id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15094 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x00007ff84c382100 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2000 in save_state File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 219 in take_snapshot File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1417 in take_snapshot File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 296 in process File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 273 in discovery File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 636 in save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 912 in save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: 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Bytes before following region: 4453363543\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10970f000-109713000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":88668}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0xa9 is not in any region. 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""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J125_003_volume_map.mrc Opened cryosparc_P388_J125_003_volume_map.mrc as #1, grid size 180,180,180, pixel 2.85, shown at level 0.612, step 1, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J181_002_volume_map.mrc Opened cryosparc_P388_J181_002_volume_map.mrc as #2, grid size 180,180,180, pixel 2.85, shown at level 0.614, step 1, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J182_002_volume_map.mrc Opened cryosparc_P388_J182_002_volume_map.mrc as #3, grid size 180,180,180, pixel 2.85, shown at level 0.611, step 1, values float32 > hide #!2 models > hide #!3 models > volume #1 level 0.5077 > volume #1 level 0.4 > volume #1 level 0.45 > volume #2 level 0.45 > volume #1 level 0.4 > volume #1 level 0.45 > volume #2 level 0.4 > volume #3 level 0.4 > volume #3 level 0.45 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P310_J405_007_volume_map.mrc Opened cryosparc_P310_J405_007_volume_map.mrc as #4, grid size 640,640,640, pixel 0.95, shown at level 0.114, step 4, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P310_J408_007_volume_map.mrc Opened cryosparc_P310_J408_007_volume_map.mrc as #5, grid size 640,640,640, pixel 0.95, shown at level 0.111, step 4, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P310_J413_009_volume_map.mrc Opened cryosparc_P310_J413_009_volume_map.mrc as #6, grid size 640,640,640, pixel 0.95, shown at level 0.114, step 4, values float32 > hide #!3 models > hide #!5 models > hide #!6 models > volume #4 step 1 > volume #4 level 0.1 > volume #4 level 0.12 > volume #5 step 1 > volume #5 level 0.12 > volume #4 level 0.1 > volume #4 level 0.12 > volume #5 level 0.1 > volume #6 step 1 > volume #6 level 0.12 > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J408_008_volume_map.mrc Opened cryosparc_P17_J408_008_volume_map.mrc as #7, grid size 294,294,294, pixel 1.9, shown at level 0.354, step 2, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc Opened cryosparc_P17_J368_007_volume_map.mrc as #8, grid size 294,294,294, pixel 1.9, shown at level 0.37, step 2, values float32 > hide #!8 models > hide #!7 models > show #!8 models > volume #8 step 1 > volume #8 level 0.4191 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J408_008_volume_map.mrc Opened cryosparc_P17_J408_008_volume_map.mrc as #9, grid size 294,294,294, pixel 1.9, shown at level 0.354, step 2, values float32 > close #9 > show #!7 models > hide #!7 models > volume #8 level 0.4 > volume #7 step 1 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J392_002_volume_map.mrc Opened cryosparc_P17_J392_002_volume_map.mrc as #9, grid size 294,294,294, pixel 1.9, shown at level 0.207, step 2, values float32 > hide #!7 models > volume #9 step 1 > volume #9 level 0.3788 > volume #9 level 0.4816 > hide #!9 models > show #!9 models > show #!8 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!9 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J411_002_volume_map.mrc Opened cryosparc_P17_J411_002_volume_map.mrc as #10, grid size 294,294,294, pixel 1.9, shown at level 0.214, step 2, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J412_002_volume_map.mrc Opened cryosparc_P17_J412_002_volume_map.mrc as #11, grid size 294,294,294, pixel 1.9, shown at level 0.289, step 2, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J413_002_volume_map.mrc Opened cryosparc_P17_J413_002_volume_map.mrc as #12, grid size 294,294,294, pixel 1.9, shown at level 0.214, step 2, values float32 > volume #10 step 1 > volume #11 step 1 > volume #12 step 1 > volume #10 level 0.5137 > volume #10 level 0.4337 > volume #12 level 0.4965 > volume #12 level 0.4561 > hide #!9 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J401_007_volume_map.mrc Opened cryosparc_P17_J401_007_volume_map.mrc as #13, grid size 294,294,294, pixel 1.9, shown at level 0.357, step 2, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J403_008_volume_map.mrc Opened cryosparc_P17_J403_008_volume_map.mrc as #14, grid size 294,294,294, pixel 1.9, shown at level 0.357, step 2, values float32 > show #!8 models > hide #!8 models > volume #13 step 1 > volume #14 step 1 > volume #13 level 0.35 > volume #13 level 0.3 > volume #14 level 0.3 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J399_007_volume_map.mrc Opened cryosparc_P17_J399_007_volume_map.mrc as #15, grid size 294,294,294, pixel 1.9, shown at level 0.357, step 2, values float32 > hide #!14 models > volume #15 step 1 > volume #15 level 0.2842 > volume #15 level 0.2923 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P388_J217_006_volume_map.mrc Opened cryosparc_P388_J217_006_volume_map.mrc as #16, grid size 294,294,294, pixel 1.9, shown at level 0.368, step 2, values float32 > hide #!15 models > volume #16 step 1 > volume #16 level 0.3641 > show #!8 models > volume #16 level 0.4 > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > open /Users/cvetkom/Downloads/cs_P17_J486_009_volume_map.mrc Opened cs_P17_J486_009_volume_map.mrc as #17, grid size 588,588,588, pixel 0.85, shown at level 0.169, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J486_005_volume_map.mrc Opened cryosparc_P17_J486_005_volume_map.mrc as #18, grid size 588,588,588, pixel 0.85, shown at level 0.169, step 4, values float32 > hide #!8 models > hide #!16 models > volume #18 step 1 > volume #17 step 1 > volume #17 level 0.1385 > volume #17 level 0.1646 > volume #17 level 0.1556 > ui tool show ""Map Coordinates"" > save /Users/cvetkom/Downloads/cs_P17_J486_009_volume_map.mrc models #17 > hide #!17 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > close #18 > open /Users/cvetkom/Downloads/cryosparc_P17_J491_011_volume_map.mrc Opened cryosparc_P17_J491_011_volume_map.mrc as #18, grid size 588,588,588, pixel 0.85, shown at level 0.166, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J492_012_volume_map.mrc Opened cryosparc_P17_J492_012_volume_map.mrc as #19, grid size 588,588,588, pixel 0.85, shown at level 0.166, step 4, values float32 > volume #18 step 1 > volume #18 level 0.139 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/initial_model_job502.mrc Opened initial_model_job502.mrc as #20, grid size 588,588,588, pixel 0.95, shown at level 0.00493, step 4, values float32 > hide #!18 models > volume #20 step 1 > volume #20 level 0.005154 > volume #20 level 0.00473 > close #20 > show #!8 models > open /Users/cvetkom/Downloads/cryosparc_P17_J429_map_sharp.mrc Opened cryosparc_P17_J429_map_sharp.mrc as #20, grid size 294,294,294, pixel 1.9, shown at level 0.000158, step 2, values float32 > hide #!8 models > volume #20 step 1 > volume #20 level 0.123 > volume #20 level 0.1118 > hide #!20 models > show #!18 models > show #!19 models > hide #!18 models > volume #19 step 1 > volume #19 level 0.1482 > show #!18 models > hide #!18 models > volume #18 level 0.14 > volume #19 level 0.14 > volume #18 level 0.135 > volume #18 level 0.13 > volume #19 level 0.13 > open /Users/cvetkom/Downloads/cryosparc_P17_J489_013_volume_map.mrc Opened cryosparc_P17_J489_013_volume_map.mrc as #21, grid size 588,588,588, pixel 0.85, shown at level 0.165, step 4, values float32 > hide #!21 models > show #!18 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!18 models > show #!18 models > hide #!19 models > show #!19 models > hide #!18 models > show #!18 models > hide #!19 models > show #!19 models > hide #!18 models > hide #!19 models > show #!21 models > volume #21 step 1 > volume #21 level 0.14 > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!21 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > hide #!19 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!20 models > close #18-21 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J491_011_volume_map.mrc Opened cryosparc_P17_J491_011_volume_map.mrc as #18, grid size 588,588,588, pixel 0.85, shown at level 0.166, step 4, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J489_013_volume_map.mrc Opened cryosparc_P17_J489_013_volume_map.mrc as #19, grid size 588,588,588, pixel 0.85, shown at level 0.165, step 4, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J492_012_volume_map.mrc Opened cryosparc_P17_J492_012_volume_map.mrc as #20, grid size 588,588,588, pixel 0.85, shown at level 0.166, step 4, values float32 > volume #18 step 2 > volume #18 step 1 > volume #19 step 1 > volume #20 step 1 > volume #18 level 0.13 > volume #19 level 0.13 > volume #20 level 0.13 > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!18 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!18 models > show #!18 models > hide #!19 models > show #!19 models > hide #!18 models > show #!18 models > hide #!19 models > show #!19 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!19 models > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job511.mrc Opened postprocess_masked_job511.mrc as #21, grid size 588,588,588, pixel 0.95, shown at level 0.00498, step 4, values float32 > hide #!18 models > show #!18 models > hide #!18 models > hide #!21 models > show #!18 models > select add #21 2 models selected > show #!21 models > ui mousemode right ""rotate selected models"" > view matrix models > #21,-0.55287,0.83087,-0.063182,166.89,-0.5876,-0.33499,0.73655,276.93,0.59081,0.44434,0.67343,-162.06 > ui mousemode right ""translate selected models"" > view matrix models > #21,-0.55287,0.83087,-0.063182,188.59,-0.5876,-0.33499,0.73655,291.89,0.59081,0.44434,0.67343,-218.35 > view matrix models > #21,-0.55287,0.83087,-0.063182,185.39,-0.5876,-0.33499,0.73655,288.19,0.59081,0.44434,0.67343,-212.32 > ui mousemode right zoom > select subtract #21 Nothing selected > ui tool show ""Fit in Map"" > fitmap #21 inMap #18 Fit map postprocess_masked_job511.mrc in map cryosparc_P17_J491_011_volume_map.mrc using 31756 points correlation = 0.8968, correlation about mean = 0.2434, overlap = 42.45 steps = 180, shift = 7, angle = 10.3 degrees Position of postprocess_masked_job511.mrc (#21) relative to cryosparc_P17_J491_011_volume_map.mrc (#18) coordinates: Matrix rotation and translation -0.51920954 0.84749667 0.11032156 127.58974848 -0.54899809 -0.42966309 0.71693147 315.34926138 0.65499813 0.31167134 0.68835923 -196.84626713 Axis -0.26099112 -0.35077655 -0.89935502 Axis point 178.92637046 159.99291122 0.00000000 Rotation angle (degrees) 129.06906427 Shift along axis 33.11776092 > hide #!18 models > volume #21 step 1 > volume #21 level 0.005527 > hide #!21 models > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job505_run_class001.mrc Opened Ref3D_job505_run_class001.mrc as #22, grid size 588,588,588, pixel 0.95, shown at level 0.005, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job507_run_class001.mrc Opened Ref3D_job507_run_class001.mrc as #23, grid size 588,588,588, pixel 0.95, shown at level 0.00501, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job505_run_class001.mrc Opened Ref3D_job505_run_class001.mrc as #24, grid size 588,588,588, pixel 0.95, shown at level 0.005, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job507_run_class001.mrc Opened Ref3D_job507_run_class001.mrc as #25, grid size 588,588,588, pixel 0.95, shown at level 0.00501, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job508_run_class001.mrc Opened Ref3D_job508_run_class001.mrc as #26, grid size 588,588,588, pixel 0.95, shown at level 0.00502, step 4, values float32 > hide #!26 models > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > show #!22 models > hide #!22 models > close #22-26 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job505_run_class001.mrc Opened Ref3D_job505_run_class001.mrc as #22, grid size 588,588,588, pixel 0.95, shown at level 0.005, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001.mrc Opened Ref3D_job506_run_class001.mrc as #23, grid size 588,588,588, pixel 0.95, shown at level 0.00502, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job507_run_class001.mrc Opened Ref3D_job507_run_class001.mrc as #24, grid size 588,588,588, pixel 0.95, shown at level 0.00501, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job508_run_class001.mrc Opened Ref3D_job508_run_class001.mrc as #25, grid size 588,588,588, pixel 0.95, shown at level 0.00502, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job509_run_class001.mrc Opened Ref3D_job509_run_class001.mrc as #26, grid size 588,588,588, pixel 0.95, shown at level 0.005, step 4, values float32 > hide #!23 models > hide #!24 models > hide #!25 models > hide #!26 models > volume #22 step 1 > volume #22 level 0.004523 > volume #22 level 0.004 > volume #23 step 1 > volume #23 level 0.004 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job514.mrc Opened postprocess_masked_job514.mrc as #27, grid size 588,588,588, pixel 0.95, shown at level 0.00499, step 4, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job515.mrc Opened postprocess_masked_job515.mrc as #28, grid size 588,588,588, pixel 0.95, shown at level 0.00499, step 4, values float32 > hide #!27 models > hide #!28 models > hide #!22 models > hide #!23 models > show #!24 models > show #!22 models > hide #!22 models > volume #24 step 1 > volume #24 level 0.004649 > show #!25 models > hide #!24 models > show #!24 models > hide #!24 models > show #!26 models > hide #!25 models > hide #!26 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!24 models > show #!25 models > volume #25 step 1 > volume #24 level 0.0045 > volume #24 level 0.0046 > hide #!24 models > volume #25 level 0.0046 > show #!24 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > hide #!24 models > show #!27 models > show #!21 models > hide #!21 models > volume #27 step 1 > volume #27 level 0.00489 > volume #28 step 1 > show #!27 models > hide #!28 models > show #!28 models > hide #!27 models > hide #!28 models > show #!23 models > volume #23 level 0.0035 > volume #23 level 0.0045 > ui tool show ""Segment Map"" Segmenting Ref3D_job506_run_class001.mrc, density threshold 0.004500 Only showing 60 of 67 regions. Showing 60 of 67 region surfaces 277 watershed regions, grouped to 67 regions Showing Ref3D_job506_run_class001.seg - 67 regions, 60 surfaces > select #29.26 1 model selected > select add #29.13 2 models selected > select add #29.6 3 models selected > select add #29.1 4 models selected > select add #29.38 5 models selected Grouped 5 regions > select add #29.11 2 models selected > select add #29.31 3 models selected Grouped 3 regions > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models Only showing 60 of 61 regions. Showing 60 of 61 region surfaces Only showing 60 of 61 regions. Showing 60 of 61 region surfaces Opened Ref3D_job506_run_class001_imasked as #30, grid size 588,588,588, pixel 0.95, shown at step 1, values float32 > hide #!23 models > hide #!29 models > show #!29 models > hide #!30 models > show #!30 models > hide #!29 models > show #!29 models > hide #!30 models Only showing 60 of 61 regions. Showing 60 of 61 region surfaces > show #!30 models > hide #!29 models > show #!29 models > hide #!30 models > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > hide #!29 models > select add #29 61 models selected > select subtract #29 Nothing selected > show #!30 models > ui tool show ""Map Eraser"" > volume erase #30 center 322.28,330.54,256.92 radius 31.628 > hide #!30 models > show #!30 models > save > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_NCP.mrc > models #30 > volume #30 level 0.004 > volume #30 level 0.0045 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map.mrc Opened cryosparc_P17_J288_006_volume_map.mrc as #31, grid size 294,294,294, pixel 1.9, shown at level 0.258, step 2, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map_sharp.mrc Opened cryosparc_P17_J288_006_volume_map_sharp.mrc as #32, grid size 294,294,294, pixel 1.9, shown at level 0.251, step 2, values float32 > volume #32 step 1 > volume #32 level 0.5717 > volume #31 step 1 > volume #31 level 0.6543 > open 4C93 fromDatabase pdb format mmcif Summary of feedback from opening 4C93 fetched from pdb --- note | Fetching compressed mmCIF 4c93 from http://files.rcsb.org/download/4c93.cif 4c93 title: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha. [more info...] Chain information for 4c93 #33 --- Chain | Description | UniProt A B C | DNA POLYMERASE ALPHA-BINDING PROTEIN | CTF4_YEAST 471-927 D E | DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A | DPOA_YEAST 137-149 > select add #33 9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected > hide (#!33 & sel) target a > cartoon (#!33 & sel) > select subtract #33 Nothing selected > select add #33 9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #33,1,0,0,277.71,0,1,0,277.7,0,0,1,412.4 > ui mousemode right ""rotate selected models"" > view matrix models > #33,0.85071,0.51833,-0.087371,264.2,-0.5256,0.83678,-0.15343,265.2,-0.0064157,0.17644,0.98429,409.11 > ui mousemode right ""translate selected models"" > view matrix models > #33,0.85071,0.51833,-0.087371,206.06,-0.5256,0.83678,-0.15343,295.57,-0.0064157,0.17644,0.98429,358 > ui mousemode right ""rotate selected models"" > view matrix models > #33,0.85087,0.50579,-0.1421,203.77,-0.52472,0.80474,-0.2776,290.42,-0.026051,0.31077,0.95013,354.26 > view matrix models > #33,0.74237,0.64892,-0.16668,199.01,-0.66761,0.73743,-0.10249,297.15,0.056405,0.18736,0.98067,358.62 > view matrix models > #33,0.61879,0.74677,-0.24378,192.29,-0.78542,0.59391,-0.17432,294.16,0.014612,0.29934,0.95404,355.21 > view matrix models > #33,0.9983,-0.034334,-0.047129,217.9,0.018839,0.95483,-0.29655,295.6,0.055182,0.29515,0.95386,355.87 > view matrix models > #33,0.9358,0.25827,-0.23996,204.12,-0.34616,0.80203,-0.48675,283.69,0.066739,0.53856,0.83994,347.46 > view matrix models > #33,0.4441,-0.059162,-0.89402,171.67,-0.18738,0.96962,-0.15725,298.59,0.87616,0.23736,0.41953,344.85 > view matrix models > #33,0.35501,0.67532,-0.64646,171.15,-0.35267,0.73716,0.57639,332.55,0.86579,0.023365,0.49987,351.35 > ui mousemode right ""translate selected models"" > view matrix models > #33,0.35501,0.67532,-0.64646,241,-0.35267,0.73716,0.57639,296.24,0.86579,0.023365,0.49987,410.46 > fitmap #33 inMap #31 Fit molecule 4c93 (#33) to map cryosparc_P17_J288_006_volume_map.mrc (#31) using 9593 atoms average map value = 0.5941, steps = 164 shifted from previous position = 8.43 rotated from previous position = 36.7 degrees atoms outside contour = 5817, contour level = 0.65427 Position of 4c93 (#33) relative to cryosparc_P17_J288_006_volume_map.mrc (#31) coordinates: Matrix rotation and translation -0.11641260 0.77432829 -0.62198377 234.06062084 -0.72447465 0.36217880 0.58648359 303.04623599 0.67940017 0.51888555 0.51881904 403.24027766 Axis -0.03403562 -0.65524703 -0.75464753 Axis point 89.28765412 -151.08833550 0.00000000 Rotation angle (degrees) 96.75980732 Shift along axis -510.84082774 > fitmap #33 inMap #31 Fit molecule 4c93 (#33) to map cryosparc_P17_J288_006_volume_map.mrc (#31) using 9593 atoms average map value = 0.5941, steps = 40 shifted from previous position = 0.00237 rotated from previous position = 0.00559 degrees atoms outside contour = 5819, contour level = 0.65427 Position of 4c93 (#33) relative to cryosparc_P17_J288_006_volume_map.mrc (#31) coordinates: Matrix rotation and translation -0.11649075 0.77431865 -0.62198114 234.06168000 -0.72442922 0.36216631 0.58654742 303.05097408 0.67943522 0.51890866 0.51875003 403.23724883 Axis -0.03405645 -0.65526960 -0.75462700 Axis point 89.27779010 -151.08286692 0.00000000 Rotation angle (degrees) 96.76441303 Shift along axis -510.84511620 > open 6SKL fromDatabase pdb format mmcif 6skl title: Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1 [more info...] Chain information for 6skl #34 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971 4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845 A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208 B | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213 C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194 D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294 E | Cell division control protein 45 | CDC45_YEAST 1-650 F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927 I | DNA fork, leading-strand template | J | DNA fork, lagging-strand template | X | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238 Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317 Non-standard residues in 6skl #34 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion ZN — zinc ion > select subtract #33 Nothing selected > select add #34 118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected > hide (#!34 & sel) target a > cartoon (#!34 & sel) > view matrix models #34,1,0,0,-105.11,0,1,0,63.093,0,0,1,60.805 > ui mousemode right ""rotate selected models"" > view matrix models > #34,0.89661,0.16888,-0.40936,-42.927,-0.024986,0.94224,0.33399,18.768,0.44212,-0.28923,0.84904,55.571 > view matrix models > #34,0.18469,0.42907,0.88419,-184.99,-0.91736,-0.24753,0.31174,429.58,0.35262,-0.86869,0.34789,275.52 > view matrix models > #34,-0.74581,-0.65341,0.12973,345.25,-0.31799,0.17808,-0.93122,453.04,0.58536,-0.73576,-0.34059,328.08 > view matrix models > #34,-0.74688,-0.65706,0.10221,351.14,-0.29136,0.1852,-0.93852,447.68,0.59773,-0.73074,-0.32976,322.69 > view matrix models > #34,-0.79277,-0.59486,-0.13289,390.85,-0.15343,0.40576,-0.90101,370.97,0.58989,-0.6939,-0.41295,332.21 > view matrix models > #34,-0.80975,-0.58676,0.0025381,368.19,-0.2818,0.38509,-0.8788,396.52,0.51467,-0.71233,-0.47718,362.38 > volume #31 level 0.5196 > volume #31 flipNormals Missing ""flipNormals"" keyword's argument > volume flip #31 Opened cryosparc_P17_J288_006_volume_map.mrc z flip as #35, grid size 294,294,294, pixel 1.9, shown at step 1, values float32 > select subtract #34 Nothing selected > select add #35 2 models selected > view matrix models > #35,0.78895,-0.57985,-0.20332,272.36,0.063773,-0.25184,0.96567,82.546,-0.61114,-0.77483,-0.16171,684.21 > view matrix models > #35,0.28797,-0.87982,-0.37814,542.26,-0.92038,-0.36335,0.14448,602.17,-0.26451,0.30642,-0.91441,478.11 > view matrix models > #35,0.19939,-0.94065,-0.27463,557.88,-0.84145,-0.30798,0.44396,488.1,-0.50219,0.14257,-0.85292,575.32 > view matrix models > #35,0.056907,-0.98144,-0.18311,586.32,-0.81292,-0.15202,0.56218,406.67,-0.57958,0.11686,-0.80649,592.58 > view matrix models > #35,-0.4142,-0.82661,-0.38098,727.63,-0.85036,0.50069,-0.16185,421.02,0.32454,0.25694,-0.91031,323.5 > view matrix models > #35,-0.05329,-0.9466,-0.31798,642.33,-0.99846,0.055466,0.0022138,544.59,0.015542,0.31761,-0.94809,404.07 > view matrix models > #35,-0.12565,-0.99206,-0.005759,595.9,-0.98907,0.12572,-0.077001,542.65,0.077114,-0.003979,-0.99701,488.13 > view matrix models > #35,-0.028832,-0.99711,0.070342,550.41,-0.98983,0.038289,0.13704,512.53,-0.13933,-0.065675,-0.98807,564.4 > ui mousemode right ""translate selected models"" > view matrix models > #35,-0.028832,-0.99711,0.070342,558.82,-0.98983,0.038289,0.13704,502.05,-0.13933,-0.065675,-0.98807,609.85 > select subtract #35 Nothing selected > fitmap #33 inMap #35 Fit molecule 4c93 (#33) to map cryosparc_P17_J288_006_volume_map.mrc z flip (#35) using 9593 atoms average map value = 0.748, steps = 156 shifted from previous position = 23.9 rotated from previous position = 52.9 degrees atoms outside contour = 2729, contour level = 0.51963 Position of 4c93 (#33) relative to cryosparc_P17_J288_006_volume_map.mrc z flip (#35) coordinates: Matrix rotation and translation 0.31609082 -0.94869655 0.00783922 290.47366164 -0.57784462 -0.18596222 0.79467833 322.70855084 -0.75245079 -0.25572037 -0.60698014 144.58037287 Axis -0.77884069 0.56373337 0.27497613 Axis point 0.00000000 302.79412564 42.56571290 Rotation angle (degrees) 137.59748776 Shift along axis -4.55497724 > volume #35 color #ffffb280 > volume #35 color #ffffb29a > ui tool show Matchmaker QDockWidget failed to find relevant screen info. screenFrom: QScreen(0x600001698de0, name=""DELL U2415"") screenTo: QScreen(0x0) wdgScreen: QScreen(0x6000016ad580, name=""Built-in Retina Display"") orgWdgScreen QScreen(0x6000016ad580, name=""Built-in Retina Display"") QDockWidget failed to find relevant screen info. screenFrom: QScreen(0x600001698de0, name=""DELL U2415"") screenTo: QScreen(0x0) wdgScreen: QScreen(0x600001698de0, name=""DELL U2415"") orgWdgScreen QScreen(0x6000016ad580, name=""Built-in Retina Display"") > matchmaker #33/A to #34/G pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6skl, chain G (#34) with 4c93, chain A (#33), sequence alignment score = 2250.7 RMSD between 395 pruned atom pairs is 0.975 angstroms; (across all 421 pairs: 1.137) > select add #33 9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected > select add #34 127813 atoms, 129087 bonds, 134 pseudobonds, 8652 residues, 6 models selected > view matrix models > #33,0.20694,0.33166,-0.92042,219.01,-0.50314,0.84292,0.19061,241.4,0.83906,0.42366,0.3413,390.93,#34,-0.80975,-0.58676,0.0025381,554.75,-0.2818,0.38509,-0.8788,387.59,0.51467,-0.71233,-0.47718,400.46 > view matrix models > #33,0.20694,0.33166,-0.92042,219.86,-0.50314,0.84292,0.19061,243.18,0.83906,0.42366,0.3413,387.91,#34,-0.80975,-0.58676,0.0025381,555.6,-0.2818,0.38509,-0.8788,389.37,0.51467,-0.71233,-0.47718,397.44 > select subtract #34 9593 atoms, 9682 bonds, 4 pseudobonds, 1331 residues, 2 models selected > select subtract #33 Nothing selected > fitmap #34 inMap #35 Fit molecule 6skl (#34) to map cryosparc_P17_J288_006_volume_map.mrc z flip (#35) using 118220 atoms average map value = 0.6269, steps = 156 shifted from previous position = 29.5 rotated from previous position = 20.7 degrees atoms outside contour = 51602, contour level = 0.51963 Position of 6skl (#34) relative to cryosparc_P17_J288_006_volume_map.mrc z flip (#35) coordinates: Matrix rotation and translation 0.46209162 -0.10482145 0.88061558 50.05829992 0.51912918 0.83705154 -0.17277039 61.05331656 -0.71901059 0.53698899 0.44121038 233.04243695 Axis 0.38201772 0.86097564 0.33583240 Axis point 167.96409560 0.00000000 110.80343384 Rotation angle (degrees) 68.27348026 Shift along axis 149.95177710 > matchmaker #33/A to #34/G pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6skl, chain G (#34) with 4c93, chain A (#33), sequence alignment score = 2250.7 RMSD between 395 pruned atom pairs is 0.975 angstroms; (across all 421 pairs: 1.137) > ui mousemode right zoom > hide #!35 models > open ""/Users/cvetkom/Downloads/ranked_0 (1).pdb"" Chain information for ranked_0 (1).pdb #36 --- Chain | Description A | No description available B C D | No description available > matchmaker #36/B to #34/H pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6skl, chain H (#34) with ranked_0 (1).pdb, chain B (#36), sequence alignment score = 2258.6 RMSD between 415 pruned atom pairs is 0.607 angstroms; (across all 425 pairs: 0.788) > show #!35 models > select #36/B 7269 atoms, 7356 bonds, 457 residues, 1 model selected > select clear > select #36/A 277 atoms, 276 bonds, 17 residues, 1 model selected > color sel red > select clear > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > open 8B9D fromDatabase pdb format mmcif files.rcsb.org failed to respond > open 8B9D fromDatabase pdb format mmcif files.rcsb.org failed to respond > open 8B9D fromDatabase pdb format mmcif Summary of feedback from opening 8B9D fetched from pdb --- warnings | Atom H1 is not in the residue template for MET /C:1 Atom H1 is not in the residue template for MET /D:1 Atom H1 is not in the residue template for MET /E:1 Atom H1 is not in the residue template for MET /P:1 note | Fetching compressed mmCIF 8b9d from http://files.rcsb.org/download/8b9d.cif 8b9d title: Human replisome bound by Pol α [more info...] Chain information for 8b9d #37 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719 A | DNA polymerase alpha subunit B | DPOA2_HUMAN 1-598 B | DNA polymerase alpha catalytic subunit | DPOLA_HUMAN 1-1462 C | Cell division control protein 45 homolog | CDC45_HUMAN 1-134 135-566 D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN 1-196 E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN 1-185 F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN 1-216 G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN 1-223 H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN 1-1129 K | Protein timeless homolog | TIM_HUMAN 1-1208 L | TIMELESS-interacting protein | TIPIN_HUMAN 1-301 M | Leading strand DNA | N | DNA Molecule | O | DNA primase small subunit | PRI1_HUMAN 1-420 P | DNA primase large subunit | PRI2_HUMAN 1-509 Q | Claspin | CLSPN_HUMAN 1-1339 Non-standard residues in 8b9d #37 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion ZN — zinc ion > hide #33-37 target a > cartoon #33-37 > hide #!37 models > hide #!35 models > show #!35 models > save > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map_zflip.mrc > models #35 > hide #36 models > hide #!35 models > hide #!34 models > hide #!33 models > show #!31 models > show #!32 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > volume #32 level 0.7272 > volume flip #32 Opened cryosparc_P17_J288_006_volume_map_sharp.mrc z flip as #38, grid size 294,294,294, pixel 1.9, shown at step 1, values float32 > volume #32 level 0.7618 > volume #38 level 0.7618 > volume #38 level 0.7272 > save > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J288_006_volume_map_sharp_zflip.mrc > models #38 > hide #!38 models > show #!34 models > select #34/E 9129 atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected > hide #!34 models > select add #34 118220 atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected > select subtract #34 Nothing selected > show #!31 models > hide #!31 models > show #!19 models > show #!27 models > hide #!27 models > hide #!19 models > open > /Users/cvetkom/Documents/AlphaFold/yMrc1_H3H4_tetr/yMrc1_H3H4_tetr_ranked_0.pdb Chain information for yMrc1_H3H4_tetr_ranked_0.pdb #39 --- Chain | Description A | No description available B C | No description available D E | No description available > select add #39 25142 atoms, 25299 bonds, 1574 residues, 1 model selected > view sel > select subtract #39 Nothing selected > hide #39 models > show #39 models > hide #39 target a > cartoon #39 > ui tool show ""Show Sequence Viewer"" > sequence chain #39/A Alignment identifier is 39/A > select #39/A:657 15 atoms, 14 bonds, 1 residue, 1 model selected > select #39/A:657-660 63 atoms, 62 bonds, 4 residues, 1 model selected > color sel red > select #39/A:678 15 atoms, 14 bonds, 1 residue, 1 model selected > select #39/A:678-712 621 atoms, 621 bonds, 35 residues, 1 model selected > select #39/A:746 11 atoms, 10 bonds, 1 residue, 1 model selected > select #39/A:746-751 96 atoms, 95 bonds, 6 residues, 1 model selected > select #39/A:612 15 atoms, 14 bonds, 1 residue, 1 model selected > select #39/A:612-616 83 atoms, 83 bonds, 5 residues, 1 model selected > select #39/A:746-747 23 atoms, 22 bonds, 2 residues, 1 model selected > select #39/A:746-751 96 atoms, 95 bonds, 6 residues, 1 model selected > select #39/A:657 15 atoms, 14 bonds, 1 residue, 1 model selected > select #39/A:657-660 63 atoms, 62 bonds, 4 residues, 1 model selected > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/mask_job518.mrc Opened mask_job518.mrc as #40, grid size 588,588,588, pixel 0.95, shown at level 5e-05, step 4, values float32 > select add #39 25142 atoms, 25299 bonds, 1574 residues, 1 model selected > select subtract #39 Nothing selected > hide #39 models > hide #!40 models > show #!30 models > show #!40 models > hide #!40 models > show #!40 models > volume #40 step 1 > volume #40 level 1 > volume #40 color #ffb2b280 > volume #40 level 1 > show #!29 models > hide #!29 models > show #!23 models > hide #!30 models > hide #!23 models > hide #!40 models > show #!30 models > volume #30 level 0.005 > volume #30 level 0.004 > volume #30 level 0.0045 > volume #30 level 0.005 > show #!40 models > hide #!40 models > show #!40 models > volume #30 level 0.0045 > close #40 > show #39 models > hide #39 models > show #!37 models > hide #!37 models > close #37 > show #36 models > hide #36 models > hide #!30 models > show #!18 models > show #!20 models > hide #!18 models > show #!19 models > hide #!20 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J492_012_volume_map_sharp.mrc Opened cryosparc_P17_J492_012_volume_map_sharp.mrc as #37, grid size 588,588,588, pixel 0.85, shown at level 0.161, step 4, values float32 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J491_011_volume_map_sharp.mrc Opened cryosparc_P17_J491_011_volume_map_sharp.mrc as #40, grid size 588,588,588, pixel 0.85, shown at level 0.17, step 4, values float32 > hide #!19 models > hide #!37 models > volume #40 level 0.2312 > volume #40 step 1 > volume #40 level 0.3499 > volume #37 level 0.1763 > volume #37 step 1 > volume #37 level 0.2223 > volume #37 level 0.2 > volume #37 level 0.1885 > volume #37 level 0.1742 > hide #!37 models > show #!8 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map_sharp.mrc Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #41, grid size 294,294,294, pixel 1.9, shown at level 0.362, step 2, values float32 > hide #!8 models > volume #41 step 1 > volume #41 level 0.4564 > hide #!41 models > show #!35 models > hide #!35 models > show #!41 models > hide #!41 models > show #!33 models > hide #!33 models > show #36 models > combine #36 > hide #36 models > show #!41 models > select add #42 22084 atoms, 22344 bonds, 1388 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #42,-0.66651,-0.41454,0.61961,272.25,-0.074937,-0.78968,-0.60893,371.9,0.74172,-0.45229,0.49526,320.86 > ui mousemode right ""rotate selected models"" > view matrix models > #42,0.88686,0.43938,0.14293,270.28,0.32258,-0.81026,0.4893,369.08,0.3308,-0.38784,-0.86032,324.19 > view matrix models > #42,0.37114,0.92855,0.0068206,265.93,0.88732,-0.3568,0.29216,367.34,0.27372,-0.10238,-0.95634,322.18 > view matrix models > #42,-0.31468,0.84864,0.42519,263.78,0.88685,0.10319,0.4504,363.22,0.33835,0.51881,-0.78509,316.9 > view matrix models > #42,-0.23757,0.91024,0.33914,263.75,0.89188,0.06608,0.44741,363.53,0.38484,0.40877,-0.82753,317.99 > ui mousemode right ""translate selected models"" > view matrix models > #42,-0.23757,0.91024,0.33914,263.29,0.89188,0.06608,0.44741,364.95,0.38484,0.40877,-0.82753,225.17 > ui tool show ""Fit in Map"" > fitmap #42 inMap #41 Fit molecule copy of ranked_0 (1).pdb (#42) to map cryosparc_P17_J368_007_volume_map_sharp.mrc (#41) using 22084 atoms average map value = 0.6576, steps = 148 shifted from previous position = 10.7 rotated from previous position = 27.8 degrees atoms outside contour = 5619, contour level = 0.45638 Position of copy of ranked_0 (1).pdb (#42) relative to cryosparc_P17_J368_007_volume_map_sharp.mrc (#41) coordinates: Matrix rotation and translation 0.11572590 0.95057234 0.28813146 269.08018829 0.98967501 -0.13504383 0.04802635 358.27183284 0.08456290 0.27959862 -0.95638576 219.12378513 Axis 0.74509125 0.65498843 0.12581411 Axis point 0.00000000 52.42448167 89.73927147 Rotation angle (degrees) 171.06008584 Shift along axis 462.72206245 > select subtract #42 Nothing selected > color #41 #99bfe584 models > color #41 #99bfe582 models > color #41 #99bfe580 models > volume #41 level 0.5 > volume #41 level 0.55 > save > /Users/cvetkom/Documents/chimera_sessions/20240502_CMGC4MCT_Fpl20MN_krios_merged_misc.cxs ===== 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: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 580~1678 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 11 days, 2 hours, 56 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2415: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 7MT016923MAL Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 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: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX