id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15239 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000002048af240 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2024-05-17 08:47:23.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.4.1 (23E224)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""1FB3BFDC-F1D6-47CC-84A1-5A83B61EDCD7""} { ""uptime"" : 180000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,2"", ""coalitionID"" : 1464, ""osVersion"" : { ""train"" : ""macOS 14.4.1"", ""build"" : ""23E224"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-05-17 08:47:17.3779 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""1FB3BFDC-F1D6-47CC-84A1-5A83B61EDCD7"", ""pid"" : 3590, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-05-14 14:35:16.2569 +0200"", ""procStartAbsTime"" : 2623362463632, ""procExitAbsTime"" : 4470309020738, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""DF51A6B6-AF2B-59DE-B219-DDB53D97F1B3"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D34F8069-E1C1-FE0D-96BE-91B1F96E2FD2"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 1, ""sleepWakeUUID"" : ""85F3721F-3792-41D2-806D-1ED4E0B57F72"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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{ }, ""deploymentId"" : 240000003 }, { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000550 } ], ""experiments"" : [ { ""treatmentId"" : ""a34d22a1-a1a5-4126-a477-0c499e502c6a"", ""experimentId"" : ""65835bc103dc58766bab2d27"", ""deploymentId"" : 400000011 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF894EF6A78)"" ] } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kgr849/Downloads/cryosparc_P48_J259_009_volume_map.mrc format > mrc Opened cryosparc_P48_J259_009_volume_map.mrc as #1, grid size 224,224,224, pixel 1.5, shown at level 0.103, step 1, values float32 > open /Users/kgr849/Downloads/cryosparc_P48_J271_002_volume_map.mrc Opened cryosparc_P48_J271_002_volume_map.mrc as #2, grid size 224,224,224, pixel 1.5, shown at level 0.0843, step 1, values float32 > volume #2 level 0.08862 > volume #2 level 0.2237 > volume #1 level 0.2715 > volume #2 level 0.2044 > volume #2 level 0.1937 > volume #2 level 0.1765 > open /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/cryosparc_P48_J179_mask.mrc Opened cryosparc_P48_J179_mask.mrc as #3, grid size 224,224,224, pixel 1.5, shown at level 0.986, step 1, values float32 > volume #1 level 0.08974 > ui mousemode right select > select #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.87861,-0.31195,-0.36157,130.48,0.25825,0.94727,-0.18972,-4.1365,0.40168,0.073313,0.91284,-65.724 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit map cryosparc_P48_J179_mask.mrc in map cryosparc_P48_J259_009_volume_map.mrc using 112393 points correlation = 0.6834, correlation about mean = 0, overlap = 8855 steps = 112, shift = 17.2, angle = 11.3 degrees Position of cryosparc_P48_J179_mask.mrc (#3) relative to cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.79903807 -0.47329137 -0.37085502 175.89742421 0.43851937 0.88069010 -0.17912485 -13.61410817 0.41138659 -0.01949953 0.91125235 -60.81880048 Axis 0.13171137 -0.64544969 0.75236083 Axis point 137.62362742 317.05268061 0.00000000 Rotation angle (degrees) 37.29841378 Shift along axis -13.80277069 > open /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_full_mask.mrc Opened hTRPM4_full_mask.mrc as #4, grid size 224,224,224, pixel 1.5, shown at level 1, step 1, values float32 > volume #4 level 0.2413 > ui mousemode right select > select #4 2 models selected Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 4 hTRPM4_full_mask.mrc > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.96447,0.24519,0.09843,-53.314,-0.23383,0.96557,-0.11405,66.18,-0.123,0.086979,0.98859,8.2529,#4,0.96447,0.24519,0.09843,-53.314,-0.23383,0.96557,-0.11405,66.18,-0.123,0.086979,0.98859,8.2529 > undo > ui mousemode right select > ui mousemode right translate > ui mousemode right select > select clear > select #4 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.89595,0.43138,-0.10575,-34.28,0.39768,-0.88517,-0.24149,296.77,-0.19778,0.17431,-0.96462,387.57 > view matrix models > #4,0.99762,-0.012445,0.067875,-10.765,-0.012722,-0.99991,0.003651,337.03,0.067824,-0.0045058,-0.99769,379.46 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99762,-0.012445,0.067875,-11.401,-0.012722,-0.99991,0.003651,335.47,0.067824,-0.0045058,-0.99769,351.28 > fitmap #4 inMap #1 Fit map hTRPM4_full_mask.mrc in map cryosparc_P48_J259_009_volume_map.mrc using 670986 points correlation = 0.6806, correlation about mean = 0.1795, overlap = 3.352e+04 steps = 112, shift = 22.7, angle = 5.13 degrees Position of hTRPM4_full_mask.mrc (#4) relative to cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99747325 -0.07104231 0.00031359 12.23312623 -0.07104235 -0.99747329 0.00011280 347.06375723 0.00030478 -0.00013480 -0.99999994 339.69726431 Axis -0.99936808 0.03554456 -0.00015450 Axis point 0.00000000 173.75995356 169.83693139 Rotation angle (degrees) 179.99290231 Shift along axis 0.05834901 > hide #!3 models > hide #!2 models > transparency sel 50 > view matrix models > #4,0.99747,-0.071042,0.00031359,12.265,-0.071042,-0.99747,0.0001128,345.2,0.00030478,-0.0001348,-1,348.04 > undo > open /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_MSP_Science_box224_resampled.mrc Opened hTRPM4_MSP_Science_box224_resampled.mrc as #5, grid size 224,224,224, pixel 1.5, shown at level 2.61, step 1, values float32 > ui mousemode right select > select clear > select #5 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.32496,-0.45287,-0.83025,454.06,-0.52063,0.81855,-0.24271,163.85,0.78952,0.35338,-0.50177,77.787 > hide #!4 models > view matrix models > #5,-0.19102,-0.97362,-0.1248,384.03,-0.98016,0.19605,-0.029213,303.16,0.05291,0.11675,-0.99175,333 > fitmap #5 inMap #1 Fit map hTRPM4_MSP_Science_box224_resampled.mrc in map cryosparc_P48_J259_009_volume_map.mrc using 112310 points correlation = 0.6009, correlation about mean = 0.09451, overlap = 5.21e+04 steps = 108, shift = 1.57, angle = 9.19 degrees Position of hTRPM4_MSP_Science_box224_resampled.mrc (#5) relative to cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.28810148 -0.95759984 -0.00030465 376.29035526 -0.95759971 0.28810161 -0.00051745 279.93026482 0.00058328 0.00014265 -0.99999982 362.98598409 Axis 0.59661478 -0.80252775 0.00011681 Axis point 292.13543335 0.00000000 181.57822196 Rotation angle (degrees) 179.96830352 Shift along axis -0.10901681 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.2881,-0.9576,-0.00030465,375.44,-0.9576,0.2881,-0.00051745,280.09,0.00058328,0.00014265,-1,349.26 > fitmap #5 inMap #1 Fit map hTRPM4_MSP_Science_box224_resampled.mrc in map cryosparc_P48_J259_009_volume_map.mrc using 112310 points correlation = 0.8253, correlation about mean = 0.5199, overlap = 9.551e+04 steps = 188, shift = 11.8, angle = 15.8 degrees Position of hTRPM4_MSP_Science_box224_resampled.mrc (#5) relative to cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.53750734 -0.84325907 0.00000317 398.86260680 -0.84325907 0.53750734 0.00002190 218.94669812 -0.00002017 0.00000909 -1.00000000 337.60277907 Axis -0.48088104 0.87678585 0.00001077 Axis point 259.47422198 0.00000000 168.79853010 Rotation angle (degrees) 179.99923719 Shift along axis 0.16753917 > volume #5 level 2.606 > volume #5 level 4.704 > volume #1 level 0.1593 > hide #!5 models > show #!4 models > show #!5 models > fitmap #4 inMap #5 Fit map hTRPM4_full_mask.mrc in map hTRPM4_MSP_Science_box224_resampled.mrc using 670986 points correlation = 0.1639, correlation about mean = 0.2324, overlap = 3.156e+05 steps = 260, shift = 2.86, angle = 50.1 degrees Position of hTRPM4_full_mask.mrc (#4) relative to hTRPM4_MSP_Science_box224_resampled.mrc (#5) coordinates: Matrix rotation and translation 0.36907779 0.92939850 0.00012167 -50.54210027 -0.92939848 0.36907781 -0.00016570 261.39451417 -0.00019891 -0.00005192 0.99999998 -4.93882849 Axis 0.00006121 0.00017246 -0.99999998 Axis point 167.25560519 167.92331954 0.00000000 Rotation angle (degrees) 68.34124665 Shift along axis 4.98081580 > ui mousemode right select > select clear Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 4 hTRPM4_full_mask.mrc , 5 hTRPM4_MSP_Science_box224_resampled.mrc > select clear > ui mousemode right translate > show #!3 models > volume resample Missing or invalid ""volumes"" argument: empty atom specifier > fitmap #3 inMap #4 Fit map cryosparc_P48_J179_mask.mrc in map hTRPM4_full_mask.mrc using 112393 points correlation = 0.9896, correlation about mean = 0, overlap = 1.055e+05 steps = 468, shift = 29.9, angle = 55 degrees Position of cryosparc_P48_J179_mask.mrc (#3) relative to hTRPM4_full_mask.mrc (#4) coordinates: Matrix rotation and translation 0.79698469 -0.52792236 -0.29345085 165.66765932 -0.58103135 -0.80281637 -0.13374770 398.48505234 -0.16497874 0.27709901 -0.94657179 357.68136780 Axis 0.94724334 -0.29620377 -0.12244747 Axis point 0.00000000 204.46084006 212.54648036 Rotation angle (degrees) 167.47506942 Shift along axis -4.90236667 > ui mousemode right select > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.93759,0.34192,-0.063402,-53.161,-0.30605,0.89791,0.31637,-83.698,0.1651,-0.27722,0.94651,-12.954 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.80011,0.36692,-0.47455,328.32,-0.38371,0.29502,0.87506,-89.321,0.46108,0.88223,-0.095254,-34.249 > view matrix models > #3,-0.70084,0.64239,-0.31009,242.81,-0.15493,0.28725,0.94524,-141.87,0.69629,0.71051,-0.10179,-51.446 > view matrix models > #3,-0.6639,0.69423,-0.27798,223.25,-0.11368,0.27371,0.95507,-149.16,0.73913,0.66567,-0.1028,-52.753 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.9193,-0.36679,0.14268,9.5783,-0.39309,-0.87352,0.28713,179.97,0.01932,-0.32004,-0.94721,364.99 > view matrix models > #3,0.91603,-0.39944,0.036538,34.032,-0.39573,-0.88513,0.24484,189.76,-0.065457,-0.23874,-0.96887,372.92 > view matrix models > #3,0.89585,-0.42947,-0.11405,69.269,-0.40554,-0.89511,0.18523,203.77,-0.18164,-0.11968,-0.97606,378.62 > view matrix models > #3,0.89504,-0.43125,-0.11365,69.582,-0.40724,-0.8942,0.1859,203.82,-0.18179,-0.12011,-0.97597,378.69 > view matrix models > #3,0.89694,-0.42872,-0.10818,67.9,-0.40398,-0.89403,0.19367,201.8,-0.17975,-0.13001,-0.97508,379.53 > view matrix models > #3,0.89101,-0.43642,-0.12506,73.096,-0.41417,-0.89423,0.16976,208.01,-0.18592,-0.099464,-0.97752,376.88 > view matrix models > #3,0.87874,-0.45,-0.15907,83.36,-0.43471,-0.89219,0.12254,220.03,-0.19707,-0.03853,-0.97963,370.9 > view matrix models > #3,0.86209,-0.46408,-0.20355,96.388,-0.46158,-0.88489,0.062579,234.77,-0.20916,0.040007,-0.97706,361.83 > view matrix models > #3,0.8347,-0.47056,-0.28608,117.24,-0.49613,-0.86802,-0.019813,253.68,-0.239,0.15847,-0.958,347.42 > view matrix models > #3,0.86316,-0.46303,-0.20139,95.658,-0.46575,-0.88416,0.036657,240.15,-0.19503,0.062155,-0.97883,356.59 > view matrix models > #3,0.88435,-0.44865,-0.12898,76.674,-0.44068,-0.8935,0.086393,227.87,-0.154,-0.019562,-0.98788,362.14 > view matrix models > #3,0.87458,-0.25119,0.41473,-48.016,-0.38412,-0.88091,0.27649,181.33,0.29589,-0.40112,-0.86692,312.13 > view matrix models > #3,0.91509,-0.39972,0.053217,31.192,-0.40325,-0.90765,0.11649,217.64,0.0017391,-0.12806,-0.99177,349.95 > view matrix models > #3,0.80651,-0.56978,0.15777,54.748,0.06778,-0.17599,-0.98206,234.15,0.58732,0.80273,-0.10332,-44.383 > view matrix models > #3,0.82253,-0.56742,0.038358,73.392,-0.55645,-0.81689,-0.15185,281.55,0.1175,0.10356,-0.98766,296.82 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.82253,-0.56742,0.038358,225.68,-0.55645,-0.81689,-0.15185,426.54,0.1175,0.10356,-0.98766,301.06 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.81869,-0.56525,0.1012,214.59,-0.55796,-0.82469,-0.092563,417.04,0.13578,0.019314,-0.99055,309.87 > view matrix models > #3,0.82466,-0.54626,0.14675,202.6,-0.54883,-0.83553,-0.025978,404.73,0.1368,-0.059115,-0.98883,320.13 > view matrix models > #3,0.82116,-0.55803,0.11957,209.8,-0.5542,-0.82974,-0.066359,412.28,0.13624,-0.011774,-0.99061,314.06 > view matrix models > #3,-0.23974,-0.94973,0.20136,437.66,-0.97081,0.23608,-0.042345,336.06,-0.0073208,-0.20563,-0.9786,364.03 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.23974,-0.94973,0.20136,340.33,-0.97081,0.23608,-0.042345,260.56,-0.0073208,-0.20563,-0.9786,366.8 > fitmap #3 inMap #4 Fit map cryosparc_P48_J179_mask.mrc in map hTRPM4_full_mask.mrc using 112393 points correlation = 0.9894, correlation about mean = 0, overlap = 1.065e+05 steps = 332, shift = 33.4, angle = 43.4 degrees Position of cryosparc_P48_J179_mask.mrc (#3) relative to hTRPM4_full_mask.mrc (#4) coordinates: Matrix rotation and translation -0.03485747 -0.99835373 0.04555035 331.92163209 0.99888090 -0.03334550 0.03354219 -1.74823673 -0.03196807 0.04666857 0.99839878 2.77069575 Axis 0.00656719 0.03878284 0.99922608 Axis point 166.88795301 159.44683403 0.00000000 Rotation angle (degrees) 92.00014878 Shift along axis 4.88054225 > hide #!4 models > transparency sel 50 > ui mousemode right select > select clear > volume resample #3 onGrid #1 Opened cryosparc_P48_J179_mask.mrc resampled as #6, grid size 224,224,224, pixel 1.5, shown at step 1, values float32 > save /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_proteomer_box224_J259fit.mrc > models #6 > volume #6 level 0.9667 > open /Users/kgr849/Downloads/cryosparc_P48_J273_mask.mrc Opened cryosparc_P48_J273_mask.mrc as #7, grid size 224,224,224, pixel 1.5, shown at level 1, step 1, values float32 > volume #7 level 0.939 Unsupported scale factor (0.000000) detected on Display1 Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 5 hTRPM4_MSP_Science_box224_resampled.mrc , 6 hTRPM4_proteomer_box224_J259fit.mrc , 7 cryosparc_P48_J273_mask.mrc > select clear Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 5 hTRPM4_MSP_Science_box224_resampled.mrc , 6 hTRPM4_proteomer_box224_J259fit.mrc , 7 cryosparc_P48_J273_mask.mrc > select clear > ui mousemode right translate > open /Users/kgr849/Downloads/cryosparc_P48_J274_002_volume_map.mrc Opened cryosparc_P48_J274_002_volume_map.mrc as #8, grid size 224,224,224, pixel 1.5, shown at level 0.089, step 1, values float32 > hide #!7 models > hide #!6 models > volume #8 level 0.1788 > hide #!5 models > open /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/cryosparc_P48_J182_mask.mrc Opened cryosparc_P48_J182_mask.mrc as #9, grid size 224,224,224, pixel 1.5, shown at level 0.734, step 1, values float32 > close #9 > open /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_cyto_mask_C4_box224_resampled.mrc Opened hTRPM4_cyto_mask_C4_box224_resampled.mrc as #9, grid size 224,224,224, pixel 1.5, shown at level 0.000529, step 1, values float32 > close #9 > open /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/hTPRM4_flexdomain_smooth_box224.mrc Opened hTPRM4_flexdomain_smooth_box224.mrc as #9, grid size 224,224,224, pixel 1.5, shown at level 0.000334, step 1, values float32 > show #!7 models > ui mousemode right select > select #9 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.96614,0.0054378,-0.25797,59.977,-0.25765,-0.0337,-0.96565,427.11,-0.013945,0.99942,-0.031158,51.819 > view matrix models > #9,-0.26269,0.60719,0.74988,2.2035,0.93009,0.36615,0.029353,-92.089,-0.25674,0.70517,-0.66092,282.46 > view matrix models > #9,-0.26621,0.60518,0.75026,3.1819,0.93195,0.36039,0.039974,-93.731,-0.24619,0.70984,-0.65994,279.31 > view matrix models > #9,0.77787,-0.27802,-0.56357,209.85,-0.49432,-0.82445,-0.27556,463.42,-0.38803,0.49294,-0.77875,369.49 > view matrix models > #9,0.59651,-0.79153,-0.13287,242.77,-0.80179,-0.59514,-0.054198,442.28,-0.036177,0.13886,-0.98965,400.09 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.59651,-0.79153,-0.13287,257.04,-0.80179,-0.59514,-0.054198,447.71,-0.036177,0.13886,-0.98965,328.93 > view matrix models > #9,0.59651,-0.79153,-0.13287,252.68,-0.80179,-0.59514,-0.054198,410.46,-0.036177,0.13886,-0.98965,319.91 > view matrix models > #9,0.59651,-0.79153,-0.13287,226.91,-0.80179,-0.59514,-0.054198,410.78,-0.036177,0.13886,-0.98965,321.01 Window position QRect(1577,869 338x98) outside any known screen, using primary screen > fitmap #9 inMap #7 Fit map hTPRM4_flexdomain_smooth_box224.mrc in map cryosparc_P48_J273_mask.mrc using 39705 points correlation = 0.7896, correlation about mean = 0.008853, overlap = 6.424e+04 steps = 132, shift = 3.33, angle = 9.68 degrees Position of hTPRM4_flexdomain_smooth_box224.mrc (#9) relative to cryosparc_P48_J273_mask.mrc (#7) coordinates: Matrix rotation and translation 0.54298402 -0.83953438 0.01871854 213.37390235 -0.83700958 -0.54287917 -0.06853588 415.49039157 0.06770013 0.02154629 -0.99747303 321.62577465 Axis 0.87826053 -0.47754844 0.02461558 Axis point 0.00000000 261.05613664 163.87050845 Rotation angle (degrees) 177.06032957 Shift along axis -3.10190996 > color #7 #b2ffb24e models > hide #!7 models > show #!5 models > hide #!8 models > hide #!5 models > volume resample #9 onGrid #1 Opened hTPRM4_flexdomain_smooth_box224.mrc resampled as #10, grid size 224,224,224, pixel 1.5, shown at step 1, values float32 > volume #10 level 0.02137 > volume gaussian #9 sDev 2 Opened hTPRM4_flexdomain_smooth_box224.mrc gaussian as #11, grid size 224,224,224, pixel 1.5, shown at step 1, values float32 > volume #11 level 0.0279 > save /Users/kgr849/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_flex_box224_J259.mrc models #11 > open /Users/kgr849/Downloads/cryosparc_P48_J276_mask.mrc Opened cryosparc_P48_J276_mask.mrc as #12, grid size 224,224,224, pixel 1.5, shown at level 0.794, step 1, values float32 > hide #!10 models > select subtract #9 Nothing selected > hide #!11 models > hide #!12 models > show #!3 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > volume #6 level 0.9903 > ui tool show ""Segment Map"" Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Showing 5 region surfaces 97910 watershed regions, grouped to 5 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 5 regions, 5 surfaces Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Showing 17 region surfaces 97910 watershed regions, grouped to 17 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 17 regions, 17 surfaces Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Only showing 60 of 5180 regions. Showing 60 of 5180 region surfaces 97910 watershed regions, grouped to 5180 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 5180 regions, 60 surfaces Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Showing 5 region surfaces 97910 watershed regions, grouped to 5 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 5 regions, 5 surfaces Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Showing 3 region surfaces 97910 watershed regions, grouped to 3 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 3 regions, 3 surfaces Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Only showing 2000 of 5180 regions. Showing 2000 of 5180 region surfaces 97910 watershed regions, grouped to 5180 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 5180 regions, 2000 surfaces Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260 Only showing 2000 of 5180 regions. Showing 2000 of 5180 region surfaces 97910 watershed regions, grouped to 5180 regions Showing hTRPM4_proteomer_box224_J259fit.seg - 5180 regions, 2000 surfaces > select #13.5 1 model selected > show #!12 models > hide #!12 models > show #!11 models > hide #!13 models > hide #!6 models > view matrix models #13.5,1,0,0,-1.2286,0,1,0,-0.85805,0,0,1,-9.2414 > show #!12 models > view matrix models #13.5,1,0,0,-6.181,0,1,0,0.076582,0,0,1,-23.628 > show #!2 models > hide #!2 models Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,2 Model Number: Z15S000HZDK/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 9 days, 1 hour, 24 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP E24 G4: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX