id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14811 Graphics crash, macOS 14.3.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff85796f7c0 (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/graphics/opengl.py"", line 2730 in draw_elements File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1740 in draw File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 840 in _draw_geometry File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 775 in draw_self File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 768 in draw File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1555 in _draw_multiple File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1542 in draw_opaque File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 247 in _draw_scene File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 177 in draw File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py"", line 288 in render File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py"", line 113 in _redraw File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 138 in invoke File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 237 in _activate File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 206 in activate File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 382 in activate_trigger File 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Total=17.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=17.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 5132K 72 \nCG raster data 8K 1 \nColorSync 260K 34 \nCoreAnimation 1972K 152 \nCoreGraphics 24K 4 \nCoreServices 132K 1 \nCoreUI image data 5448K 42 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 17.0G 5246 \nMALLOC guard page 64K 16 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 120K 30 \nStack 158.2M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 351.8M 288 \n__CTF 824 1 \n__DATA 51.3M 787 \n__DATA_CONST 44.3M 405 \n__DATA_DIRTY 1804K 220 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 212.5M 154 \n__OBJC_RO 71.1M 1 \n__OBJC_RW 2172K 2 \n__TEXT 1.0G 785 \ndyld private memory 552K 7 \nmapped file 259.1M 75 \nshared memory 3512K 30 \n=========== ======= ======= \nTOTAL 19.2G 8403 \nTOTAL, minus reserved VM space 19.2G 8403 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""b4a247c3140ca50fca655b30c097195351bc180b"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000368 } ], ""experiments"" : [ { ""treatmentId"" : ""a3f9ec09-b145-49f3-8142-da4a1f338456"", ""experimentId"" : ""65f21aa774b6f500a45abd7d"", ""deploymentId"" : 400000002 } ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/puehrit/Downloads/cryosparc_P370_J835_003_volume_map.mrc Opened cryosparc_P370_J835_003_volume_map.mrc as #1, grid size 512,512,512, pixel 0.95, shown at level 0.19, step 2, values float32 > open /Users/puehrit/Downloads/cryosparc_P370_J835_003_volume_map.mrc Opened cryosparc_P370_J835_003_volume_map.mrc as #2, grid size 512,512,512, pixel 0.95, shown at level 0.19, step 2, values float32 > volume #1 level 0.2764 > volume #1 level 0.335 > volume #1 level 0.1851 > volume #1 step 1 > volume #1 level 0.2623 > ui tool show ""Side View"" > open /Users/puehrit/Downloads/cryosparc_P370_J855_class_00_final_volume.mrc Opened cryosparc_P370_J855_class_00_final_volume.mrc as #3, grid size 192,192,192, pixel 2.53, shown at level 0.437, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P370_J855_class_01_final_volume.mrc Opened cryosparc_P370_J855_class_01_final_volume.mrc as #4, grid size 192,192,192, pixel 2.53, shown at level 0.471, step 1, values float32 > close #1 > close #2 > tile 2 models tiled > volume #3 level 0.2832 > volume #4 level 0.8113 > volume #3 level 0.6759 > close #3 > close #4 > open /Users/puehrit/Downloads/cryosparc_P370_J856_class_00_final_volume.mrc Opened cryosparc_P370_J856_class_00_final_volume.mrc as #1, grid size 192,192,192, pixel 2.53, shown at level 0.395, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P370_J856_class_01_final_volume.mrc Opened cryosparc_P370_J856_class_01_final_volume.mrc as #2, grid size 192,192,192, pixel 2.53, shown at level 0.434, step 1, values float32 > tile 2 models tiled > volume #2 level 0.9826 > volume #2 level 0.8096 > volume #1 level 0.8728 > close #1 > close #2 > open /Users/puehrit/Downloads/cryosparc_P370_J865_003_volume_map.mrc Opened cryosparc_P370_J865_003_volume_map.mrc as #1, grid size 512,512,512, pixel 0.95, shown at level 0.187, step 2, values float32 > volume #1 step 1 > volume #1 level 0.2634 > close #1 > open /Users/puehrit/Downloads/cryosparc_P370_J869_006_volume_map.mrc Opened cryosparc_P370_J869_006_volume_map.mrc as #1, grid size 256,256,256, pixel 1.9, shown at level 0.433, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P370_J868_006_volume_map.mrc Opened cryosparc_P370_J868_006_volume_map.mrc