id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14411 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-14.2.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002970bb000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002960af000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002950a3000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000294097000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000029308b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000029207f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000291073000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000290067000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028f05b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028e04f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000028d043000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00000001d9849000 (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"":""2024-01-17 22:09:53.00 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All rights reserved. How to cite UCSF ChimeraX > open /Users/ihansol/Documents/Lab_Roh/2024_internship/7xw2.pdb 7xw2.pdb title: Cryo-em structure of human dicer-pre-miRNA In A dicing state [more info...] Chain information for 7xw2.pdb #1 --- Chain | Description | UniProt A | endoribonuclease dicer | DICER_HUMAN 1-1922 C | RNA (73-mer) | Non-standard residues in 7xw2.pdb #1 --- CA — calcium ion > open /Users/ihansol/Documents/Lab_Roh/2024_internship/emd_33489.map Opened emd_33489.map as #2, grid size 280,280,280, pixel 0.849, shown at level 0.0531, step 2, values float32 > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.1408 > volume #2 step 1 > volume #2 level 0.355 > volume #2 level 0.1499 > volume #2 level 0.1134 > show #!1 models > transparency 50 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J762_007_volume_map.mrc Opened cryosparc_P4_J762_007_volume_map.mrc as #3, grid size 450,450,450, pixel 1.08, shown at level 0.00638, step 2, values float32 > hide #!1 models > hide #!2 models > volume #3 level -0.02735 > volume #3 level 0.0163 > show #!2 models > close session > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J762_007_volume_map.mrc > format mrc Opened cryosparc_P4_J762_007_volume_map.mrc as #1, grid size 450,450,450, pixel 1.08, shown at level 0.00638, step 2, values float32 > volume #1 level 0.02225 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_00_00281_volume.mrc Opened cryosparc_P4_J628_class_00_00281_volume.mrc as #2, grid size 168,168,168, pixel 2.89, shown at level 0.0338, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_01_00281_volume.mrc Opened cryosparc_P4_J628_class_01_00281_volume.mrc as #3, grid size 168,168,168, pixel 2.89, shown at level 0.0338, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_02_00281_volume.mrc Opened cryosparc_P4_J628_class_02_00281_volume.mrc as #4, grid size 168,168,168, pixel 2.89, shown at level 0.0371, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_03_00281_volume.mrc Opened cryosparc_P4_J628_class_03_00281_volume.mrc as #5, grid size 168,168,168, pixel 2.89, shown at level 0.0378, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_04_00281_volume.mrc Opened cryosparc_P4_J628_class_04_00281_volume.mrc as #6, grid size 168,168,168, pixel 2.89, shown at level 0.0349, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_05_00281_volume.mrc Opened cryosparc_P4_J628_class_05_00281_volume.mrc as #7, grid size 168,168,168, pixel 2.89, shown at level 0.0322, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_06_00281_volume.mrc Opened cryosparc_P4_J628_class_06_00281_volume.mrc as #8, grid size 168,168,168, pixel 2.89, shown at level 0.0315, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_07_00281_volume.mrc Opened cryosparc_P4_J628_class_07_00281_volume.mrc as #9, grid size 168,168,168, pixel 2.89, shown at level 0.0315, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_08_00281_volume.mrc Opened cryosparc_P4_J628_class_08_00281_volume.mrc as #10, grid size 168,168,168, pixel 2.89, shown at level 0.0319, step 1, values float32 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628_class_09_00281_volume.mrc Opened cryosparc_P4_J628_class_09_00281_volume.mrc as #11, grid size 168,168,168, pixel 2.89, shown at level 0.0314, step 1, values float32 > volume #11 level 0.1987 > volume #10 level 0.2681 > volume #9 level 0.2027 > volume #8 level 0.1658 > volume #7 level 0.32 > volume #6 level 0.3003 > volume #5 level 0.3925 > volume #4 level 0.5084 > volume #3 level 0.2929 > volume #2 level 0.1345 > volume #3 level 0.2032 > volume #4 level 0.08478 > volume #5 level 0.09519 > volume #6 level 0.06286 > volume #7 level 0.05658 > volume #8 level 0.06986 > volume #9 level 0.1362 > volume #10 level 0.07732 > volume #11 level 0.06489 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J637_004_volume_map.mrc Opened cryosparc_P4_J637_004_volume_map.mrc as #12, grid size 450,450,450, pixel 1.08, shown at level 0.00971, step 2, values float32 > volume #12 step 1 > volume #12 level 0.03285 > volume #6 level 0.0908 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J628__mask_solvent.mrc Opened cryosparc_P4_J628__mask_solvent.mrc as #13, grid size 168,168,168, pixel 2.89, shown at level 0.369, step 1, values float32 > hide #!1-13 target m > volume #13 level 0.1645 > ui mousemode right ""map eraser"" > volume erase #13 center 247.68,320.3,258.76 radius 39.366 Opened cryosparc_P4_J628__mask_solvent.mrc copy as #15, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume erase #15 center 249.07,272.84,282.79 radius 39.366 > volume erase #15 center 247.55,229.8,277.28 radius 39.366 > volume erase #15 center 244.71,198.34,276.38 radius 39.366 > volume erase #15 center 236.42,172.27,255.93 radius 39.366 > volume erase #15 center 203.93,231.34,282.94 radius 39.366 > volume erase #15 center 287.67,230.12,271.24 radius 39.366 > volume erase #15 center 288.1,254.01,273.7 radius 39.366 > volume erase #15 center 219.51,267.66,284.45 radius 39.366 > volume erase #15 center 195.34,221.92,270.84 radius 39.366 > volume erase #15 center 305.61,238.97,252.49 radius 39.366 > volume erase #15 center 301.63,280.66,247.38 radius 39.366 > volume erase #15 center 279.68,300.27,260.37 radius 39.366 > volume erase #15 center 258.62,315.49,259.64 radius 39.366 > volume erase #15 center 246.98,313.49,258.11 radius 39.366 > volume erase #15 center 217.18,190.29,265.24 radius 39.366 > volume erase #15 center 200.42,193.68,261.27 radius 39.366 > volume erase #15 center 265.5,184.92,266.15 radius 39.366 > ui mousemode right select > ui mousemode right ""translate selected models"" > select add #15 2 models selected > view matrix models #15,1,0,0,-3.496,0,1,0,54.992,0,0,1,-127.27 > ui mousemode right ""map eraser"" > volume erase #15 center 228.15,254.76,186.75 radius 39.366 > ui mousemode right ""translate selected models"" > view matrix models #15,1,0,0,-41.409,0,1,0,-35.442,0,0,1,-30.179 > view matrix models #15,1,0,0,-32.266,0,1,0,-78.28,0,0,1,-6.6445 > volume #15 level 1 > view matrix models #15,1,0,0,-42.821,0,1,0,-121.44,0,0,1,-27.723 > save > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask.mrc > models #15 > volume #15 gaussian 10 Expected a keyword > molmap #15 10 No atoms specified > volume #15 level 1 > view matrix models #15,1,0,0,-33.65,0,1,0,-68.387,0,0,1,-11.048 > view matrix models #15,1,0,0,-20.912,0,1,0,-60.78,0,0,1,-9.8763 > view matrix models #15,1,0,0,-13.717,0,1,0,-60.179,0,0,1,-4.9026 > view matrix models #15,1,0,0,-9.9415,0,1,0,-53.629,0,0,1,2.5346 > view matrix models #15,1,0,0,-10.972,0,1,0,-50.663,0,0,1,-1.5542 > gaussian #15 10 Unknown command: gaussian #15 10 > toolshed show > ui mousemode right ""contour level"" > ui mousemode right ""map eraser"" > ui mousemode right ""translate selected models"" > volume #15 level 1 > view matrix models #15,1,0,0,-10.943,0,1,0,-50.86,0,0,1,-1.9568 > ui tool show ""Hide Dust"" > surface dust #15 size 17.36 > ui tool show ""Map Coordinates"" > ui tool show ""Map Statistics"" > measure mapstats sel Map Hsp90_side_mask.mrc #15, minimum 0, maximum 1, mean 0.003797, SD 0.05919, RMS 0.05931 > ui tool show ""Measure Volume and Area"" > ui tool show ""Measure and Color Blobs"" > ui tool show ""Segment Map"" > ui tool show ""Show Volume Menu"" > ui tool show ""Volume Viewer"" > ui tool show ""Show Volume Menu"" > volume gaussian #15 sDev 10 Opened Hsp90_side_mask.mrc gaussian as #16, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #16 level 0.8772 > measure blob #!16.1 triangleNumber 1610 color #0000ccff outline true Surface Hsp90_side_mask.mrc gaussian #16.1 blob: volume = 1.2811e+05 area = 12868 size = 73.274 59.14 50.995 > ui mousemode right ""pick blobs"" > ui mousemode right ""translate selected models"" > view matrix models #15,1,0,0,-10.73,0,1,0,-50.037,0,0,1,-2.1026 > view matrix models #15,1,0,0,-4.6413,0,1,0,-23.883,0,0,1,-20.686 > ui mousemode right ""pick blobs"" > ui mousemode right ""map eraser"" > ui mousemode right ""pick blobs"" > ui mousemode right ""translate selected models"" > view matrix models #15,1,0,0,28.989,0,1,0,-53.863,0,0,1,-33.833 > hide #!16 models > show #!16 models > select add #16 5 models selected > select subtract #15 3 models selected > view matrix models #16,1,0,0,17.505,0,1,0,-76.371,0,0,1,-13.216 > view matrix models #16,1,0,0,13.211,0,1,0,-40.586,0,0,1,10.077 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.32653,-0.50733,-0.79749,615.5,-0.025284,-0.83875,0.54393,306.31,-0.94485,0.19777,0.26105,336.53 > view matrix models > #16,-0.84434,-0.47578,-0.24641,620.33,0.0088869,-0.47227,0.88141,140.24,-0.53573,0.74202,0.40299,76.738 > view matrix models > #16,-0.7913,-0.55068,-0.26569,629.9,0.035228,-0.47489,0.87934,135.01,-0.61041,0.68647,0.39518,109.78 > view matrix models > #16,-0.74101,-0.61727,-0.26434,633.93,0.069313,-0.46188,0.88423,122.68,-0.6679,0.6369,0.38504,137.71 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.74101,-0.61727,-0.26434,634.33,0.069313,-0.46188,0.88423,122.11,-0.6679,0.6369,0.38504,144.08 > volume #16 level 0.807 No map chosen to save > save > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask_0.807.mrc > models #16 > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask_0.807.mrc Opened Hsp90_side_mask_0.807.mrc as #17, grid size 168,168,168, pixel 2.89, shown at level 0.0306, step 1, values float32 > volume #17 level 0.844 > volume #16 style image > volume #16 style surface > save > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Hsp90_side_mask_0.807.mrc > models #16 > close #17 > view matrix models > #16,-0.74101,-0.61727,-0.26434,629.61,0.069313,-0.46188,0.88423,164.74,-0.6679,0.6369,0.38504,150.17 > volume #16 change image level -2.29e-16,0 level 0.03057,0.8 level 0.9991,1 > volume #16 level 0.7996 > view matrix models > #16,-0.74101,-0.61727,-0.26434,628.25,0.069313,-0.46188,0.88423,98.537,-0.6679,0.6369,0.38504,134.8 > volume gaussian #11 sDev 10 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #17, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #17 level 0.007198 > volume gaussian #17 sDev 20 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #18, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #18 level 0.004995 > volume gaussian #18 sDev 20 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #19, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #19 level 0.004625 > volume gaussian #19 sDev 20 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #20, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #20 level 0.004777 > volume gaussian #20 sDev 20 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #21, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #21 level 0.002647 > volume gaussian #21 sDev 20 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #22, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #22 level 0.001976 > ui mousemode right ""map eraser"" Can only have one displayed volume when erasing > volume #22 level 0.002122 > volume gaussian #22 sDev 20 Opened cryosparc_P4_J628_class_09_00281_volume.mrc gaussian as #23, grid size 168,168,168, pixel 2.89, shown at step 1, values float32 > volume #23 level 0.001856 No map chosen to save > save > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/J628_mask_0.00186.mrc > models #23 > save /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Mask_making.cxs > open > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/cryosparc_P4_J826_class_00_final_volume.mrc Opened cryosparc_P4_J826_class_00_final_volume.mrc as #24, grid size 192,192,192, pixel 2.53, shown at level 0.0456, step 1, values float32 > hide #14 models > ui mousemode right ""translate selected models"" > volume #24 level 0.1245 > close #22 > close #20 > close #21 > close #19 > close #18 > close #17 > view matrix models > #16,-0.74101,-0.61727,-0.26434,615.77,0.069313,-0.46188,0.88423,102.42,-0.6679,0.6369,0.38504,181.5 > view matrix models > #16,-0.74101,-0.61727,-0.26434,613.81,0.069313,-0.46188,0.88423,100.68,-0.6679,0.6369,0.38504,173.94 > view matrix models > #16,-0.74101,-0.61727,-0.26434,613.96,0.069313,-0.46188,0.88423,101.83,-0.6679,0.6369,0.38504,172.53 > volume #24 level 0.1087 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.33169,0.15469,-0.93062,461.39,-0.45283,-0.8915,0.013213,507.66,-0.8276,0.42579,0.36575,266.32 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.33169,0.15469,-0.93062,469.01,-0.45283,-0.8915,0.013213,510.72,-0.8276,0.42579,0.36575,265.42 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.17387,0.30096,-0.93765,396.86,-0.48568,-0.85451,-0.18421,549.34,-0.85667,0.42337,0.29474,287.29 > view matrix models > #16,-0.13114,0.30798,-0.94231,385.87,-0.8357,-0.54567,-0.062046,532.66,-0.5333,0.77935,0.32894,115.87 > view matrix models > #16,-0.16063,0.25482,-0.95356,408.21,-0.82899,-0.55918,-0.0097837,523.82,-0.5357,0.78891,0.30106,119.72 > view matrix models > #16,-0.23167,0.14386,-0.9621,454.11,-0.80783,-0.57946,0.10788,499.99,-0.54198,0.8022,0.25046,128.18 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.23167,0.14386,-0.9621,454.36,-0.80783,-0.57946,0.10788,497.04,-0.54198,0.8022,0.25046,129.71 > save > /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/J827_side_mask_0.8.mrc > models #16 > save /Users/ihansol/Documents/Lab_Roh/Dicer/maps/20240117/Mask_making.cxs Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: You can double click a model's Name or ID in the model panel to edit those fields 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 M1 Pro 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: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15J004J4KH/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 26 days, 18 hours, 58 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG FULL HD: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX