id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6468 Crash in Qt event loop after saving sessions with maps chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000075ed000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1284 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00000001106b8600 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.3.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"":""2022-03-25 21:46:23.00 -0400"",""app_version"":""1.3.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.3.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.2.1 (21D62)"",""incident_id"":""E762CDE2-18D6-419B-9643-01360E6DEE38"",""name"":""ChimeraX""} { ""uptime"" : 630000, ""procLaunch"" : ""2022-03-25 20:45:30.0594 -0400"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""procStartAbsTime"" : 627203471819743, ""coalitionID"" : 41917, ""osVersion"" : { ""train"" : ""macOS 12.2.1"", ""build"" : ""21D62"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-03-25 21:46:14.5340 -0400"", ""incident"" : ""E762CDE2-18D6-419B-9643-01360E6DEE38"", ""bug_type"" : ""309"", ""pid"" : 48042, ""procExitAbsTime"" : 630847951425409, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.3.0"",""CFBundleVersion"":""1.3.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D925C038-417C-5232-8E26-B18684AC4B44"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""67FBC4A0-8B5F-1AB5-AADA-75EAE622406F"", ""wakeTime"" : 5885, ""bridgeVersion"" : {""build"":""19P744"",""train"":""6.2""}, ""sleepWakeUUID"" : ""F40FE598-E502-4EE8-A029-208F07F02700"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/kate/Desktop/Modelling/cryosparc_J207.cxs Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size 128,128,128, pixel 2.59, shown at level 0.322, step 1, values float32 Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size 128,128,128, pixel 2.59, shown at level 0.514, step 1, values float32 Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size 128,128,128, pixel 2.59, shown at level 0.315, step 1, values float32 Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size 128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size 128,128,128, pixel 2.59, shown at level 0.381, step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size 128,128,128, pixel 2.59, shown at level 0.222, step 1, values float32 Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size 128,128,128, pixel 2.59, shown at level 0.28, step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size 128,128,128, pixel 2.59, shown at level 0.325, step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size 128,128,128, pixel 2.59, shown at level 0.225, step 1, values float32 Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size 128,128,128, pixel 2.59, shown at level 0.464, step 1, values float32 Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size 400,400,400, pixel 0.83, shown at level 0.0773, step 1, values float32 opened ChimeraX session > select #17 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #17,0.99982,0.017549,0.0076871,-3.913,-0.018067,0.99713,0.073491,-8.432,-0.0063754,-0.073616,0.99727,11.472 > ui tool show ""Fit in Map"" Fit molecule 3lz0 (#15) to map cryosparc_P18_J209_005_volume_map.mrc z flip (#17) using 11908 atoms average map value = 0.09375, steps = 64 shifted from previous position = 1.11 rotated from previous position = 3.95 degrees atoms outside contour = 3912, contour level = 0.077264 Position of 3lz0 (#15) relative to cryosparc_P18_J209_005_volume_map.mrc z flip (#17) coordinates: Matrix rotation and translation -0.01066791 -0.98142446 0.19155217 145.42854530 -0.92976680 -0.06076261 -0.36309998 163.03020845 0.36799441 -0.18197237 -0.91184767 218.58520600 Axis 0.70181525 -0.68366085 0.20015793 Axis point 0.00000000 142.57591251 97.16426346 Rotation angle (degrees) 172.58574997 Shift along axis 34.35816382 > open /Users/kate/Desktop/Modelling/cryosparc_J207.cxs Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size 128,128,128, pixel 2.59, shown at level 0.322, step 1, values float32 Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size 128,128,128, pixel 2.59, shown at level 0.514, step 1, values float32 Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size 128,128,128, pixel 2.59, shown at level 0.315, step 1, values float32 Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size 128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size 128,128,128, pixel 2.59, shown at level 0.381, step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size 128,128,128, pixel 2.59, shown at level 0.222, step 1, values float32 Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size 128,128,128, pixel 2.59, shown at level 0.28, step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size 128,128,128, pixel 2.59, shown at level 0.325, step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size 128,128,128, pixel 2.59, shown at level 0.225, step 1, values float32 Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size 128,128,128, pixel 2.59, shown at level 0.464, step 1, values float32 Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size 400,400,400, pixel 0.83, shown at level 0.0773, step 1, values float32 opened ChimeraX session ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/kate/Desktop/Modelling/cryosparc_J207.cxs Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size 128,128,128, pixel 2.59, shown at level 0.322, step 1, values float32 Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size 128,128,128, pixel 2.59, shown at level 0.514, step 1, values float32 Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size 128,128,128, pixel 2.59, shown at level 0.315, step 1, values float32 Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size 128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size 128,128,128, pixel 2.59, shown at level 0.381, step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size 128,128,128, pixel 2.59, shown at level 0.222, step 1, values float32 Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size 128,128,128, pixel 2.59, shown at level 0.28, step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size 128,128,128, pixel 2.59, shown at level 0.325, step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size 128,128,128, pixel 2.59, shown at level 0.225, step 1, values float32 Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size 128,128,128, pixel 2.59, shown at level 0.464, step 1, values float32 Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size 128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32 Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size 400,400,400, pixel 0.83, shown at level 0.0773, step 1, values float32 Log from Fri Mar 25 20:46:34 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/behrouzi/Downloads/cryosparc_P18_J203_class_02_00142_volume.mrc Opened cryosparc_P18_J203_class_02_00142_volume.mrc as #1, grid size 128,128,128, pixel 2.59, shown at level 0.292, step 1, values float32 > open /home/behrouzi/Downloads/cryosparc_P18_J203_class_01_00142_volume.mrc Opened cryosparc_P18_J203_class_01_00142_volume.mrc as #2, grid size 128,128,128, pixel 2.59, shown at level 0.266, step 1, values float32 > open /home/behrouzi/Downloads/cryosparc_P18_J203_class_00_00142_volume.mrc Opened cryosparc_P18_J203_class_00_00142_volume.mrc as #3, grid size 128,128,128, pixel 2.59, shown at level 0.276, step 1, values float32 > hide #!2 models > hide #!3 models > volume #1 level 0.4142 > volume #1 level 0.3302 > vop flip #1-3 Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > close #1 > close #2 > close #3 > volume #4 level 0.2507 > volume #4 level 0.2601 > volume #4 level 0.3864 > volume #4 level 0.4121 > 1ubq Unknown command: 1ubq > open 1ubq 1ubq title: Structure of ubiquitin refined At 1.8 angstroms resolution [more info...] Chain information for 1ubq #1 --- Chain | Description | UniProt A | ubiquitin | UBIQ_HUMAN > select #1 660 atoms, 608 bonds, 134 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,123.07,0,1,0,71.882,0,0,1,128.61 > view matrix models #1,1,0,0,124.38,0,1,0,127.68,0,0,1,105.11 > ui tool show ""Fit in Map"" Fit molecule 1ubq (#1) to map cryosparc_P18_J203_class_02_00142_volume.mrc z flip (#4) using 660 atoms average map value = 0.3686, steps = 160 shifted from previous position = 7.72 rotated from previous position = 85.3 degrees atoms outside contour = 492, contour level = 0.41212 Position of 1ubq (#1) relative to cryosparc_P18_J203_class_02_00142_volume.mrc z flip (#4) coordinates: Matrix rotation and translation 0.97144537 -0.18611259 -0.14715975 136.19150881 -0.12832275 0.10956376 -0.98566174 165.28304353 0.19956743 0.97640047 0.08255273 83.48543591 Axis 0.98432828 -0.17394625 0.02899204 Axis point 0.00000000 50.36749314 141.19726907 Rotation angle (degrees) 85.30905899 Shift along axis 107.72720008 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.87175,-0.46961,-0.13971,200.65,0.36294,-0.42739,-0.82802,164.15,0.32913,-0.77253,0.54302,125.29 > view matrix models > #1,-0.92246,-0.37312,-0.099221,198.49,0.29136,-0.50415,-0.81298,168.41,0.25332,-0.77886,0.57377,127.23 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.92246,-0.37312,-0.099221,201.04,0.29136,-0.50415,-0.81298,173.4,0.25332,-0.77886,0.57377,122.67 > volume #4 level 0.3706 > hide #1 models > volume #5 level 0.2151 > volume #5 level 0.2887 > volume #5 level 0.2726 > volume #6 level 0.2491 > volume #6 level 0.3154 > volume #5 level 0.5694 > volume #4 level 0.2576 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J185_class_00_00162_volume.mrc Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size 128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J185_class_01_00162_volume.mrc Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size 128,128,128, pixel 2.59, shown at level 0.269, step 1, values float32 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J185_class_02_00162_volume.mrc Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size 128,128,128, pixel 2.59, shown at level 0.25, step 1, values float32 > hide #!4 models > hide #!2 models > hide #!3 models > hide #!7 models > show #!7 models > vop flip #3 Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #8, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > vop flip #2 Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #9, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > vop flip #7 Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > ~select #1 Nothing selected > show #!4 models > hide #!4 models > show #!4 models > hide #!9 models > hide #!10 models > hide #!8 models > volume #3 level 0.3807 > volume #7 level 0.2219 > close #10 > close #9 > close #8 > vop flip #2,3,7 Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > volume #10 level 0.2247 > volume #9 level 0.239 > volume #8 level 0.1833 > volume #8 level 0.2797 > volume #9 level 0.325 > show #!4 models > hide #!9 models > show #!5 models > hide #!4 models > hide #!5 models > show #!4 models > show #!5 models > show #!6 models > volume #5 level 0.2887 > hide #!6 models > hide #!4 models > volume #5 level 0.2358 > hide #!5 models > show #!6 models > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_00_00102_volume.mrc Opened cryosparc_P18_J207_class_00_00102_volume.mrc as #11, grid size 128,128,128, pixel 2.59, shown at level 0.292, step 1, values float32 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_01_00102_volume.mrc Opened cryosparc_P18_J207_class_01_00102_volume.mrc as #12, grid size 128,128,128, pixel 2.59, shown at level 0.262, step 1, values float32 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_02_00102_volume.mrc Opened cryosparc_P18_J207_class_02_00102_volume.mrc as #13, grid size 128,128,128, pixel 2.59, shown at level 0.306, step 1, values float32 > hide #!6 models > hide #!12 models > hide #!13 models > volume #11 level 0.4088 > volume #11 level 0.2873 > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > vop flip #13 Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > volume #13 level 0.4081 > hide #!13 models > show #!4 models > volume #4 level 0.3222 > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > hide #!4 models > show #!5 models > show #!14 models > open 3lz0 3lz0 title: Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) [more info...] Chain information for 3lz0 #15 --- Chain | Description | UniProt A E | Histone H3.2 | H32_XENLA B F | Histone H4 | H4_XENLA C G | Histone H2A | Q6AZJ8_XENLA D H | Histone H2B 1.1 | H2B11_XENLA I | DNA (145-mer) | J | DNA (145-mer) | Non-standard residues in 3lz0 #15 --- CL — chloride ion MN — manganese (II) ion > select #15 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 3 models selected > view matrix models #15,1,0,0,225.86,0,1,0,44.811,0,0,1,16.474 > view matrix models #15,1,0,0,173,0,1,0,128.83,0,0,1,143.44 > view matrix models #15,1,0,0,187.87,0,1,0,188.43,0,0,1,113.43 > ui mousemode right ""rotate selected models"" > view matrix models > #15,0.087514,-0.98792,-0.12789,153.13,0.9308,0.035359,0.36381,171.17,-0.35489,-0.15088,0.92265,106.15 > hide #!14 models > volume #5 level 0.5142 > hide sel atoms > show sel cartoons > view matrix models > #15,0.4357,-0.82483,-0.3603,173.92,0.87658,0.29795,0.37793,175.04,-0.20438,-0.4805,0.85285,105.27 > view matrix models > #15,0.37177,-0.91265,0.16986,147.74,-0.89372,-0.40136,-0.20044,148.38,0.25111,-0.077286,-0.96487,202.08 > view matrix models > #15,-0.043627,-0.87192,0.4877,126.21,-0.93044,-0.14232,-0.33769,159.1,0.36385,-0.4685,-0.80506,189.15 > view matrix models > #15,-0.065002,-0.88689,0.45739,126.76,-0.9292,-0.11332,-0.35178,160.35,0.36381,-0.44787,-0.81673,190.1 > view matrix models > #15,-0.19304,-0.94641,0.25891,131.43,-0.90688,0.071369,-0.4153,167.51,0.37456,-0.31497,-0.87206,195.56 > ui mousemode right ""translate selected models"" > view matrix models > #15,-0.19304,-0.94641,0.25891,141.27,-0.90688,0.071369,-0.4153,164.53,0.37456,-0.31497,-0.87206,199.89 Fit molecule 3lz0 (#15) to map cryosparc_P18_J203_class_02_00142_volume.mrc z flip (#4) using 11908 atoms average map value = 0.5527, steps = 80 shifted from previous position = 12.4 rotated from previous position = 10.5 degrees atoms outside contour = 1025, contour level = 0.32218 Position of 3lz0 (#15) relative to cryosparc_P18_J203_class_02_00142_volume.mrc z flip (#4) coordinates: Matrix rotation and translation -0.02418109 -0.97986826 0.19817536 145.21368009 -0.92678755 -0.05234851 -0.37191997 163.55384603 0.37480676 -0.19265989 -0.90686386 215.74768192 Axis 0.69697531 -0.68675480 0.20638136 Axis point 0.00000000 143.64511866 95.01294070 Rotation angle (degrees) 172.61138207 Shift along axis 33.41526061 > hide #!5 models > color sel bychain > show #!14 models > close #13 > close #12 > close #11 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_00_00102_volume.mrc Opened cryosparc_P18_J207_class_00_00102_volume.mrc as #11, grid size 128,128,128, pixel 2.59, shown at level 0.292, step 1, values float32 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_01_00102_volume.mrc Opened cryosparc_P18_J207_class_01_00102_volume.mrc as #12, grid size 128,128,128, pixel 2.59, shown at level 0.262, step 1, values float32 > select up 12568 atoms, 13308 bonds, 334 pseudobonds, 1185 residues, 28 models selected > select up 12568 atoms, 13308 bonds, 334 pseudobonds, 1185 residues, 28 models selected > vop flip #11,12 Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > ~select #1 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 27 models selected > show #1 models > hide #1 models > ~select #2 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 25 models selected > ~select #3 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 23 models selected > ~select #4 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 21 models selected > ~select #5 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 19 models selected > ~select #6 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 17 models selected > ~select #7 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 15 models selected > ~select #8 11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 13 models selected > ~select #15 10 models selected > ~select #14 8 models selected > ~select #12 6 models selected > ~select #11 4 models selected > ~select #10 2 models selected > ~select #9 Nothing selected > hide #!13 models > hide #!14 models > volume #16 level 0.5822 > volume #16 level 0.1861 > hide #!16 models > show #!14 models Fit molecule 3lz0 (#15) to map cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) using 11908 atoms average map value = 0.5131, steps = 36 shifted from previous position = 0.0965 rotated from previous position = 0.148 degrees atoms outside contour = 996, contour level = 0.30581 Position of 3lz0 (#15) relative to cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates: Matrix rotation and translation -0.02279591 -0.97949752 0.20016232 145.20081148 -0.92652134 -0.05451162 -0.37227232 163.51565359 0.37555099 -0.19394095 -0.90628272 215.79936649 Axis 0.69749224 -0.68598269 0.20720118 Axis point -0.00000000 143.55390536 94.92324854 Rotation angle (degrees) 172.65535069 Shift along axis 33.82141608 > volume #14 level 0.5607 > volume #14 level 0.4751 > volume #14 level 0.278 > volume #14 level 0.4472 > volume #14 level 0.3829 > show #!13 models > hide #!14 models > close #11 > close #12 > volume #13 level 0.4971 > volume #13 level 0.337 > volume #13 level 0.6234 > volume #13 level 0.2603 > volume #13 level 0.2378 > volume #13 level 0.3167 > show #!16 models > volume #16 level 0.2875 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_03_00102_volume.mrc Opened cryosparc_P18_J207_class_03_00102_volume.mrc as #11, grid size 128,128,128, pixel 2.59, shown at level 0.297, step 1, values float32 > hide #!11 models > hide #!13 models > show #!11 models > hide #!16 models > vop flip #11 Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size 128,128,128, pixel 2.59, shown at step 1, values float32 > close #11 > show #!16 models > hide #!16 models > volume #12 level 0.4054 > volume #12 level 0.2819 > hide #!15 models > show #!13 models > volume #13 level 0.2829 > show #!14 models > show #!16 models > hide #!16 models > hide #!13 models > hide #!12 models > volume #14 level 0.2437 > show #!15 models > volume #14 level 0.2115 > hide #!15 models > show #!16 models > volume #16 level 0.282 > volume #13 level 0.282 > volume #14 level 0.282 > hide #!16 models > hide #!14 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!12 models > hide #!13 models > show #!14 models > show #!13 models > hide #!14 models > hide #!13 models > show #!14 models > hide #!14 models > show #!16 models > hide #!16 models > show #!14 models > show #1 models > color #1 #a40000 transparency 0 > volume #14 level 0.4641 > volume #14 level 0.5069 > show #!15 models > volume #14 level 0.4812 > volume #14 level 0.4512 > select #1 660 atoms, 608 bonds, 134 residues, 1 model selected > view matrix models > #1,-0.92246,-0.37312,-0.099221,203.04,0.29136,-0.50415,-0.81298,170.03,0.25332,-0.77886,0.57377,120.14 > view matrix models > #1,-0.92246,-0.37312,-0.099221,198.97,0.29136,-0.50415,-0.81298,202.36,0.25332,-0.77886,0.57377,127.84 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.94635,-0.23064,-0.22632,197.56,0.12458,-0.90665,0.40307,198.23,-0.29816,0.35325,0.88674,104.1 > view matrix models > #1,-0.91358,-0.3343,-0.23156,199.85,0.20275,-0.86802,0.45324,193.78,-0.35252,0.36712,0.86078,105.78 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.91358,-0.3343,-0.23156,201.93,0.20275,-0.86802,0.45324,178.94,-0.35252,0.36712,0.86078,94.219 > view matrix models > #1,-0.91358,-0.3343,-0.23156,189.86,0.20275,-0.86802,0.45324,235.61,-0.35252,0.36712,0.86078,83.543 > view matrix models > #1,-0.91358,-0.3343,-0.23156,211.69,0.20275,-0.86802,0.45324,174.44,-0.35252,0.36712,0.86078,98.339 > view matrix models > #1,-0.91358,-0.3343,-0.23156,206.95,0.20275,-0.86802,0.45324,172.73,-0.35252,0.36712,0.86078,99.432 > view matrix models > #1,-0.91358,-0.3343,-0.23156,229.89,0.20275,-0.86802,0.45324,152.59,-0.35252,0.36712,0.86078,107.72 > volume #14 level 0.4255 > view matrix models > #1,-0.91358,-0.3343,-0.23156,192.78,0.20275,-0.86802,0.45324,112.64,-0.35252,0.36712,0.86078,119.18 > view matrix models > #1,-0.91358,-0.3343,-0.23156,134.98,0.20275,-0.86802,0.45324,148.14,-0.35252,0.36712,0.86078,83.719 > view matrix models > #1,-0.91358,-0.3343,-0.23156,137.97,0.20275,-0.86802,0.45324,171.15,-0.35252,0.36712,0.86078,138.9 > view matrix models > #1,-0.91358,-0.3343,-0.23156,169.05,0.20275,-0.86802,0.45324,184.36,-0.35252,0.36712,0.86078,125.81 > view matrix models > #1,-0.91358,-0.3343,-0.23156,169.58,0.20275,-0.86802,0.45324,175.53,-0.35252,0.36712,0.86078,135.52 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.44579,-0.03476,-0.89446,157.95,0.091297,0.99227,-0.084063,131.12,0.89047,-0.11914,-0.43917,135.93 > view matrix models > #1,-0.75265,-0.2316,-0.61635,168.37,-0.15504,0.97211,-0.17595,140.83,0.63991,-0.036865,-0.76757,146.82 > view matrix models > #1,-0.81251,-0.50783,-0.28625,172.84,-0.39309,0.83989,-0.37425,155.64,0.43048,-0.19155,-0.88204,159.96 > view matrix models > #1,-0.1411,-0.68594,-0.71384,165.58,-0.97557,0.21898,-0.017587,186.1,0.16838,0.69392,-0.70009,137.38 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.1411,-0.68594,-0.71384,165.3,-0.97557,0.21898,-0.017587,187.87,0.16838,0.69392,-0.70009,131.8 > view matrix models > #1,-0.1411,-0.68594,-0.71384,166.4,-0.97557,0.21898,-0.017587,186.54,0.16838,0.69392,-0.70009,135.08 > view matrix models > #1,-0.1411,-0.68594,-0.71384,164.23,-0.97557,0.21898,-0.017587,187.69,0.16838,0.69392,-0.70009,132.54 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.025945,-0.46002,-0.88753,155.29,-0.98681,0.13011,-0.096284,192.16,0.15977,0.87833,-0.45058,122.69 > view matrix models > #1,-0.24119,0.50465,-0.82895,132.61,-0.13084,0.82946,0.54303,133.32,0.96162,0.23943,-0.13403,112.46 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.24119,0.50465,-0.82895,77.704,-0.13084,0.82946,0.54303,156.48,0.96162,0.23943,-0.13403,177.24 > view matrix models > #1,-0.24119,0.50465,-0.82895,150.97,-0.13084,0.82946,0.54303,139.34,0.96162,0.23943,-0.13403,137.09 > view matrix models > #1,-0.24119,0.50465,-0.82895,155.5,-0.13084,0.82946,0.54303,133.79,0.96162,0.23943,-0.13403,125.53 > view matrix models > #1,-0.24119,0.50465,-0.82895,150.77,-0.13084,0.82946,0.54303,129.54,0.96162,0.23943,-0.13403,111.28 > view matrix models > #1,-0.24119,0.50465,-0.82895,137.26,-0.13084,0.82946,0.54303,135.08,0.96162,0.23943,-0.13403,118.23 > volume #14 level 0.2413 > volume #14 level 0.4362 Fit molecule 1ubq (#1) to map cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) using 660 atoms average map value = 0.4132, steps = 76 shifted from previous position = 10.6 rotated from previous position = 34 degrees atoms outside contour = 422, contour level = 0.43624 Position of 1ubq (#1) relative to cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates: Matrix rotation and translation 0.04614331 0.73031158 -0.68155395 118.39545684 -0.52465781 0.59831732 0.60559934 158.31374099 0.85006175 0.32963824 0.41077202 101.90968678 Axis -0.13803319 -0.76610004 -0.62772411 Axis point 61.46613916 0.00000000 46.86111250 Rotation angle (degrees) 88.41749967 Shift along axis -201.59783434 > view matrix models > #1,0.046143,0.73031,-0.68155,124.18,-0.52466,0.59832,0.6056,154.92,0.85006,0.32964,0.41077,99.561 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.13443,-0.36502,0.92124,126.8,-0.85717,0.42361,0.29293,175.94,-0.49717,-0.82904,-0.25594,187.94 > view matrix models > #1,0.48172,-0.30197,-0.82266,145.3,0.25998,-0.84725,0.46323,178.23,-0.83688,-0.43702,-0.32963,187.46 > view matrix models > #1,-0.28143,0.90719,-0.31272,122.1,0.35997,-0.20228,-0.91077,179.72,-0.8895,-0.36889,-0.26964,185.89 > view matrix models > #1,-0.17293,0.89292,0.41568,106.32,0.046398,0.42895,-0.90213,169.62,-0.98384,-0.13672,-0.11561,178.85 > view matrix models > #1,-0.23774,0.9641,0.11826,111.37,0.21833,0.17167,-0.96066,173.38,-0.94647,-0.20256,-0.25131,182.16 > view matrix models > #1,-0.1952,0.97781,0.076099,110.41,0.13299,0.10326,-0.98572,178.52,-0.97171,-0.18229,-0.15019,180.51 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.1952,0.97781,0.076099,106.6,0.13299,0.10326,-0.98572,178.15,-0.97171,-0.18229,-0.15019,188.32 > view matrix models > #1,-0.1952,0.97781,0.076099,109.95,0.13299,0.10326,-0.98572,171.27,-0.97171,-0.18229,-0.15019,174.94 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.76479,-0.64398,0.019477,131.85,-0.27485,-0.29878,0.91389,162.28,-0.5827,-0.70429,-0.4055,183.78 > view matrix models > #1,0.47248,-0.078137,0.87787,108.03,-0.88061,-0.082248,0.46664,181.91,0.035742,-0.99354,-0.10767,168.66 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.47248,-0.078137,0.87787,105.78,-0.88061,-0.082248,0.46664,184.73,0.035742,-0.99354,-0.10767,166.73 > view matrix models > #1,0.47248,-0.078137,0.87787,106.32,-0.88061,-0.082248,0.46664,189.27,0.035742,-0.99354,-0.10767,166.01 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.50961,-0.083959,0.8563,105.76,-0.8568,-0.14055,0.49613,189.82,0.078696,-0.98651,-0.14356,165.13 > view matrix models > #1,0.57307,-0.35122,0.74043,114.13,-0.79908,-0.039035,0.59995,183.1,-0.18181,-0.93548,-0.30302,174.28 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.57307,-0.35122,0.74043,120.2,-0.79908,-0.039035,0.59995,180.62,-0.18181,-0.93548,-0.30302,173.65 > volume #14 level 0.387 > open > /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J209_005_volume_map.mrc Opened cryosparc_P18_J209_005_volume_map.mrc as #11, grid size 400,400,400, pixel 0.83, shown at level 0.0549, step 2, values float32 > hide #!14 models > vop flip #11 Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size 400,400,400, pixel 0.83, shown at step 1, values float32 Fit map cryosparc_P18_J209_005_volume_map.mrc z flip in map cryosparc_P18_J207_class_02_00102_volume.mrc z flip using 639858 points correlation = 0.9935, correlation about mean = 0.9268, overlap = 2.568e+04 steps = 52, shift = 2.23, angle = 0.523 degrees Position of cryosparc_P18_J209_005_volume_map.mrc z flip (#17) relative to cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates: Matrix rotation and translation 0.99995836 0.00469834 -0.00782269 0.71936693 -0.00469611 0.99998893 0.00030346 0.75861923 0.00782403 -0.00026671 0.99996936 -3.50246066 Axis -0.03122682 -0.85691938 -0.51450371 Axis point 373.74992925 0.00000000 94.47855415 Rotation angle (degrees) 0.52309649 Shift along axis 1.12948994 Fit map cryosparc_P18_J209_005_volume_map.mrc z flip in map cryosparc_P18_J207_class_02_00102_volume.mrc z flip using 639858 points correlation = 0.9935, correlation about mean = 0.9268, overlap = 2.568e+04 steps = 24, shift = 0.00305, angle = 0.0232 degrees Position of cryosparc_P18_J209_005_volume_map.mrc z flip (#17) relative to cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates: Matrix rotation and translation 0.99996159 0.00464670 -0.00743210 0.65975411 -0.00464525 0.99998919 0.00021226 0.76603634 0.00743300 -0.00017773 0.99997236 -3.44947842 Axis -0.02224140 -0.84775622 -0.52991953 Axis point 381.43699002 0.00000000 90.28237028 Rotation angle (degrees) 0.50233677 Shift along axis 1.16386004 > volume #14 level 0.4641 > close #11 > volume #17 level 0.07726 > transparency #17 60 > save /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_J207.cxs > includeMaps true ——— End of log from Fri Mar 25 20:46:34 2022 ——— opened ChimeraX session OpenGL version: 4.1 ATI-4.7.103 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc.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: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0) OS Loader Version: 540.80.2~11 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 34 days 10:24 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 Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 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 Family: Supported, Metal GPUFamily macOS 2 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: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 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sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Sessions can't reproduce all ChimeraX