as #2, grid size 256,256,256, pixel 1.9, shown at level 0.409, step 1, values float32 > volume #1 level 0.6049 > volume #2 level 0.6545 > close #2 > close #1 > open /Users/puehrit/Downloads/cryosparc_P370_J739_006_volume_map.mrc format > mrc No such file/path: /Users/puehrit/Downloads/cryosparc_P370_J739_006_volume_map.mrc > open /Users/puehrit/Downloads/cryosparc_P370_J739_006_volume_map.mrc format > mrc No such file/path: /Users/puehrit/Downloads/cryosparc_P370_J739_006_volume_map.mrc > open ""/Users/puehrit/Dropbox (The Francis Crick)/Thomas_Alessandro_CMG- > Assembly-Intermediates/preIC/preIC_csJ293_2xbinned.mrc"" Opened preIC_csJ293_2xbinned.mrc as #1, grid size 256,256,256, pixel 1.9, shown at level 0.522, step 1, values float32 > volume #1 level 0.7216 > open ""/Users/puehrit/Dropbox (The Francis Crick)/Thomas_Alessandro_CMG- > Assembly-Intermediates/preIC/preIC_modeling_March2024.cxs"" > set bgColor #ffffff00 opened ChimeraX session > open ""/Users/puehrit/Dropbox (The Francis Crick)/Thomas_Alessandro_CMG- > Assembly-Intermediates/preIC/preIC_csJ293_2xbinned.mrc"" Opened preIC_csJ293_2xbinned.mrc as #2, grid size 256,256,256, pixel 1.9, shown at level 0.522, step 1, values float32 > select #2 2 models selected > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,56.117,0,1,0,106.31,0,0,1,27.346 > undo > select #1 95664 atoms, 97296 bonds, 76 pseudobonds, 11942 residues, 3 models selected > view matrix models #1,1,0,0,52.703,0,1,0,98.823,0,0,1,25.119 > view matrix models > #1,-0.38901,0.2101,0.89696,80.207,-0.87181,-0.3986,-0.28473,438.5,0.2977,-0.89274,0.33822,197.81 > view matrix models > #1,-0.81757,0.54881,-0.17432,270.19,-0.54177,-0.63053,0.55581,286.18,0.19512,0.54885,0.81283,-39.736 > view matrix models > #1,-0.56432,0.65293,-0.5052,274.45,-0.81936,-0.5178,0.24603,361.02,-0.10095,0.55278,0.82719,-0.67216 > view matrix models > #1,-0.68988,0.35174,-0.63273,349.37,-0.58687,-0.78347,0.20435,367.32,-0.42384,0.51231,0.74693,62.704 > view matrix models > #1,-0.68988,0.35174,-0.63273,365.03,-0.58687,-0.78347,0.20435,418.34,-0.42384,0.51231,0.74693,82.167 > view matrix models > #1,-0.68988,0.35174,-0.63273,367.29,-0.58687,-0.78347,0.20435,424.99,-0.42384,0.51231,0.74693,84.581 > view matrix models > #1,-0.45702,0.47913,-0.74937,337.41,-0.66064,-0.74698,-0.074697,475.46,-0.59556,0.46092,0.65792,129.33 > view matrix models > #1,-0.50588,0.43283,-0.74616,349.46,-0.66954,-0.74241,0.02328,460.53,-0.54388,0.51136,0.66536,114.67 > view matrix models > #1,-0.50412,0.43279,-0.74736,349.41,-0.6698,-0.74222,0.021987,460.75,-0.54519,0.51167,0.66405,115.02 > view matrix models > #1,-0.34774,0.63817,-0.68689,292.55,-0.87627,-0.48181,-0.0040167,462.22,-0.33351,0.6005,0.72675,64.247 > view matrix models > #1,-0.34774,0.63817,-0.68689,317.19,-0.87627,-0.48181,-0.0040167,423.99,-0.33351,0.6005,0.72675,99.626 > view matrix models > #1,-0.25374,-0.43193,0.86548,187.21,-0.75312,-0.47326,-0.45698,477.79,0.60698,-0.76776,-0.20521,282.75 > view matrix models > #1,0.12151,-0.56824,-0.81384,418.7,-0.99192,-0.099548,-0.078597,405.47,-0.036355,0.81682,-0.57574,238.92 > view matrix models > #1,-0.075378,-0.61948,-0.78139,447.61,-0.9968,0.025809,0.075697,366.21,-0.026726,0.78459,-0.61944,248.47 > view matrix models > #1,-0.075378,-0.61948,-0.78139,450.18,-0.9968,0.025809,0.075697,374.63,-0.026726,0.78459,-0.61944,246.05 > fitmap #1 inMap #2 Fit molecule mergedpreICDNA.pdb (#1) to map preIC_csJ293_2xbinned.mrc (#2) using 95664 atoms average map value = 0.631, steps = 132 shifted from previous position = 11.7 rotated from previous position = 16.8 degrees atoms outside contour = 37431, contour level = 0.52178 Position of mergedpreICDNA.pdb (#1) relative to preIC_csJ293_2xbinned.mrc (#2) coordinates: Matrix rotation and translation 0.04192346 -0.80575610 -0.59076180 434.60856342 -0.99705145 -0.07177564 0.02714092 389.75515298 -0.06427127 0.58788207 -0.80638939 296.45548769 Axis 0.70746938 -0.66425645 -0.24135129 Axis point 0.00000000 356.43006807 277.04396546 Rotation angle (degrees) 156.65288273 Shift along axis -22.97503796 > volume #2 level 0.5617 > color #2 #b2b2b2ab models > select clear > volume #2 level 0.6177 > open /Users/puehrit/Downloads/ranked_1.pdb Chain information for ranked_1.pdb #3 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available > matchmaker #3/B to #1D pairing ss Invalid ""to"" argument: invalid atoms specifier > matchmaker #3/B to #1/D 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 mergedpreICDNA.pdb, chain D (#1) with ranked_1.pdb, chain B (#3), sequence alignment score = 1241.4 RMSD between 218 pruned atom pairs is 0.768 angstroms; (across all 242 pairs: 2.439) > hide atoms > show cartoons > ~cartoon #3 > cartoon #3/F > volume #2 level 0.7056 > volume #2 level 0.8095 > open /Users/puehrit/Downloads/cryosparc_P370_J876_class_00_final_volume.mrc Opened cryosparc_P370_J876_class_00_final_volume.mrc as #4, grid size 128,128,128, pixel 3.8, shown at level 0.752, step 1, values float32 > hide #!1 models > hide #3 models > volume #4 level 0.4621 > volume #4 level 0.4747 > volume #4 level 0.8909 > open /Users/puehrit/Downloads/cryosparc_P370_J873_004_volume_map.mrc Opened cryosparc_P370_J873_004_volume_map.mrc as #5, grid size 256,256,256, pixel 1.9, shown at level 0.309, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P370_J871_004_volume_map.mrc Opened cryosparc_P370_J871_004_volume_map.mrc as #6, grid size 256,256,256, pixel 1.9, shown at level 0.313, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P370_J870_004_volume_map.mrc Opened cryosparc_P370_J870_004_volume_map.mrc as #7, grid size 256,256,256, pixel 1.9, shown at level 0.324, step 1, values float32 > close #3#1-2,4 > tile 3 models tiled > tile spacingFactor 1.2 3 models tiled > volume all level 0.5 > volume all level 0.6 > volume #5 level 1.018 > volume #5 level 0.8311 > volume #6 level 1.003 > volume all level 0.8 > ~tile > hide #!7 models > hide #!6 models > open /Users/puehrit/Downloads/cryosparc_P370_J880_003_volume_map.mrc Opened cryosparc_P370_J880_003_volume_map.mrc as #1, grid size 256,256,256, pixel 1.9, shown at level 0.33, step 1, values float32 > hide #!1 models > open /Users/puehrit/Downloads/cryosparc_P370_J879_004_volume_map.mrc Opened cryosparc_P370_J879_004_volume_map.mrc as #2, grid size 256,256,256, pixel 1.9, shown at level 0.337, step 1, values float32 > tile 2 models tiled > volume all level 0.5 > volume all level 0.6 > volume all level 0.7 > volume #2 level 0.9017 > volume #1 level 1.165 > volume #1 level 0.9129 > lighting full > open /Users/puehrit/Downloads/cryosparc_P370_J878_002_volume_map.mrc Opened cryosparc_P370_J878_002_volume_map.mrc as #3, grid size 128,128,128, pixel 3.8, shown at level 1.05, step 1, values float32 > volume #3 level 1.334 > volume #3 level 0.9306 > lighting simple > open /Users/puehrit/Downloads/cryosparc_P370_J885_001_volume_map.mrc Opened cryosparc_P370_J885_001_volume_map.mrc as #4, grid size 128,128,128, pixel 3.8, shown at level 1.03, step 1, values float32 > volume #4 level 0.854 > volume #4 level 0.8454 > open /Users/puehrit/Downloads/cryosparc_P119_J1321_volume_map.mrc Opened cryosparc_P119_J1321_volume_map.mrc as #8, grid size 120,120,120, pixel 4.03, shown at level 2.84, step 1, values float32 > volume #8 level 4.521 > volume #8 level 3.035 > volume #8 level 1.775 > volume #8 level 2.292 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_00_00081_volume.mrc"" Opened J1201_class_00_00081_volume.mrc as #9, grid size 108,108,108, pixel 4.48, shown at level 2.21, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_01_00081_volume.mrc"" Opened J1201_class_01_00081_volume.mrc as #10, grid size 108,108,108, pixel 4.48, shown at level 2.23, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_02_00081_volume.mrc"" Opened J1201_class_02_00081_volume.mrc as #11, grid size 108,108,108, pixel 4.48, shown at level 2.28, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_03_00081_volume.mrc"" Opened J1201_class_03_00081_volume.mrc as #12, grid size 108,108,108, pixel 4.48, shown at level 2.32, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_04_00081_volume.mrc"" Opened J1201_class_04_00081_volume.mrc as #13, grid size 108,108,108, pixel 4.48, shown at level 2.39, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_05_00081_volume.mrc"" Opened J1201_class_05_00081_volume.mrc as #14, grid size 108,108,108, pixel 4.48, shown at level 2.38, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_06_00081_volume.mrc"" Opened J1201_class_06_00081_volume.mrc as #15, grid size 108,108,108, pixel 4.48, shown at level 2.42, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_07_00081_volume.mrc"" Opened J1201_class_07_00081_volume.mrc as #16, grid size 108,108,108, pixel 4.48, shown at level 2.4, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_08_00081_volume.mrc"" Opened J1201_class_08_00081_volume.mrc as #17, grid size 108,108,108, pixel 4.48, shown at level 2.4, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_09_00081_volume.mrc"" Opened J1201_class_09_00081_volume.mrc as #18, grid size 108,108,108, pixel 4.48, shown at level 2.42, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_10_00081_volume.mrc"" Opened J1201_class_10_00081_volume.mrc as #19, grid size 108,108,108, pixel 4.48, shown at level 2.43, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_11_00081_volume.mrc"" Opened J1201_class_11_00081_volume.mrc as #20, grid size 108,108,108, pixel 4.48, shown at level 2.44, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_12_00081_volume.mrc"" Opened J1201_class_12_00081_volume.mrc as #21, grid size 108,108,108, pixel 4.48, shown at level 2.71, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_13_00081_volume.mrc"" Opened J1201_class_13_00081_volume.mrc as #22, grid size 108,108,108, pixel 4.48, shown at level 2.47, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_14_00081_volume.mrc"" Opened J1201_class_14_00081_volume.mrc as #23, grid size 108,108,108, pixel 4.48, shown at level 2.49, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_15_00081_volume.mrc"" Opened J1201_class_15_00081_volume.mrc as #24, grid size 108,108,108, pixel 4.48, shown at level 2.65, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_16_00081_volume.mrc"" Opened J1201_class_16_00081_volume.mrc as #25, grid size 108,108,108, pixel 4.48, shown at level 2.75, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_17_00081_volume.mrc"" Opened J1201_class_17_00081_volume.mrc as #26, grid size 108,108,108, pixel 4.48, shown at level 2.8, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_18_00081_volume.mrc"" Opened J1201_class_18_00081_volume.mrc as #27, grid size 108,108,108, pixel 4.48, shown at level 2.78, step 1, values float32 > open ""/Users/puehrit/Downloads/cryosparc_P119_J1201_00081_volume_series > 2/J1201_class_19_00081_volume.mrc"" Opened J1201_class_19_00081_volume.mrc as #28, grid size 108,108,108, pixel 4.48, shown at level 2.85, step 1, values float32 > tile 20 models tiled > volume all level 2 > volume #21 level 2.281 > volume #21 level 2.751 > volume all level 2 > volume all level 2.3 > volume all level 2.5 > volume all level 2.9 > volume all level 2.7 > volume all level 2.8 > volume all level 3 > volume all level 2.5 > volume all level 2.8 > volume #21 level 2.929 > volume #5 level 2.436 > volume #11 level 3.337 > volume #11 level 2.263 > volume #12 level 2.239 > volume #13 level 2.44 > volume #9 level 2.994 > volume #10 level 3.381 > volume #9 level 3.516 > volume #10 level 3.587 > hide #!9-28 target m > open /Users/puehrit/Downloads/cryosparc_P119_J1227_class_01_00142_volume.mrc Opened cryosparc_P119_J1227_class_01_00142_volume.mrc as #29, grid size 128,128,128, pixel 3.78, shown at level 2.67, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P119_J1230_class_01_00082_volume.mrc Opened cryosparc_P119_J1230_class_01_00082_volume.mrc as #30, grid size 128,128,128, pixel 3.78, shown at level 2.7, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P119_J1230_class_00_00082_volume.mrc Opened cryosparc_P119_J1230_class_00_00082_volume.mrc as #31, grid size 128,128,128, pixel 3.78, shown at level 2.66, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P119_J1229_class_01_00102_volume.mrc Opened cryosparc_P119_J1229_class_01_00102_volume.mrc as #32, grid size 128,128,128, pixel 3.78, shown at level 2.68, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P119_J1228_class_01_00142_volume.mrc Opened cryosparc_P119_J1228_class_01_00142_volume.mrc as #33, grid size 128,128,128, pixel 3.78, shown at level 2.56, step 1, values float32 > ~tile > tile 5 models tiled > volume #31 level 3.856 > volume #31 level 3.465 > volume #31 level 1.415 > volume #31 level 1.659 > volume #31 level 3.002 > volume #30 level 3.447 > ~tile > volume #30 level 2.967 > volume #29 level 2.896 > open 7p30 7p30 title: 3.0 A resolution structure of a DNA-loaded MCM double hexamer [more info...] Chain information for 7p30 #34 --- Chain | Description | UniProt 2 A | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 B | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971 4 C | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 D | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 E | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 F | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845 X | DNA (53-MER) | Y | DNA (53-MER) | Non-standard residues in 7p30 #34 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide atoms > show cartoons > select #34 123819 atoms, 125026 bonds, 244 pseudobonds, 7780 residues, 4 models selected > view matrix models #34,1,0,0,-41.786,0,1,0,60.479,0,0,1,48.17 > view matrix models > #34,0.44617,0.61091,0.654,-142.72,-0.85333,0.51065,0.10516,232.54,-0.26973,-0.605,0.74915,205.67 > view matrix models > #34,0.44617,0.61091,0.654,-98.855,-0.85333,0.51065,0.10516,278.11,-0.26973,-0.605,0.74915,173.6 > view matrix models > #34,0.28619,0.63047,0.72153,-88.895,-0.86274,0.49716,-0.092214,309.38,-0.41686,-0.5961,0.68622,201.81 > view matrix models > #34,0.1271,0.67754,0.72442,-73.694,-0.94947,0.29441,-0.10877,352.05,-0.28697,-0.67399,0.68072,195.34 > view matrix models > #34,0.1271,0.67754,0.72442,11.211,-0.94947,0.29441,-0.10877,301.04,-0.28697,-0.67399,0.68072,250.72 > view matrix models > #34,0.1271,0.67754,0.72442,7.4472,-0.94947,0.29441,-0.10877,341.39,-0.28697,-0.67399,0.68072,258.32 > view matrix models > #34,0.1271,0.67754,0.72442,29.017,-0.94947,0.29441,-0.10877,347.75,-0.28697,-0.67399,0.68072,263.39 > view matrix models > #34,0.12506,0.71816,0.68455,29.318,-0.9582,0.26638,-0.1044,352.25,-0.25732,-0.64288,0.72145,249.14 > view matrix models > #34,0.13078,0.79626,0.59065,31.006,-0.96185,0.24631,-0.11909,357.64,-0.24031,-0.55254,0.7981,223.28 > view matrix models > #34,0.319,0.75814,0.56874,13.206,-0.92637,0.37617,0.018151,315.09,-0.20018,-0.53266,0.82231,211.48 > view matrix models > #34,0.31889,0.78709,0.52802,14.984,-0.92989,0.36759,0.013644,317.42,-0.18335,-0.49535,0.84912,200.13 > view matrix models > #34,0.32082,0.73606,0.59607,12.139,-0.92077,0.38985,0.014177,312.98,-0.22194,-0.55339,0.80281,220.17 > view matrix models > #34,0.28503,0.7458,0.60211,14.908,-0.93047,0.36613,-0.01303,321.5,-0.23017,-0.55654,0.7983,222.4 > view matrix models > #34,0.23249,0.48605,0.84244,24.203,-0.96727,0.20613,0.14801,325.99,-0.10171,-0.84927,0.51806,285.12 > view matrix models > #34,0.23249,0.48605,0.84244,21.468,-0.96727,0.20613,0.14801,324.84,-0.10171,-0.84927,0.51806,298.23 > view matrix models > #34,0.22916,0.46666,0.85424,22.954,-0.96803,0.20125,0.14975,325.38,-0.10203,-0.86124,0.49785,302.82 > view matrix models > #34,0.2546,0.42908,0.86664,22.875,-0.93502,0.33794,0.10738,307.78,-0.2468,-0.83767,0.48724,321.21 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!29 models > show #!29 models > hide #!30 models > volume #29 level 3.49 > fitmap #34 inMap #29 Fit molecule 7p30 (#34) to map cryosparc_P119_J1227_class_01_00142_volume.mrc (#29) using 123819 atoms average map value = 3.228, steps = 60 shifted from previous position = 1.46 rotated from previous position = 6.95 degrees atoms outside contour = 73356, contour level = 3.4897 Position of 7p30 (#34) relative to cryosparc_P119_J1227_class_01_00142_volume.mrc (#29) coordinates: Matrix rotation and translation -0.43880053 -0.89851209 0.01140690 426.61308233 0.89858281 -0.43873974 0.00750857 176.77923876 -0.00174189 0.01354481 0.99990675 94.43182872 Axis 0.00335877 0.00731645 0.99996759 Axis point 158.16663368 221.16176974 0.00000000 Rotation angle (degrees) 116.02840999 Shift along axis 97.15506228 > color #34/2,A pink > color #34/3,B cyan > color #34/4,C forestgreen > color #34/5,D yellow > color #34/6,E orange > color #34/7,F medium blue > color #34/X red > color #34/Y white > select clear > ui mousemode right translate > ~tile > select #34 123819 atoms, 125026 bonds, 244 pseudobonds, 7780 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #34,-0.42402,-0.6453,0.63545,280.94,0.72881,-0.65966,-0.18356,340.16,0.53763,0.38529,0.75001,-146.72 > view matrix models > #34,-0.41652,-0.65446,0.63103,281.8,0.82887,-0.55851,-0.032145,290.59,0.37347,0.50965,0.77509,-144.74 > view matrix models > #34,-0.41652,-0.65446,0.63103,287.39,0.82887,-0.55851,-0.032145,288.03,0.37347,0.50965,0.77509,-240.73 > view matrix models > #34,-0.41652,-0.65446,0.63103,285.83,0.82887,-0.55851,-0.032145,286.13,0.37347,0.50965,0.77509,-213.07 > view matrix models > #34,-0.39338,-0.8604,0.32398,354.96,0.90127,-0.43048,-0.048921,260.61,0.18156,0.27275,0.9448,-177.49 > view matrix models > #34,-0.39338,-0.8604,0.32398,340.87,0.90127,-0.43048,-0.048921,179.56,0.18156,0.27275,0.9448,28.201 > view matrix models > #34,-0.39338,-0.8604,0.32398,366.98,0.90127,-0.43048,-0.048921,180.23,0.18156,0.27275,0.9448,28.812 > view matrix models > #34,-0.364,-0.92972,-0.055948,426.59,0.92991,-0.35938,-0.078166,170.5,0.052566,-0.080479,0.99537,88.768 > hide #!30 models > hide #!31 models > hide #!32 models > fitmap #34 inMap #29 Fit molecule 7p30 (#34) to map cryosparc_P119_J1227_class_01_00142_volume.mrc (#29) using 123819 atoms average map value = 2.714, steps = 80 shifted from previous position = 13.8 rotated from previous position = 3.49 degrees atoms outside contour = 89495, contour level = 3.4897 Position of 7p30 (#34) relative to cryosparc_P119_J1227_class_01_00142_volume.mrc (#29) coordinates: Matrix rotation and translation 0.32891517 0.45029262 0.83009118 18.28786046 -0.92448582 0.33291500 0.18572447 299.31622433 -0.19271944 -0.82849512 0.52578994 302.72323427 Axis -0.50935600 0.51367054 -0.69043396 Axis point 162.01470339 273.88782984 0.00000000 Rotation angle (degrees) 84.61716487 Shift along axis -64.57550539 > show #!31 models > show #!32 models > show #!33 models > hide #!33 models > hide #!32 models > hide #!31 models > show #!32 models > select clear > select #34 123819 atoms, 125026 bonds, 244 pseudobonds, 7780 residues, 4 models selected > view matrix models > #34,-0.31159,-0.94951,-0.036598,413.57,0.94905,-0.30908,-0.061361,156.82,0.046951,-0.053853,0.99744,102.24 > view matrix models > #34,-0.20263,-0.56737,0.79814,226.44,0.9561,-0.29081,0.036006,139.45,0.21168,0.7704,0.60139,20.872 > hide #!32 models > fitmap #34 inMap #29 Fit molecule 7p30 (#34) to map cryosparc_P119_J1227_class_01_00142_volume.mrc (#29) using 123819 atoms average map value = 3.227, steps = 68 shifted from previous position = 9.07 rotated from previous position = 3.14 degrees atoms outside contour = 73402, contour level = 3.4897 Position of 7p30 (#34) relative to cryosparc_P119_J1227_class_01_00142_volume.mrc (#29) coordinates: Matrix rotation and translation 0.43925801 0.89828974 0.01131123 53.97012348 -0.89835962 0.43920089 0.00725014 304.85260504 0.00154482 -0.01334623 0.99990974 97.70907241 Axis -0.01146284 0.00543546 -0.99991953 Axis point 271.04438222 110.34732875 0.00000000 Rotation angle (degrees) 63.94815062 Shift along axis -96.66284563 > select clear > volume #29 level 2.645 > volume #29 color #b2b2b299 > ui mousemode right translate > volume #29 level 3.284 > volume #29 level 2.188 > molmap #34 res 7 Missing or invalid ""resolution"" argument: Expected a number > molmap #34 7 Opened 7p30 map 7 as #35, grid size 110,93,78, pixel 2.33, shown at level 0.105, step 1, values float32 > molmap #34 8 Opened 7p30 map 8 as #35, grid size 99,83,70, pixel 2.67, shown at level 0.101, step 1, values float32 > hide #!34 models > hide #!29 models > volume #35 level 0.3954 > show #!34 models > color #35 #b2ffb287 models > show #!29 models > volume #29 color #b2b2b2 > volume #29 level 3.17 > hide #!29 models > show #!33 models > show #!29 models > show #!30 models > show #!31 models > show #!32 models > select #33 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.34915,-0.47618,0.80706,352.42,0.35859,-0.8636,-0.35442,515.23,0.86574,0.16566,0.47228,52.887 > view matrix models > #33,-0.34915,-0.47618,0.80706,288.02,0.35859,-0.8636,-0.35442,377.34,0.86574,0.16566,0.47228,-60.721 > view matrix models > #33,-0.42939,-0.62877,0.64829,382.65,0.46944,-0.76863,-0.43456,346.73,0.77153,0.11774,0.6252,-63.066 > view matrix models > #33,-0.44799,-0.68217,0.57789,417.03,0.51325,-0.72549,-0.45852,331.43,0.73204,0.09119,0.67513,-59.074 > view matrix models > #33,-0.94569,-0.16103,0.28239,485.63,-0.025766,-0.82883,-0.55891,512.73,0.32406,-0.53583,0.77966,166.1 > view matrix models > #33,-0.9745,-0.1371,0.17761,512.28,0.12792,-0.98983,-0.062183,393.59,0.18433,-0.037878,0.98214,32.092 > view matrix models > #33,-0.9745,-0.1371,0.17761,477.63,0.12792,-0.98983,-0.062183,401.72,0.18433,-0.037878,0.98214,-31.667 > view matrix models > #33,-0.9745,-0.1371,0.17761,479.14,0.12792,-0.98983,-0.062183,442.85,0.18433,-0.037878,0.98214,-2.3638 > view matrix models > #33,-0.87488,-0.078259,0.47798,368.01,-0.012456,-0.9829,-0.18373,505,0.48419,-0.16669,0.85894,-15.298 > view matrix models > #33,-0.87307,-0.068755,0.48273,364.14,-0.017428,-0.98498,-0.17181,503.84,0.48729,-0.15842,0.85875,-17.998 > view matrix models > #33,-0.83357,-0.16387,0.52755,366.42,0.099885,-0.98396,-0.14782,469.01,0.54331,-0.070526,0.83657,-47.454 > view matrix models > #33,-0.40985,-0.045601,0.91101,141.43,-0.23119,-0.96094,-0.15211,545.78,0.88237,-0.27296,0.3833,27.396 > view matrix models > #33,-0.35098,-0.016351,0.93624,113.88,-0.25102,-0.96161,-0.1109,540.84,0.90211,-0.27393,0.33341,34.842 > view matrix models > #33,-0.28586,-0.14633,0.94703,126.45,-0.12008,-0.97501,-0.1869,530.29,0.95072,-0.16715,0.26114,14.774 > view matrix models > #33,-0.28586,-0.14633,0.94703,137.95,-0.12008,-0.97501,-0.1869,539.9,0.95072,-0.16715,0.26114,12.245 > view matrix models > #33,-0.66075,-0.25307,0.70666,313.62,0.062382,-0.95671,-0.28429,514.27,0.74801,-0.14376,0.64793,-37.079 > view matrix models > #33,-0.69214,-0.3141,0.64983,349.68,0.15515,-0.94404,-0.29106,490.1,0.70489,-0.10064,0.70214,-49.935 > view matrix models > #33,-0.73732,-0.35266,0.57619,387.81,0.21249,-0.9307,-0.29772,474.44,0.64126,-0.097079,0.76116,-49.434 > view matrix models > #33,-0.73732,-0.35266,0.57619,376.14,0.21249,-0.9307,-0.29772,477.1,0.64126,-0.097079,0.76116,-62.031 > hide #!32 models > hide #!31 models > hide #!29 models > hide #!33 models > hide #!35 models > show #!33 models > hide #!34 models > fitmap #33 inMap #30 Fit map cryosparc_P119_J1228_class_01_00142_volume.mrc in map cryosparc_P119_J1230_class_01_00082_volume.mrc using 20963 points correlation = 0.9885, correlation about mean = 0.8469, overlap = 2.853e+05 steps = 108, shift = 15.8, angle = 27.2 degrees Position of cryosparc_P119_J1228_class_01_00142_volume.mrc (#33) relative to cryosparc_P119_J1230_class_01_00082_volume.mrc (#30) coordinates: Matrix rotation and translation 0.99999809 -0.00194811 -0.00016360 0.53147829 0.00194810 0.99999810 -0.00005874 -0.32934493 0.00016371 0.00005842 0.99999998 0.15484846 Axis 0.02994941 -0.08367591 0.99604286 Axis point 160.82980819 269.61948765 0.00000000 Rotation angle (degrees) 0.11206198 Shift along axis 0.19771140 > ui mousemode right translate > show #!34 models > hide #!30 models > volume #33 color #ffb2ffb8 > volume sel style mesh > volume sel style surface > volume #33 level 2.373 > hide #!33 models > show #!32 models > volume #32 color #b2b2ffa0 > volume #32 color #b2b2ffa1 > volume #32 level 3.526 > volume #32 level 2.786 > volume #32 level 3.103 > volume #31 level 1.44 > volume #31 level 2.416 > volume #31 color #b2ffff9c > volume #31 level 3.099 > volume #31 level 1.806 > volume #31 level 4.1 > volume #30 color #ffffb280 > open /Users/puehrit/Downloads/cryosparc_P119_J1362_002_volume_map.mrc Opened cryosparc_P119_J1362_002_volume_map.mrc as #36, grid size 120,120,120, pixel 4.03, shown at level 2.8, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P119_J1363_002_volume_map.mrc Opened cryosparc_P119_J1363_002_volume_map.mrc as #37, grid size 120,120,120, pixel 4.03, shown at level 2.92, step 1, values float32 > hide #!34 models > volume #36 level 6.407 > volume #36 level 5.13 > volume #36 level 3.816 > ui mousemode right zoom > volume #36 level 4.942 > show #!34 models > select #36 2 models selected > select /F:92 22 atoms, 21 bonds, 1 residue, 1 model selected > select #36 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #36,0.5208,0.088437,0.84909,-105.54,-0.22186,0.97447,0.034584,51.725,-0.82435,-0.20639,0.52712,360.91 > fitmap #34 inMap #36 Fit molecule 7p30 (#34) to map cryosparc_P119_J1362_002_volume_map.mrc (#36) using 123819 atoms average map value = 4.057, steps = 72 shifted from previous position = 5.36 rotated from previous position = 6.4 degrees atoms outside contour = 87731, contour level = 4.9423 Position of 7p30 (#34) relative to cryosparc_P119_J1362_002_volume_map.mrc (#36) coordinates: Matrix rotation and translation -0.44001386 -0.89799098 -0.00003121 428.38451062 0.89799096 -0.44001386 0.00018747 178.09682999 -0.00018207 0.00005446 0.99999999 96.34648926 Axis -0.00007406 0.00008400 0.99999999 Axis point 158.66785738 222.61663518 0.00000000 Rotation angle (degrees) 116.10476609 Shift along axis 96.32972433 > show #!37 models > select #37 2 models selected > view matrix models > #37,0.597,0.01914,0.80201,-100.99,-0.27413,0.94441,0.18152,35.834,-0.75395,-0.32822,0.56906,365.65 > view matrix models > #37,0.61846,0.10543,0.77871,-121.31,-0.17966,0.98368,0.0095017,45.113,-0.765,-0.14578,0.62731,310.35 > hide #!36 models > fitmap #34 inMap #37 Fit molecule 7p30 (#34) to map cryosparc_P119_J1363_002_volume_map.mrc (#37) using 123819 atoms average map value = 3.906, steps = 72 shifted from previous position = 5.1 rotated from previous position = 7.58 degrees atoms outside contour = 34351, contour level = 2.9168 Position of 7p30 (#34) relative to cryosparc_P119_J1363_002_volume_map.mrc (#37) coordinates: Matrix rotation and translation -0.44120178 -0.89740788 -0.00032234 428.40488739 0.89740793 -0.44120177 -0.00010303 178.35303227 -0.00004976 -0.00033472 0.99999995 96.31910121 Axis -0.00012909 -0.00015187 0.99999998 Axis point 158.67565255 222.56733511 0.00000000 Rotation angle (degrees) 116.18058583 Shift along axis 96.23670895 > select clear > volume #37 color #99bfe595 > volume #37 color #99bfe594 > ui mousemode right zoom > ui mousemode right translate > select #36 2 models selected > ui tool show ""Fit in Map"" > fitmap #36 inMap #37 Fit map cryosparc_P119_J1362_002_volume_map.mrc in map cryosparc_P119_J1363_002_volume_map.mrc using 7008 points correlation = 0.9896, correlation about mean = 0.7852, overlap = 2.854e+05 steps = 72, shift = 4.91, angle = 7.59 degrees Position of cryosparc_P119_J1362_002_volume_map.mrc (#36) relative to cryosparc_P119_J1363_002_volume_map.mrc (#37) coordinates: Matrix rotation and translation 0.99999941 -0.00077162 -0.00075997 0.33574362 0.00077126 0.99999959 -0.00046586 -0.09458641 0.00076032 0.00046528 0.99999960 -0.41387977 Axis 0.39493573 -0.64481738 0.65439767 Axis point 187.47675261 474.51599460 0.00000000 Rotation angle (degrees) 0.06754332 Shift along axis -0.07725384 > fitmap #36 inMap #37 Fit map cryosparc_P119_J1362_002_volume_map.mrc in map cryosparc_P119_J1363_002_volume_map.mrc using 7008 points correlation = 0.9896, correlation about mean = 0.7854, overlap = 2.854e+05 steps = 44, shift = 0.00872, angle = 0.0136 degrees Position of cryosparc_P119_J1362_002_volume_map.mrc (#36) relative to cryosparc_P119_J1363_002_volume_map.mrc (#37) coordinates: Matrix rotation and translation 0.99999940 -0.00082974 -0.00071415 0.34545475 0.00082925 0.99999942 -0.00069097 -0.05052497 0.00071472 0.00069038 0.99999951 -0.45490435 Axis 0.53357905 -0.55193782 0.64082606 Axis point 114.03814139 467.25232280 0.00000000 Rotation angle (degrees) 0.07416469 Shift along axis -0.07930051 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/puehrit/Downloads/cryosparc_P119_J1363_002_volume_map.mrc Opened cryosparc_P119_J1363_002_volume_map.mrc as #1, grid size 120,120,120, pixel 4.03, shown at level 2.92, step 1, values float32 > open /Users/puehrit/Downloads/cryosparc_P119_J1362_002_volume_map.mrc Opened cryosparc_P119_J1362_002_volume_map.mrc as #2, grid size 120,120,120, pixel 4.03, shown at level 2.8, step 1, values float32 > volume #2 level 1.306 > volume #2 level 1.963 > volume #2 level 1.89 > volume #1 level 1.883 > volume #1 level 3.986 > volume #1 level 1.848 > volume gaussian #1 sDev 2 Opened cryosparc_P119_J1363_002_volume_map.mrc gaussian as #3, grid size 120,120,120, pixel 4.03, shown at step 1, values float32 > volume #3 level 1.597 > volume gaussian #2 sDev 2 Opened cryosparc_P119_J1362_002_volume_map.mrc gaussian as #4, grid size 120,120,120, pixel 4.03, shown at step 1, values float32 > volume #4 level 1.6 > volume #4 level 1.82 > open 7p30 7p30 title: 3.0 A resolution structure of a DNA-loaded MCM double hexamer [more info...] Chain information for 7p30 #5 --- Chain | Description | UniProt 2 A | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 B | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971 4 C | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 D | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 E | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 F | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845 X | DNA (53-MER) | Y | DNA (53-MER) | Non-standard residues in 7p30 #5 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide atoms > show cartoons > color #5/A,2 pink > color #5/B,3 cyan > color #5/C,4 darkgreen > color #5/C,4 mediumblue green Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5/C,4 green > color #5/D,5 yellow > color #5/E,6 orange > color #5/F,7 medium blue > color #5/X red > color #5/Y white > select #5 123819 atoms, 125026 bonds, 244 pseudobonds, 7780 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #5,1,0,0,24.227,0,1,0,65.771,0,0,1,33.089 > view matrix models > #5,0.31745,-0.022615,-0.94801,257.34,-0.89854,0.31233,-0.30834,330.57,0.30306,0.9497,0.078829,-10.311 > volume #4 level 3.088 > view matrix models > #5,0.31745,-0.022615,-0.94801,322.19,-0.89854,0.31233,-0.30834,362.61,0.30306,0.9497,0.078829,54.438 > view matrix models > #5,0.04135,-0.97634,0.21223,328.38,-0.96384,0.01699,0.26595,331.13,-0.26326,-0.21555,-0.94033,440.57 > view matrix models > #5,0.14346,-0.96612,0.21455,312.41,-0.97356,-0.098823,0.20596,357.14,-0.17778,-0.23842,-0.95475,433.89 > view matrix models > #5,-0.0248,-0.96463,0.26245,328.83,-0.99841,0.0372,0.042384,364.93,-0.050648,-0.26098,-0.96401,420.64 > view matrix models > #5,-0.0248,-0.96463,0.26245,339.49,-0.99841,0.0372,0.042384,374.63,-0.050648,-0.26098,-0.96401,412.51 > view matrix models > #5,-0.071862,-0.87721,0.4747,303.68,-0.99659,0.082538,0.0016565,373.86,-0.040634,-0.47296,-0.88015,428.69 > view matrix models > #5,-0.02563,-0.8475,0.53017,285.21,-0.99685,0.061517,0.050148,369.92,-0.075115,-0.52722,-0.8464,436.25 > view matrix models > #5,-0.02563,-0.8475,0.53017,288.1,-0.99685,0.061517,0.050148,363.71,-0.075115,-0.52722,-0.8464,439.47 > view matrix models > #5,0.2371,0.76253,0.60194,17.126,-0.96369,0.26296,0.046477,331.57,-0.12285,-0.5911,0.79719,221.2 > view matrix models > #5,0.28583,0.95629,-0.061754,77.781,-0.95828,0.28504,-0.021402,337.4,-0.0028639,0.065295,0.99786,84.543 > view matrix models > #5,0.43154,0.8991,-0.073462,67.106,-0.90073,0.43393,0.019663,302.81,0.049557,0.057684,0.9971,78.407 > fitmap #5 inMap #4 Fit molecule 7p30 (#5) to map cryosparc_P119_J1362_002_volume_map.mrc gaussian (#4) using 123819 atoms average map value = 3.838, steps = 56 shifted from previous position = 3.65 rotated from previous position = 4.38 degrees atoms outside contour = 33864, contour level = 3.0877 Position of 7p30 (#5) relative to cryosparc_P119_J1362_002_volume_map.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.44135224 0.89733394 -0.00006329 55.44889217 -0.89733386 0.44135223 0.00039192 305.40408937 0.00037962 -0.00011618 0.99999992 96.24630498 Axis -0.00028312 -0.00024679 -0.99999993 Axis point 272.97102390 108.17938480 0.00000000 Rotation angle (degrees) 63.80981147 Shift along axis -96.33736804 > volume #4 color #b2b2ffa2 > select clear > volume #4 level 4.21 > volume #2 level 3.58 > volume #2 color #ffffb2a5 > volume #2 color #ffffb2a6 > set bgColor white > volume #2 level 4.105 > volume #2 level 2.528 > volume #1 level 3.205 > volume #1 color #b2b2b2ac > volume #1 color #b2b2b2ab > volume #4 level 3.527 > volume #4 level 2.649 > volume #3 level 1.857 > volume #3 color #b2ffff93 > volume #3 color #b2ffff94 > volume #3 level 2.686 > volume #3 level 2.023 > volume #3 level 1.786 > volume #1 level 1.921 OpenGL version: 4.1 INTEL-22.1.29 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. 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: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.80.5.0.1 (iBridge: 21.16.3049.0.0,0) OS Loader Version: 580~1337 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 6 days, 33 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX