184,1.7199 > view matrix models > #3,-0.074648,-0.95635,-0.28253,242.56,-0.27276,0.2921,-0.91667,102.64,0.95918,0.0086345,-0.28266,-125.93 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.074648,-0.95635,-0.28253,247.26,-0.27276,0.2921,-0.91667,116.15,0.95918,0.0086345,-0.28266,-100.44 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.074648,-0.95635,-0.28253,259.84,-0.27276,0.2921,-0.91667,94.672,0.95918,0.0086345,-0.28266,-27.137 > ui tool show ""Fit in Map"" > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.05093, steps = 108 shifted from previous position = 9.4 rotated from previous position = 21.1 degrees atoms outside contour = 3015, contour level = 0.024615 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.29378473 -0.49848044 0.81560271 137.08527599 -0.94940490 0.25125346 -0.18841983 193.99411200 -0.11099940 -0.82969208 -0.54707420 121.99586260 Axis -0.52834586 0.76342987 -0.37151782 Axis point 165.18429441 0.00000000 74.29225667 Rotation angle (degrees) 142.63662752 Shift along axis 30.34882418 > color #3 #ffffb261 models > color #3 #ffffb254 models > select subtract #3 Nothing selected > ui mousemode right zoom > volume #3 level 0.02462 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.05093, steps = 36 shifted from previous position = 0.00527 rotated from previous position = 0.0174 degrees atoms outside contour = 3015, contour level = 0.024615 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.29376450 -0.49834870 0.81569050 137.08295966 -0.94943441 0.25103723 -0.18855932 193.98994804 -0.11080039 -0.82983666 -0.54689523 121.98399704 Axis -0.52835976 0.76335226 -0.37165750 Axis point 165.18831934 0.00000000 74.30930524 Rotation angle (degrees) 142.63743111 Shift along axis 30.31727756 > volume #3 level 0.05266 > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.73456,-0.39363,0.5527,37.875,0.15633,0.8908,0.42665,-16.771,-0.66029,-0.227,0.71588,99.696 > view matrix models > #2,-0.32214,-0.83816,0.44012,103.42,0.074832,0.44091,0.89443,-19.195,-0.94373,0.32107,-0.079313,129.28 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.32214,-0.83816,0.44012,102.21,0.074832,0.44091,0.89443,-12.272,-0.94373,0.32107,-0.079313,125.24 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.06159, steps = 160 shifted from previous position = 6.63 rotated from previous position = 48.3 degrees atoms outside contour = 3219, contour level = 0.052655 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.94142895 -0.33520250 -0.03675354 178.48497876 -0.20705056 0.66062920 -0.72159485 147.29478215 0.26616086 -0.67172044 -0.69133932 91.35292844 Axis 0.14992281 -0.91056269 0.38522557 Axis point 95.88871198 0.00000000 85.53974950 Rotation angle (degrees) 170.42528326 Shift along axis -72.17067934 > view matrix models > #2,0.19309,-0.41699,0.88816,78.969,-0.047675,0.90014,0.43298,5.1131,-0.98002,-0.12595,0.15393,119.78 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.66784,-0.70326,0.24375,134.55,-0.28676,0.54531,0.78766,15.211,-0.68684,0.45614,-0.56585,110.24 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.66784,-0.70326,0.24375,136.73,-0.28676,0.54531,0.78766,16.889,-0.68684,0.45614,-0.56585,107.87 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.77688,-0.62962,-0.0053813,145.82,-0.40146,0.48874,0.77457,23.872,-0.48506,0.60391,-0.63246,96.513 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.77688,-0.62962,-0.0053813,143.62,-0.40146,0.48874,0.77457,23.554,-0.48506,0.60391,-0.63246,97.654 > view matrix models > #2,-0.77688,-0.62962,-0.0053813,145.64,-0.40146,0.48874,0.77457,26.346,-0.48506,0.60391,-0.63246,92.396 > view matrix models > #2,-0.77688,-0.62962,-0.0053813,143.19,-0.40146,0.48874,0.77457,25.169,-0.48506,0.60391,-0.63246,94.185 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.041321,-0.72568,0.68679,90.008,-0.14613,0.68437,0.71434,10.896,-0.9884,-0.070841,-0.13432,117.04 > view matrix models > #2,0.76604,-0.13176,0.62914,44.25,-0.17214,0.90096,0.39829,16.696,-0.61931,-0.41341,0.66749,84.849 > view matrix models > #2,0.96243,-0.19645,0.18746,30.523,0.041942,0.78962,0.61216,-0.13741,-0.26828,-0.5813,0.76819,57.92 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.96243,-0.19645,0.18746,30.297,0.041942,0.78962,0.61216,-1.0603,-0.26828,-0.5813,0.76819,63.591 > view matrix models > #2,0.96243,-0.19645,0.18746,26.634,0.041942,0.78962,0.61216,-3.2555,-0.26828,-0.5813,0.76819,63.741 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.06016, steps = 124 shifted from previous position = 5.09 rotated from previous position = 24.7 degrees atoms outside contour = 3237, contour level = 0.052655 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.35609382 -0.68376823 0.63691303 132.76435885 -0.92725360 0.17413081 -0.33148035 186.53007699 0.11574955 -0.70861800 -0.69603346 104.09621171 Axis -0.54828955 0.75767691 -0.35398344 Axis point 147.37033065 0.00000000 78.04754571 Rotation angle (degrees) 159.88399714 Shift along axis 31.68788612 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #2,0.88066,0.084716,0.46612,39.851,-0.27982,0.88694,0.36748,19.614,-0.38228,-0.45406,0.80479,74.531 > volume #3 level 0.05266 > volume #3 level 0.03463 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.06015, steps = 56 shifted from previous position = 3.77 rotated from previous position = 0.0373 degrees atoms outside contour = 2961, contour level = 0.034629 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.35617066 -0.68382777 0.63680612 132.76394754 -0.92714560 0.17374686 -0.33198352 186.50488296 0.11637649 -0.70865479 -0.69589144 104.05750959 Axis -0.54830583 0.75756934 -0.35418838 Axis point 147.35052728 0.00000000 78.07803663 Rotation angle (degrees) 159.91056850 Shift along axis 31.63917348 > hide #!3 models > select /X 2117 atoms, 2155 bonds, 267 residues, 1 model selected > color sel cornflower blue > color sel purple > color sel hot pink > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/cryosparc_P2_J77_003_volume_map.mrc"" Opened cryosparc_P2_J77_003_volume_map.mrc as #4, grid size 128,128,128, pixel 1.9, shown at level 0.0217, step 1, values float32 > ui mousemode right zoom > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected > select subtract #2 1 model selected > select add #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-20.836,0,1,0,-68.443,0,0,1,-117 > view matrix models #4,1,0,0,-25.221,0,1,0,-82.034,0,0,1,-140.68 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.044338,-0.5894,-0.80662,267.96,-0.45672,0.73006,-0.50835,66.432,0.88851,0.34586,-0.30156,-131.42 > view matrix models > #4,-0.18322,-0.83702,0.51558,155.33,-0.68629,0.48441,0.54254,-2.9827,-0.70387,-0.25443,-0.6632,174.42 > view matrix models > #4,-0.53398,-0.77518,-0.3376,292.2,0.45572,-0.60019,0.65734,-19.459,-0.71217,0.19715,0.67375,-41.047 > volume #4 level 0.0849 > view matrix models > #4,-0.78371,-0.57972,-0.22298,284.57,0.28505,-0.65465,0.70013,3.0711,-0.55185,0.48514,0.6783,-97.154 > volume #4 level 0.186 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.78371,-0.57972,-0.22298,279.51,0.28505,-0.65465,0.70013,-9.4399,-0.55185,0.48514,0.6783,-120.78 > view matrix models > #4,-0.78371,-0.57972,-0.22298,340.7,0.28505,-0.65465,0.70013,-42.227,-0.55185,0.48514,0.6783,-50.205 > view matrix models > #4,-0.78371,-0.57972,-0.22298,290.59,0.28505,-0.65465,0.70013,-72.535,-0.55185,0.48514,0.6783,-14.639 > ui mousemode right ""rotate selected models"" > fitmap #2 inMap #4 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J77_003_volume_map.mrc (#4) using 5098 atoms average map value = 0.1274, steps = 312 shifted from previous position = 13.4 rotated from previous position = 58.3 degrees atoms outside contour = 3496, contour level = 0.18604 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J77_003_volume_map.mrc (#4) coordinates: Matrix rotation and translation 0.39366624 0.59082543 -0.70423874 98.72670212 -0.68342782 -0.32424308 -0.65405875 151.96230908 -0.61477908 0.73877719 0.27614298 185.24165720 Axis 0.73698981 -0.04733570 -0.67424428 Axis point -0.00000000 8.99711411 209.82744806 Rotation angle (degrees) 109.09994115 Shift along axis -59.33079535 > ui mousemode right zoom > select subtract #4 Nothing selected > volume #4 color #b2ffff51 > volume #4 color #b2ffff52 > volume #4 level 0.2073 > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/cryosparc_P2_J87_002_volume_map.mrc"" Opened cryosparc_P2_J87_002_volume_map.mrc as #5, grid size 128,128,128, pixel 1.9, shown at level 0.0297, step 1, values float32 > hide #!2 models > hide #!4 models > volume #5 level 0.05848 > volume #5 level 0.1277 > volume #5 level 0.1997 > volume #5 level 0.2459 > show #!2 models > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.22476,-0.4398,0.86952,108.59,0.12919,0.89792,0.42077,2.9535,-0.96581,0.017763,0.25864,145.08 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.74892,-0.61014,0.25856,173.69,0.59433,-0.4459,0.66928,-50.862,-0.29307,0.65491,0.69657,108.37 > view matrix models > #2,-0.9943,-0.033639,0.10122,200.01,0.068816,-0.92735,0.36781,-22.002,0.081491,0.37268,0.92438,77.781 > view matrix models > #2,-0.066109,-0.62352,0.77901,125.75,0.91541,-0.34856,-0.20131,-69.798,0.39705,0.6998,0.59382,61.953 > view matrix models > #2,0.92421,-0.21728,0.31404,65.162,0.37945,0.42982,-0.81932,-19.522,0.043043,0.87638,0.47969,89.249 > view matrix models > #2,0.32734,0.78112,-0.53169,123.53,-0.64369,-0.22759,-0.73066,39.961,-0.69174,0.58142,0.4283,135 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.32734,0.78112,-0.53169,144.97,-0.64369,-0.22759,-0.73066,57.339,-0.69174,0.58142,0.4283,143.42 > view matrix models > #2,0.32734,0.78112,-0.53169,131.98,-0.64369,-0.22759,-0.73066,46.342,-0.69174,0.58142,0.4283,139.13 > view matrix models > #2,0.32734,0.78112,-0.53169,87.732,-0.64369,-0.22759,-0.73066,140.3,-0.69174,0.58142,0.4283,190.72 > view matrix models > #2,0.32734,0.78112,-0.53169,107.92,-0.64369,-0.22759,-0.73066,137.64,-0.69174,0.58142,0.4283,188.27 > fitmap #2 inMap #5 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J87_002_volume_map.mrc (#5) using 5098 atoms average map value = 0.1252, steps = 140 shifted from previous position = 11.6 rotated from previous position = 15.9 degrees atoms outside contour = 4024, contour level = 0.24585 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J87_002_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.36600272 0.59827985 -0.71281360 100.71411204 -0.63516086 -0.39922110 -0.66120587 146.17749312 -0.68015637 0.69475445 0.23388794 188.29332461 Axis 0.73961915 -0.01781314 -0.67278987 Axis point 0.00000000 7.25894503 204.23978094 Rotation angle (degrees) 113.55725141 Shift along axis -54.79563603 > ui mousemode right zoom > volume #5 color #b2b2ff51 > volume #5 color #b2b2ff52 > volume #5 color #19192152 > volume #5 color #393a4b52 > volume #5 color #393a4b3f > select subtract #2 1 model selected > fitmap #2 inMap #5 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J87_002_volume_map.mrc (#5) using 5098 atoms average map value = 0.1252, steps = 44 shifted from previous position = 0.0428 rotated from previous position = 0.00667 degrees atoms outside contour = 4023, contour level = 0.24585 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J87_002_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.36600862 0.59836584 -0.71273840 100.69519040 -0.63514354 -0.39915343 -0.66126336 146.15604994 -0.68016938 0.69471927 0.23395460 188.32529532 Axis 0.73960666 -0.01776443 -0.67280489 Axis point -0.00000000 7.23374201 204.24684075 Rotation angle (degrees) 113.55286922 Shift along axis -54.82772575 > volume #5 level 0.2055 > volume #5 level 0.243 > fitmap #2 inMap #5 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J87_002_volume_map.mrc (#5) using 5098 atoms average map value = 0.1252, steps = 48 shifted from previous position = 0.00828 rotated from previous position = 0.0321 degrees atoms outside contour = 4002, contour level = 0.24297 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J87_002_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.36623911 0.59849787 -0.71250910 100.68754770 -0.63471780 -0.39924714 -0.66161548 146.12130127 -0.68044267 0.69455167 0.23365734 188.33473421 Axis 0.73973553 -0.01749097 -0.67267036 Axis point 0.00000000 7.18817744 204.20538771 Rotation angle (degrees) 113.55788430 Shift along axis -54.76084090 > select /A 2981 atoms, 2893 bonds, 11 pseudobonds, 499 residues, 2 models selected > select /X 2117 atoms, 2155 bonds, 267 residues, 1 model selected > color sel purple > select /A:13 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:13-83 572 atoms, 581 bonds, 71 residues, 1 model selected > select /A:83 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:13-83 572 atoms, 581 bonds, 71 residues, 1 model selected > select /A:83 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:83 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > style sel sphere Changed 14 atom styles > style sel stick Changed 14 atom styles > style sel ball Changed 14 atom styles > style sel sphere Changed 14 atom styles > style sel stick Changed 14 atom styles > show sel surfaces > hide sel surfaces > color (#!2 & sel) forest green > surface (#!2 & sel) > hide sel surfaces > select /X 2117 atoms, 2155 bonds, 267 residues, 1 model selected > color sel hot pink > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/data > analysis/cryosparc_P2_J93_class_00_00042_volume_sharp.mrc"" Opened cryosparc_P2_J93_class_00_00042_volume_sharp.mrc as #6, grid size 128,128,128, pixel 1.9, shown at level 0.0874, step 1, values float32 > hide #!6 models > open ""/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan > Taylor lab/PKA project/cryosparc_P2_J113_001_volume_map.mrc"" Opened cryosparc_P2_J113_001_volume_map.mrc as #7, grid size 128,128,128, pixel 1.9, shown at level 0.0245, step 1, values float32 > hide #!5 models > volume #7 level 0.123 > volume #7 level 0.1723 > volume #7 level 0.2172 > fitmap #2 inMap #7 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J113_001_volume_map.mrc (#7) using 5098 atoms average map value = 0.1267, steps = 148 shifted from previous position = 2.04 rotated from previous position = 6.86 degrees atoms outside contour = 3811, contour level = 0.21723 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J113_001_volume_map.mrc (#7) coordinates: Matrix rotation and translation 0.39057817 0.58373066 -0.71183370 98.62046944 -0.70449973 -0.30820089 -0.63929050 154.18215555 -0.59256124 0.75117956 0.29086155 184.35062168 Axis 0.73211332 -0.06279959 -0.67828187 Axis point 0.00000000 11.22910299 212.05667907 Rotation angle (degrees) 108.26307881 Shift along axis -62.52290126 > volume #7 color #ffb2b221 > volume #7 color #100d0d21 > volume #7 color #00000021 > volume #7 color #0000001e > volume #7 color #00000022 > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected > select subtract #2 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:196-197 25 atoms, 26 bonds, 2 residues, 1 model selected > select /A:197 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:196-197 25 atoms, 26 bonds, 2 residues, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel sphere Changed 14 atom styles > select /A:196-197 25 atoms, 26 bonds, 2 residues, 1 model selected > select /A:196-197 25 atoms, 26 bonds, 2 residues, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:196-197 25 atoms, 26 bonds, 2 residues, 1 model selected > select clear > hide atoms > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:196 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel sphere Changed 14 atom styles > style sel sphere Changed 14 atom styles > show sel surfaces > hide sel surfaces > show sel cartoons > hide sel cartoons > style sel ball Changed 14 atom styles > show sel cartoons > show sel atoms > style sel sphere Changed 14 atom styles > style sel sphere Changed 14 atom styles > style sel stick Changed 14 atom styles > color (#!2 & sel) red > color (#!2 & sel) blue > color (#!2 & sel) purple > color (#!2 & sel) red > ui tool show ""Show Sequence Viewer"" > sequence chain /X Alignment identifier is 2/X > select /X:333 11 atoms, 10 bonds, 1 residue, 1 model selected > select /X:333 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > hide #!2 models > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected > select subtract #2 1 model selected > select add #7 2 models selected > select subtract #7 Nothing selected > show #!2 models > show #!3 models > select add #3 2 models selected > select subtract #3 Nothing selected > hide #!7 models > ui mousemode right ""translate selected models"" > select add #3 2 models selected > view matrix models > #3,-0.074648,-0.95635,-0.28253,276.53,-0.27276,0.2921,-0.91667,100.86,0.95918,0.0086345,-0.28266,-19.251 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.3773,-0.55695,-0.7399,223.28,-0.89686,-0.41889,-0.14202,177.74,-0.23084,0.71717,-0.65755,84.057 > view matrix models > #3,0.62876,-0.16127,-0.76069,143.86,-0.388,-0.91284,-0.12719,175.13,-0.67388,0.37512,-0.63653,180.62 > view matrix models > #3,0.8915,-0.21096,-0.4009,74.618,-0.26493,-0.96063,-0.083633,160.63,-0.36748,0.18077,-0.91229,199.68 > view matrix models > #3,0.88975,-0.16358,-0.42613,71.795,-0.23866,-0.96252,-0.12883,162.94,-0.38908,0.21633,-0.89544,195.86 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.88975,-0.16358,-0.42613,132.26,-0.23866,-0.96252,-0.12883,203.09,-0.38908,0.21633,-0.89544,207.64 > view matrix models > #3,0.88975,-0.16358,-0.42613,101.95,-0.23866,-0.96252,-0.12883,280.72,-0.38908,0.21633,-0.89544,266.33 > view matrix models > #3,0.88975,-0.16358,-0.42613,96.156,-0.23866,-0.96252,-0.12883,280.56,-0.38908,0.21633,-0.89544,263.96 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.43696,-0.85083,-0.29182,224.47,-0.89926,-0.42045,-0.12066,293.32,-0.020031,0.31515,-0.94883,211.48 > view matrix models > #3,-0.39973,-0.88665,-0.23254,326.82,-0.87374,0.44525,-0.19579,188.8,0.27713,0.12492,-0.95268,198.93 > view matrix models > #3,-0.94979,-0.043862,-0.3098,297.57,0.021627,0.97855,-0.20485,9.7963,0.31214,-0.20127,-0.92847,233.21 > view matrix models > #3,-0.21573,0.29563,-0.93063,235.99,0.82921,0.55875,-0.014727,-60.46,0.51563,-0.77486,-0.36568,214.03 > view matrix models > #3,0.038708,-0.73188,-0.68033,305.28,-0.61711,0.51798,-0.59234,194.4,0.78592,0.44277,-0.4316,32.936 > view matrix models > #3,0.9344,0.34936,0.069565,-33.524,0.34675,-0.8473,-0.40231,224.97,-0.08161,0.40004,-0.91286,204.12 > view matrix models > #3,0.19066,0.97371,0.12462,-26.379,0.98165,-0.18935,-0.022342,16.605,0.0018417,0.12659,-0.99195,237.86 > view matrix models > #3,-0.48477,0.84051,-0.24197,118.66,0.80173,0.53759,0.26119,-87.037,0.34961,-0.06738,-0.93447,212.18 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.0614, steps = 100 shifted from previous position = 21.3 rotated from previous position = 21.9 degrees atoms outside contour = 2872, contour level = 0.034629 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.94646621 -0.31941109 0.04667200 179.16600157 -0.22422298 0.54650840 -0.80687832 151.03200437 0.23221925 -0.77414800 -0.58887104 95.16030130 Axis 0.15505241 -0.87898758 0.45093190 Axis point 99.19680830 0.00000000 92.00400008 Rotation angle (degrees) 173.94137523 Shift along axis -62.06432087 > select subtract #3 Nothing selected > ui mousemode right zoom > volume #3 color #49493954 > select add #2 5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.21416,0.8015,-0.55832,133.01,-0.8187,-0.16448,-0.55016,161.41,-0.53279,0.57492,0.62097,177.63 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.0614, steps = 72 shifted from previous position = 3.55 rotated from previous position = 0.00786 degrees atoms outside contour = 2873, contour level = 0.034629 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.94648466 -0.31935511 0.04668087 179.17256337 -0.22422557 0.54661287 -0.80680684 151.03507502 0.23214152 -0.77409734 -0.58896827 95.16521404 Axis 0.15503143 -0.87901774 0.45088032 Axis point 99.19987136 0.00000000 91.99864336 Rotation angle (degrees) 173.94442183 Shift along axis -62.07701012 > volume #3 level 0.01861 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.0614, steps = 44 shifted from previous position = 0.0317 rotated from previous position = 0.0109 degrees atoms outside contour = 2549, contour level = 0.018607 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.94653338 -0.31920084 0.04674819 179.15137286 -0.22420415 0.54668375 -0.80676476 151.04794544 0.23196352 -0.77411091 -0.58902056 95.18695634 Axis 0.15497641 -0.87903893 0.45085792 Axis point 99.18958904 0.00000000 92.00148022 Rotation angle (degrees) 173.95260840 Shift along axis -62.09699446 > volume #3 level 0.02462 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.0614, steps = 76 shifted from previous position = 0.0304 rotated from previous position = 0.0134 degrees atoms outside contour = 2680, contour level = 0.024615 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.94647583 -0.31938887 0.04662890 179.17030664 -0.22421381 0.54664835 -0.80678606 151.03562989 0.23218888 -0.77405835 -0.58900084 95.16305799 Axis 0.15503644 -0.87902748 0.45085961 Axis point 99.19720649 0.00000000 91.99839384 Rotation angle (degrees) 173.94123400 Shift along axis -62.08136327 > volume #3 level 0.03864 > fitmap #2 inMap #3 Fit molecule flipback_hetdimer (1).pdb (#2) to map cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms average map value = 0.0614, steps = 40 shifted from previous position = 0.0206 rotated from previous position = 0.0153 degrees atoms outside contour = 2942, contour level = 0.038635 Position of flipback_hetdimer (1).pdb (#2) relative to cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates: Matrix rotation and translation -0.94652531 -0.31922142 0.04677096 179.15789005 -0.22419175 0.54653311 -0.80687026 151.03792152 0.23200839 -0.77420879 -0.58887423 95.17923569 Axis 0.15498649 -0.87899585 0.45093845 Axis point 99.19305835 0.00000000 92.00521562 Rotation angle (degrees) 173.95158637 Shift along axis -62.07467665 > select subtract #2 1 model selected > select /X:113 11 atoms, 10 bonds, 1 residue, 1 model selected > select /X:113-333 1757 atoms, 1789 bonds, 221 residues, 1 model selected > color sel cyan > color sel cornflower blue > color sel blue > color sel cyan > select clear Failed to lock QIOSurfaceGraphicsBuffer(0x600000270420, surface=0x0, size=QSize(-2147483648, -2147483648), isLocked=false, isInUse=false) -536870206 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Locale: UTF-8 Qt version: PyQt6 6.2.3, Qt 6.2.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MJ123LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 1 day, 5 hours, 35 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Usb Display: Va2055 Series (Usb): Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Usb Display: Lg Hdr Wfhd (Usb): Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array) UI Looks like: 2560 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.36.2 ChimeraX-AtomicLibrary: 6.1.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.2 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202203190100 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.5 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.31.1 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.4.0 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt6-commercial: 6.2.3 PyQt6-sip: 13.2.0 PyQt6-WebEngine-commercial: 6.2.1 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX