id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17972 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000031b163000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a157000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031914b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031813f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000317133000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000316127000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031511b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File 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recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003120f7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File 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recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f0d3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fc094840 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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""d272b91e-f9f0-3854-b5b9-508b21c25dcc"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=5.5G written=3237K(0%) resident=3237K(0%) swapped_out=0K(0%) unallocated=5.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 2256K 69 \nColorSync 656K 33 \nCoreAnimation 4432K 163 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 5744K 48 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.4G 142 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 800K 50 \nStack 400.7M 51 \nStack Guard 56.0M 1 \nVM_ALLOCATE 412.1M 364 \nVM_ALLOCATE (reserved) 160.0M 4 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 34.1M 1092 \n__DATA_CONST 34.7M 1111 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 643.2M 185 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1131 \n__TPRO_CONST 272K 2 \ndyld private memory 48K 2 \nmapped file 594.3M 83 \nowned unmapped memory 156.1M 1 \npage table in kernel 3237K 1 \nshared memory 3664K 24 \n=========== ======= ======= \nTOTAL 8.2G 6533 \nTOTAL, minus reserved VM space 8.1G 6533 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""d433786abb8cb197a80310973d7e14fb5333d889"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""654d8c0661e7447155256fcd"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""67fda5a79dc968490af7a32e"" }, ""deploymentId"" : 240000311 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet > lighting soft UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/aorta/Downloads/cryosparc_P405_J285_class_01_00400_volume.mrc Opened cryosparc_P405_J285_class_01_00400_volume.mrc as #1, grid size 64,64,64, pixel 2.89, shown at level 0.0544, step 1, values float32 > open ""/Users/aorta/Downloads/cryosparc_P405_J251_002_volume_map (1).mrc"" Opened cryosparc_P405_J251_002_volume_map (1).mrc as #2, grid size 100,100,100, pixel 2.96, shown at level 0.00914, step 1, values float32 > hide #!2 models > volume #1 level 0.3495 > show #!2 models > volume #2 level 0.3601 > open /Users/aorta/Downloads/cryosparc_P402_J837_003_volume_map_sharp.mrc Opened cryosparc_P402_J837_003_volume_map_sharp.mrc as #3, grid size 350,350,350, pixel 0.74, shown at level 0.0294, step 2, values float32 > open /Users/aorta/Downloads/cryosparc_P402_J837_003_volume_map.mrc Opened cryosparc_P402_J837_003_volume_map.mrc as #4, grid size 350,350,350, pixel 0.74, shown at level 0.0288, step 2, values float32 > hide #!2 models > hide #!1 models > volume #3 step 1 > volume #4 step 1 > ui tool show ""Side View"" > open /Users/aorta/Documents/p450/phenix/p450_trimer_Start5.pdb Chain information for p450_trimer_Start5.pdb #5 --- Chain | Description A B C | No description available > select clear Drag select of 8 residues > ui mousemode right ""translate selected models"" > view matrix models > #5,0.014042,-0.44774,0.89405,80.854,-0.076946,0.89101,0.44742,-8.0799,-0.99694,-0.075077,-0.02194,250.14 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!3 models > fitmap #5 inMap #4 Fit molecule p450_trimer_Start5.pdb (#5) to map cryosparc_P402_J837_003_volume_map.mrc (#4) using 11571 atoms average map value = 0.04953, steps = 120 shifted from previous position = 7.72 rotated from previous position = 7.16 degrees atoms outside contour = 2574, contour level = 0.028826 Position of p450_trimer_Start5.pdb (#5) relative to cryosparc_P402_J837_003_volume_map.mrc (#4) coordinates: Matrix rotation and translation 0.02929752 -0.39469402 0.91834540 69.02294252 0.03111921 0.91865459 0.39383413 -20.42510557 -0.99908620 0.01703982 0.03919687 240.58756768 Axis -0.18840104 0.95873560 0.21291101 Axis point 155.11604041 0.00000000 84.97593883 Rotation angle (degrees) 90.36815682 Shift along axis 18.63747281 > hide #!4 models > select /B:508@FE 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > view sel > show #!4 models > color #4 #b2b2ff9a models > color #4 #b2b2ff89 models > hide #!4 models > show #!3 models > color #3 #b2ffff82 models > volume #3 level 0.0393 > select /B:215 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 73 atoms, 74 bonds, 8 residues, 1 model selected > show sel atoms > hide #!3 models > select /B:305 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 127 atoms, 129 bonds, 16 residues, 1 model selected > show sel atoms > show #!3 models > select clear > select /B:211@CG 1 atom, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 73 atoms, 74 bonds, 8 residues, 1 model selected > select up 2097 atoms, 2151 bonds, 260 residues, 1 model selected > color sel white > select up 2141 atoms, 2195 bonds, 266 residues, 1 model selected > select up 3814 atoms, 3908 bonds, 474 residues, 1 model selected > color sel #ff9bdcff > color sel #706effff > color sel #6c6effff > color sel #6970ffff > color sel #6375ffff > color sel #6478ffff > color sel #6799ffff > color sel #689cffff > color sel #699effff > color sel #6da7ffff > color sel #6faaffff > color sel #75b6ffff > color sel #75b7ffff > color sel #76b7ffff > color sel #75b7ffff > color sel #74b7ffff > color sel #6db5ffff > color sel #6cb5ffff > color sel #62b0ffff > color sel #60b0ffff > color sel #5fafffff > color sel #5eafffff > color sel #59acffff > color sel #57abffff > color sel #55a9ffff > color sel #52a5ffff > color sel #51a3ffff > color sel #4e9effff > color sel #4a97ffff > color sel #4894ffff > color sel #4995ffff > color sel #4a96ffff > select clear > color byhetero > volume #3 level 0.04001 > select add #5 11571 atoms, 11862 bonds, 18 pseudobonds, 1425 residues, 3 models selected > show sel atoms > select clear > volume #3 level 0.03506 > volume #3 level 0.04142 > view name inh > view > color #3 #b2ffffff models > open /Users/aorta/Downloads/cryosparc_P402_J820_004_volume_map_sharp.mrc Opened cryosparc_P402_J820_004_volume_map_sharp.mrc as #6, grid size 400,400,400, pixel 0.74, shown at level 0.0301, step 2, values float32 > volume #6 step 1 > volume #6 level 0.07703 > hide #!5 models > select #6 2 models selected > view matrix models #6,1,0,0,-13.959,0,1,0,-17.085,0,0,1,5.1992 > view matrix models > #6,0.95721,0.28868,-0.020171,-47.538,-0.2865,0.95519,0.07433,18.151,0.040724,-0.06537,0.99703,9.6243 > fitmap #6 inMap #3 Fit map cryosparc_P402_J820_004_volume_map_sharp.mrc in map cryosparc_P402_J837_003_volume_map_sharp.mrc using 205942 points correlation = 0.8619, correlation about mean = 0.3974, overlap = 2327 steps = 204, shift = 25, angle = 4.54 degrees Position of cryosparc_P402_J820_004_volume_map_sharp.mrc (#6) relative to cryosparc_P402_J837_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.95226164 0.30528295 0.00028219 -56.66301923 -0.30528294 0.95226169 -0.00006788 33.79384754 -0.00028944 -0.00002151 0.99999996 -18.99733894 Axis 0.00007595 0.00093623 -0.99999956 Axis point 79.66538249 198.07053863 0.00000000 Rotation angle (degrees) 17.77519561 Shift along axis 19.02466585 > show #!5 models > hide #!3 models > surface dust #6 size 7.4 > select clear > view inh > color #6 #ffb2ff7f models > color #6 #ffb2ff60 models > color #6 #ffb2ff61 models > color #6 #ffb2ffa4 models > ui tool show ""Color Zone"" > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 25 atoms, 24 bonds, 3 residues, 1 model selected > select up 2097 atoms, 2151 bonds, 260 residues, 1 model selected > select up 2141 atoms, 2195 bonds, 266 residues, 1 model selected > select up 3814 atoms, 3908 bonds, 474 residues, 1 model selected > color #6 #cac0ffa3 models > color #6 #a39dffa3 models > undo > redo > color sel #9aedffa3 > color sel #a0bdffa3 > color sel #9fbbffa3 > color sel #a5d1ffa3 > color sel #b6e7ffa3 > color sel #b8e9ffa3 > color sel #b7e8ffa3 > color sel #b5e6ffa3 > color sel #b4e2ffa3 > color sel #b1ddffa3 > color sel #7f82ffa3 > color sel #7d7cffa3 > color sel #7d78ffa3 > color sel #7e75ffa3 > color sel #7e72ffa3 > color sel #7e6fffa3 > color sel #7d6bffa3 > color sel #7a6affa3 > color sel #7366ffa3 > color sel #6c62ffa3 > color sel #675fffa3 > color sel #5e5bffa3 > color sel #5e5bffa4 > color sel #5e5bffff > select #6 4 models selected > select clear > hide #!6 models > select /B:508@FE 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > color sel #ffb999ff > color sel #ffa676ff > color sel #ffab74ff > color sel #ff875eff > color sel #ff755eff > color sel #ff9977ff > color sel #ffa174ff > select clear > show #!6 models > color zone #6 near #5 distance 4.44 > color zone #6 near #5 distance 3 > color zone #6 near #5 distance 2 > color zone #6 near #5 distance 2.5 > transparency #6.1 0 > color zone #6 near #5 distance 2.5 transparency #6 50 Expected a keyword > hide #!6 models Drag select of 26 atoms, 12 residues, 19 bonds > select up 113 atoms, 112 bonds, 13 residues, 1 model selected > select down 103 atoms, 19 bonds, 13 residues, 1 model selected > select up 113 atoms, 112 bonds, 13 residues, 1 model selected > select up 424 atoms, 429 bonds, 50 residues, 1 model selected > select up 3814 atoms, 3908 bonds, 474 residues, 1 model selected > color sel #bcbaffff > color sel #9fabffff > color sel #99a0ffff > color sel #9190ffff > color sel #918fffff > color sel #685fffff > color sel #685effff > color sel #675dffff > color sel #675cffff > color sel #5e50ffff > color sel #6253ffff > color sel #6656ffff > color sel #6a5affff > color sel #6d5cffff > color sel #6f5effff > color sel #6f5eff88 > color sel #6f5eff7a > select /B:508@FE 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 3857 atoms, 3954 bonds, 475 residues, 1 model selected > select down 43 atoms, 46 bonds, 1 residue, 1 model selected > color sel #ff97687a > color sel #ff4d4f7a > color sel #ff6f617a > color sel #ff6e617a > color sel #ff6e637a > color sel #ff6e667a > color sel #ff6f6a7a > color sel #ff965c7a > select clear > color zone #6 near #5 distance 2.5 > hide #!6 models Drag select of 26 atoms, 8 residues, 25 bonds Drag select of 3 atoms, 3 residues, 2 bonds > select clear Drag select of 77 atoms, 30 residues, 80 bonds > select up 593 atoms, 616 bonds, 73 residues, 1 model selected > select up 4194 atoms, 4302 bonds, 520 residues, 1 model selected > select up 4282 atoms, 4390 bonds, 532 residues, 1 model selected > select up 7628 atoms, 7816 bonds, 948 residues, 1 model selected > select up 7714 atoms, 7908 bonds, 950 residues, 1 model selected > select up 11571 atoms, 11862 bonds, 1425 residues, 1 model selected > color sel #8dabff7a > color sel #909eff7a > color sel #909dff7a > color sel #8899ff7a > color sel #8798ff7a > color sel #8596ff7a > color sel #7f91ff7a > color sel #7b8eff7a > color sel #778cff7a > color sel #768cff7a > color sel #788eff7a > color sel #7c99ff7a > color sel #7e9fff7a > color sel #7fa6ff7a > color sel #7fa9ff7a > color sel #7ba7ff7a > color sel #79a6ff7a > color sel #78a6ff7a > color sel #78a8ff7a > color sel #79abff7a > color sel #79b0ff7a > color sel #79b5ff7a > color sel #79beff7a > color sel #7abcff7a > color sel #7abbff7a > select /B:508@FE 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 3857 atoms, 3954 bonds, 475 residues, 1 model selected > select down 43 atoms, 46 bonds, 1 residue, 1 model selected > color sel #ff996c7a > color sel #ff8e637a > color sel #ff91677a > color sel #ff966c7a > color sel #ffa87e7a > color sel #ffb5897a > color sel #ffbd8f7a > color sel #ffc0917a > color sel #ffbe8f7a > color sel #ffba8d7a > color sel #ffb3897a > color sel #ffa27d7a > color sel #ff9a787a > color sel #ff94747a > color sel #ff93747a > color sel #ff92727a > color sel #ff8e6f7a > color sel #ff87697a > color sel #ff85677a > color sel #ff83657a > color sel #ff7f627a > color sel #ff7d607a > color sel #ff7a5d7a > color sel #ff795d7a > color sel #ff785b7a > color sel #ff74587a > color sel #ff72567a > color sel #ff71537a > color sel #ff70517a > color sel #ff6f507a > color sel #ff704f7a > color sel #ff6f4f7a > color sel #ff6f4e7a > color sel #ff69447a > color sel #ff68417a > color sel #ff683e7a > color sel #ff683c7a > color sel #ff683b7a > color sel #ff683a7a > color sel #ff69367a > color sel #ff6a347a > color sel #ff6b327a > color sel #ff6c307a > color sel #ff6e2e7a > color sel #ff6f2c7a > color sel #ff722b7a > color sel #ff732a7a > select clear > color zone #6 near #5 distance 2.5 > select add #5 11571 atoms, 11862 bonds, 18 pseudobonds, 1425 residues, 3 models selected > hide #!6 target m > show #!6 target m > hide #!5 target m > show #!5 target m > hide #!6 target m > show #!4 target m > hide #!5 target m > show #!5 target m > hide #!4 target m > show #!6 target m > hide #!5 target m > select clear > hide #!6 models > show #!5 models Drag select of 117 atoms, 28 residues, 104 bonds > select up 260 atoms, 255 bonds, 36 residues, 1 model selected > select up 312 atoms, 311 bonds, 36 residues, 1 model selected > select up 685 atoms, 694 bonds, 84 residues, 1 model selected > select up 3814 atoms, 3908 bonds, 474 residues, 1 model selected > select up 3857 atoms, 3954 bonds, 475 residues, 1 model selected > select up 11571 atoms, 11862 bonds, 1425 residues, 1 model selected > select down 3857 atoms, 3954 bonds, 475 residues, 1 model selected > select down 3814 atoms, 3908 bonds, 474 residues, 1 model selected > color sel #b2b9ff7a > color sel #a3c2ff7a > color sel #8596ff7a > color sel #8596ff7c > color sel #8596ffbb > color sel #8596ffff > color sel #8c9effff > color sel #7b92ffff > color sel #7790ffff > color sel #6a80ffff > show #!6 models > hide #!6 models > select /B:508@FE 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > color sel #ffb9a8ff > color sel #ff9a74ff > color sel #ff9975ff > color sel #ffaf55ff > color sel #ffaf54ff > color sel #ffaf50ff > color sel #ffae4fff > color sel #ffa242ff > color sel #ffa241ff > color sel #ffa43eff > color sel #ffa43dff > color sel #ffa53cff > color sel #ffa135ff > color sel #ffa035ff > color sel #ff9f34ff > color sel #ff9030ff > color sel #ffa43eff > color sel #ffa236ff > color sel #ff9d31ff > color sel #ff921fff > color sel #ff9019ff > color sel #ff911aff > color sel #ff931cff > select clear > view inh > hide #!6 models Drag select of 72 atoms, 16 residues, 62 bonds > select up 154 atoms, 152 bonds, 19 residues, 1 model selected > select up 174 atoms, 175 bonds, 19 residues, 1 model selected > select up 603 atoms, 612 bonds, 73 residues, 1 model selected > select up 3814 atoms, 3908 bonds, 474 residues, 1 model selected > hide sel atoms > select clear > show #!6 models > volume splitbyzone #6 Opened cryosparc_P402_J820_004_volume_map_sharp.mrc 0 as #7.1, grid size 400,400,400, pixel 0.74, shown at level 0.077, step 1, values float32 Opened cryosparc_P402_J820_004_volume_map_sharp.mrc 1 as #7.2, grid size 400,400,400, pixel 0.74, shown at level 0.077, step 1, values float32 Opened cryosparc_P402_J820_004_volume_map_sharp.mrc 2 as #7.3, grid size 400,400,400, pixel 0.74, shown at level 0.077, step 1, values float32 > surface dust #7.1 size 7.4 > surface dust #7.2 size 7.4 > surface dust #7.3 size 7.4 > volume #7.1 level 0.07359 > volume #7.1 level 0.0737 > volume #7.1 level 0.077 > select clear > view name inh > view > select add #5 11571 atoms, 11862 bonds, 18 pseudobonds, 1425 residues, 3 models selected > select clear > hide #!5 models > show #!6 models > hide #!7 models > color #6 #b0aeffa3 models > color #6 #b0aeffff models > color #6 #6c91ffff models > hide #!6 models > show #!5 models > hide #!5 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > open /Users/aorta/Downloads/fold_gfp_dimer/fold_gfp_dimer_model_0.cif Chain information for fold_gfp_dimer_model_0.cif #8 --- Chain | Description A B | . Computing secondary structure > view > select clear Drag select of 13 residues > view matrix models > #8,0.96683,-0.12759,-0.22126,98.402,0.22227,0.84707,0.48278,39.823,0.12582,-0.51595,0.84733,66.961 > view matrix models > #8,0.96683,-0.12759,-0.22126,63.954,0.22227,0.84707,0.48278,65.008,0.12582,-0.51595,0.84733,76.849 > view matrix models > #8,0.97545,-0.16714,-0.1434,65.876,0.21921,0.79927,0.55957,83.326,0.021087,-0.57726,0.81629,79.746 > view matrix models > #8,0.86187,-0.37484,-0.34158,67.015,0.50353,0.71268,0.48842,83.938,0.060358,-0.59294,0.80298,79.852 > view matrix models > #8,0.86187,-0.37484,-0.34158,68.521,0.50353,0.71268,0.48842,84.166,0.060358,-0.59294,0.80298,83.317 > select up 397 atoms, 401 bonds, 51 residues, 1 model selected > select up 1903 atoms, 1946 bonds, 239 residues, 1 model selected > fitmap #8 inMap #1 Fit molecule fold_gfp_dimer_model_0.cif (#8) to map cryosparc_P405_J285_class_01_00400_volume.mrc (#1) using 3806 atoms average map value = 0.154, steps = 352 shifted from previous position = 11.7 rotated from previous position = 60.2 degrees atoms outside contour = 3119, contour level = 0.34953 Position of fold_gfp_dimer_model_0.cif (#8) relative to cryosparc_P405_J285_class_01_00400_volume.mrc (#1) coordinates: Matrix rotation and translation 0.98149312 0.11064508 0.15629752 69.88765237 -0.08190877 0.98031958 -0.17962313 95.14970690 -0.17309593 0.16349673 0.97123973 89.45719463 Axis 0.66867272 0.64192267 -0.37524936 Axis point 0.00000000 -658.34794788 336.53054224 Rotation angle (degrees) 14.86650817 Shift along axis 74.24196461 > undo > view matrix models > #8,0.98149,0.11065,0.1563,65.9,-0.081909,0.98032,-0.17962,96.459,-0.1731,0.1635,0.97124,89.333 > view matrix models > #8,0.96562,0.059612,0.25304,65.656,-0.13604,0.94532,0.29642,94.773,-0.22153,-0.32065,0.92093,90.602 > close #8 > open > /Users/aorta/Downloads/fold_gfp_dimer_with_nanobody/fold_gfp_dimer_with_nanobody_model_0.cif Chain information for fold_gfp_dimer_with_nanobody_model_0.cif #8 --- Chain | Description A B | . C D | . Computing secondary structure > select #8/D:189 6 atoms, 5 bonds, 1 residue, 1 model selected > view matrix models > #8,0.025962,-0.21925,0.97532,53.155,-0.6384,-0.75443,-0.1526,12.594,0.76927,-0.61868,-0.15955,12.412 > view matrix models > #8,0.75514,-0.54435,-0.3653,66.249,-0.001304,0.55598,-0.83119,5.6769,0.65556,0.62815,0.41913,17.788 > view matrix models > #8,0.75514,-0.54435,-0.3653,54.358,-0.001304,0.55598,-0.83119,89.595,0.65556,0.62815,0.41913,71.017 > view matrix models > #8,0.80863,-0.58094,0.092867,92.37,0.54344,0.67713,-0.49616,72.17,0.22536,0.45168,0.86325,71.285 > view matrix models > #8,0.93485,-0.32194,0.14969,95.806,0.32539,0.6082,-0.72403,85.959,0.14205,0.72556,0.67333,72.893 > view matrix models > #8,0.93485,-0.32194,0.14969,160.58,0.32539,0.6082,-0.72403,99.417,0.14205,0.72556,0.67333,113.33 > select clear > color #8 bychain > hide #!1 models Drag select of 145 residues > select clear Drag select of 37 residues > select up 536 atoms, 536 bonds, 84 residues, 1 model selected > select up 4068 atoms, 4134 bonds, 558 residues, 1 model selected > select up 7874 atoms, 8026 bonds, 1036 residues, 1 model selected > select down 4068 atoms, 4134 bonds, 558 residues, 1 model selected > select ::name=""CYS"" 186 atoms, 155 bonds, 31 residues, 2 models selected > show sel & #8 atoms > close #8 > open > /Users/aorta/Downloads/fold_gfp_dimer_with_nanobody/fold_gfp_dimer_with_nanobody_model_1.cif Chain information for fold_gfp_dimer_with_nanobody_model_1.cif #8 --- Chain | Description A B | . C D | . Computing secondary structure > view > color #8 bychain > select ::name=""CYS"" 186 atoms, 155 bonds, 31 residues, 2 models selected > select #8/D:273 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/C:274 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > interfaces #8 & ~solvent 4 buried areas: D B 1531, C A 1484, C D 1259, A B 638 > show sel atoms > color sel byhetero > select clear > save /Users/aorta/Documents/TEST/test1.png width 739 height 705 supersample > 4 transparentBackground true > select #8/C:246 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 51 atoms, 51 bonds, 6 residues, 1 model selected > select up 2034 atoms, 2067 bonds, 279 residues, 1 model selected > color sel cornflower blue > select clear > save /Users/aorta/Documents/TEST/test1.png width 739 height 705 supersample > 4 transparentBackground true > hide #8 models > open > /Users/aorta/Downloads/fold_atad329_dimer/fold_atad329_dimer_model_0.cif Chain information for fold_atad329_dimer_model_0.cif #9 --- Chain | Description A B | . Computing secondary structure > color #9 bychain > select #9/B:258 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 129 atoms, 131 bonds, 17 residues, 1 model selected > select up 2429 atoms, 2473 bonds, 306 residues, 1 model selected > hide sel cartoons > open /Users/aorta/Downloads/cryosparc_P405_J337_class_03_final_volume.mrc Opened cryosparc_P405_J337_class_03_final_volume.mrc as #10, grid size 192,192,192, pixel 1.54, shown at level 0.0175, step 1, values float32 > view > volume #10 level 0.05597 > select clear Drag select of 26 residues > view matrix models #9,1,0,0,116.39,0,1,0,104.06,0,0,1,211.72 > view matrix models > #9,0.38328,-0.26563,-0.88461,126.36,-0.46773,0.77005,-0.43389,103.73,0.79645,0.58006,0.1709,213.83 > view matrix models > #9,0.38328,-0.26563,-0.88461,143.65,-0.46773,0.77005,-0.43389,131.22,0.79645,0.58006,0.1709,216.47 > view matrix models > #9,0.38328,-0.26563,-0.88461,136.38,-0.46773,0.77005,-0.43389,134.26,0.79645,0.58006,0.1709,179.77 > surface dust #10 size 15.4 > fitmap #9 inMap #10 Fit molecule fold_atad329_dimer_model_0.cif (#9) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 4858 atoms average map value = 0.06642, steps = 340 shifted from previous position = 17.9 rotated from previous position = 31.3 degrees atoms outside contour = 3154, contour level = 0.055966 Position of fold_atad329_dimer_model_0.cif (#9) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation 0.78847871 -0.08610931 -0.60900452 151.35768216 -0.42736971 0.63537969 -0.64315456 137.34779106 0.44233070 0.76738376 0.46418284 168.28176002 Axis 0.78711621 -0.58667175 -0.19043197 Axis point 0.00000000 -48.46518572 246.96935300 Rotation angle (degrees) 63.63930450 Shift along axis 6.51178854 > view matrix models > #9,0.79137,-0.062038,-0.60818,151.41,-0.38616,0.72051,-0.57598,139.28,0.47393,0.69067,0.54623,170.44 > volume #10 level 0.1328 > view matrix models > #9,0.78957,-0.059353,-0.61078,151.32,-0.39075,0.71882,-0.57499,139.21,0.47317,0.69266,0.54437,170.39 > view matrix models > #9,0.76035,-0.1246,-0.63746,151.13,-0.37484,0.71733,-0.58731,139.4,0.53044,0.68551,0.49871,171.08 > view matrix models > #9,0.36113,-0.23281,-0.90299,138.8,-0.46091,0.79722,-0.38987,141.3,0.81065,0.55699,0.18059,170.71 > view matrix models > #9,0.36113,-0.23281,-0.90299,142.62,-0.46091,0.79722,-0.38987,142.06,0.81065,0.55699,0.18059,173.82 > fitmap #9 inMap #10 Fit molecule fold_atad329_dimer_model_0.cif (#9) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 4858 atoms average map value = 0.06642, steps = 292 shifted from previous position = 10.2 rotated from previous position = 32.9 degrees atoms outside contour = 3937, contour level = 0.13282 Position of fold_atad329_dimer_model_0.cif (#9) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation 0.78809691 -0.08609755 -0.60950019 151.32659082 -0.42771762 0.63548755 -0.64281663 137.35216893 0.44267472 0.76729576 0.46400033 168.27638923 Axis 0.78677925 -0.58706624 -0.19060862 Axis point 0.00000000 -48.40174972 246.91892487 Rotation angle (degrees) 63.65389777 Shift along axis 6.35086933 > hide #9 models > show #8 models Drag select of 21 atoms, 238 residues, 16 bonds > select up 1839 atoms, 1862 bonds, 239 residues, 1 model selected > select up 2888 atoms, 2930 bonds, 396 residues, 1 model selected > select up 5971 atoms, 6080 bonds, 797 residues, 1 model selected > hide sel cartoons > hide sel atoms Drag select of 239 residues > view matrix models > #8,0.88051,0.46779,-0.076663,157.75,-0.35874,0.55186,-0.75284,114.74,-0.30987,0.69038,0.65373,141.6 > view matrix models > #8,0.36593,0.11179,0.9239,159.54,-0.67867,0.71135,0.18273,146.21,-0.63679,-0.6939,0.33617,147.57 > view matrix models > #8,0.36593,0.11179,0.9239,163.37,-0.67867,0.71135,0.18273,143.29,-0.63679,-0.6939,0.33617,150.94 > fitmap #8 inMap #10 Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms average map value = 0.05868, steps = 292 shifted from previous position = 18.2 rotated from previous position = 64 degrees atoms outside contour = 6524, contour level = 0.13282 Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation -0.24060228 -0.69113193 0.68150363 152.62194254 -0.45173709 0.70118603 0.55160833 151.37558460 -0.85909496 -0.17514225 -0.48091688 139.23598980 Axis -0.42249226 0.89561810 0.13917081 Axis point 152.28219193 -0.00000000 -2.82241039 Rotation angle (degrees) 120.67492509 Shift along axis 90.47070984 > select clear > color #10 #99bfe5a1 models > select clear > select #8/A:117 4 atoms, 3 bonds, 1 residue, 1 model selected > view matrix models > #8,-0.27676,-0.66343,0.69518,150.22,-0.45131,0.72842,0.51548,150.03,-0.84836,-0.17108,-0.50101,135.57 > view matrix models > #8,-0.28778,-0.75054,0.59487,150.16,-0.66791,0.60244,0.43698,145.18,-0.68635,-0.27157,-0.67467,139.65 > fitmap #8 inMap #10 Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms average map value = 0.06221, steps = 252 shifted from previous position = 10.4 rotated from previous position = 41.3 degrees atoms outside contour = 6450, contour level = 0.13282 Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation -0.39299873 -0.91592827 0.08140881 145.66133610 -0.45028465 0.26888116 0.85143799 154.75052529 -0.80174542 0.29795691 -0.51809840 139.61892558 Axis -0.48485230 0.77364770 0.40790623 Axis point 140.84131681 0.00000000 -10.90722527 Rotation angle (degrees) 145.19586190 Shift along axis 106.04958316 > undo > select #8/A:204 7 atoms, 6 bonds, 1 residue, 1 model selected > view matrix models > #8,-0.92834,-0.3169,-0.19429,131.72,-0.32256,0.42701,0.84476,155.05,-0.18474,0.8469,-0.49864,146.37 > view matrix models > #8,-0.93302,-0.24776,-0.26092,130.9,-0.32085,0.9011,0.29166,150.11,0.16286,0.35585,-0.92024,158.78 > view matrix models > #8,-0.79835,-0.60219,-0.0030833,130.91,-0.59774,0.79305,-0.11736,139.35,0.073118,-0.09185,-0.99308,155.34 > fitmap #8 inMap #10 Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms average map value = 0.05102, steps = 144 shifted from previous position = 11.4 rotated from previous position = 10.2 degrees atoms outside contour = 6756, contour level = 0.13282 Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation -0.77795001 -0.61049006 0.14864611 139.00440758 -0.62010903 0.78411673 -0.02501490 146.72596161 -0.10128456 -0.11163714 -0.98857402 152.17601903 Axis -0.32725809 0.94423595 -0.03634042 Axis point 100.39651883 0.00000000 73.01113281 Rotation angle (degrees) 172.39485181 Shift along axis 87.52347074 > volume #10 level 0.1328 > view matrix models > #8,-0.77795,-0.61049,0.14865,163.29,-0.62011,0.78412,-0.025015,154.98,-0.10128,-0.11164,-0.98857,163.24 > view matrix models > #8,-0.62824,-0.76608,0.13577,134.17,-0.77543,0.63077,-0.028983,142.14,-0.063439,-0.12349,-0.99032,153.8 > view matrix models > #8,-0.62824,-0.76608,0.13577,133.27,-0.77543,0.63077,-0.028983,141.79,-0.063439,-0.12349,-0.99032,152.94 > select up 81 atoms, 82 bonds, 10 residues, 1 model selected > select up 1903 atoms, 1946 bonds, 239 residues, 1 model selected > fitmap #8 inMap #10 Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms average map value = 0.06221, steps = 384 shifted from previous position = 21.3 rotated from previous position = 60.6 degrees atoms outside contour = 6452, contour level = 0.13282 Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation -0.39296935 -0.91593970 0.08142207 145.64878333 -0.45019525 0.26884261 0.85149744 154.77153450 -0.80181003 0.29795657 -0.51799861 139.61449382 Axis -0.48484931 0.77362756 0.40794797 Axis point 140.84205807 0.00000000 -10.92652726 Rotation angle (degrees) 145.19131351 Shift along axis 106.07326236 > undo > select up 81 atoms, 82 bonds, 10 residues, 1 model selected > select up 1903 atoms, 1946 bonds, 239 residues, 1 model selected > ui tool show ""Fit in Map"" > fitmap sel inMap #10 Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 1903 atoms average map value = 0.1408, steps = 88 shifted from previous position = 2.78 rotated from previous position = 16.9 degrees atoms outside contour = 1015, contour level = 0.13282 Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates: Matrix rotation and translation -0.50315903 -0.81044765 0.30000933 139.05500724 -0.79921935 0.56845295 0.19521698 143.32764189 -0.32875433 -0.14154808 -0.93374768 146.07696079 Axis -0.47208381 0.88141314 0.01574004 Axis point 123.08753529 0.00000000 54.10220943 Rotation angle (degrees) 159.10359942 Shift along axis 62.98450599 > select clear > show #9 models > hide #9 models > show #9 models > color #9 #d95bf2ff > select add #9 4858 atoms, 4946 bonds, 612 residues, 1 model selected > view matrix models > #9,0.98679,-0.11025,-0.11872,165.48,-0.028938,0.60103,-0.7987,131.4,0.15941,0.79158,0.5899,124.18 > view matrix models > #9,0.98679,-0.11025,-0.11872,169.35,-0.028938,0.60103,-0.7987,177.95,0.15941,0.79158,0.5899,117.51 > view matrix models > #9,0.98679,-0.11025,-0.11872,165.77,-0.028938,0.60103,-0.7987,165.6,0.15941,0.79158,0.5899,128.63 > view matrix models > #9,0.75203,0.22798,0.61844,174.46,0.4061,0.57877,-0.70718,175.55,-0.51916,0.78297,0.34267,111.24 > view matrix models > #9,0.75203,0.22798,0.61844,177.22,0.4061,0.57877,-0.70718,207.96,-0.51916,0.78297,0.34267,94.077 > close #9 > open > /Users/aorta/Downloads/fold_gfpatad329_dimer/fold_gfpatad329_dimer_model_0.cif Chain information for fold_gfpatad329_dimer_model_0.cif #9 --- Chain | Description A B | . Computing secondary structure > select clear > color #8-9 bychain > select clear Drag select of 91 residues > select up 1114 atoms, 1131 bonds, 139 residues, 1 model selected > select up 4404 atoms, 4494 bonds, 554 residues, 1 model selected > select down 1114 atoms, 1131 bonds, 139 residues, 1 model selected > select up 4404 atoms, 4494 bonds, 554 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 553 residues > view matrix models #9,1,0,0,12.531,0,1,0,35.385,0,0,1,51.688 > view matrix models > #9,-0.31285,-0.19585,0.92939,163.27,0.56121,0.75131,0.34724,93.163,-0.76627,0.63022,-0.12513,128.46 > select clear > mmaker #9 to #8 Computing secondary structure Parameters --- Chain pairing | bb 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 fold_gfp_dimer_with_nanobody_model_1.cif, chain A (#8) with fold_gfpatad329_dimer_model_0.cif, chain A (#9), sequence alignment score = 1226.7 RMSD between 231 pruned atom pairs is 0.255 angstroms; (across all 239 pairs: 2.159) > select clear Drag select of 2 residues > view matrix models > #9,-0.90216,0.11625,0.41545,149.95,0.39246,0.62101,0.67847,157.12,-0.17913,0.77513,-0.60587,125.15 > view matrix models > #9,-0.90216,0.11625,0.41545,150.01,0.39246,0.62101,0.67847,160.8,-0.17913,0.77513,-0.60587,124.03 > open /Users/aorta/Downloads/cryosparc_P405_J346_003_volume_map_sharp.mrc Opened cryosparc_P405_J346_003_volume_map_sharp.mrc as #11, grid size 200,200,200, pixel 1.48, shown at level 0.0176, step 1, values float32 > volume #11 level 0.07876 > volume #11 level 0.1558 > view matrix models > #9,-0.90216,0.11625,0.41545,150.82,0.39246,0.62101,0.67847,160.67,-0.17913,0.77513,-0.60587,125.21 > view matrix models > #9,-0.63121,0.52898,0.56723,145.33,0.72635,0.65964,0.19312,155.14,-0.27201,0.53391,-0.8006,127.36 > view matrix models > #9,-0.78761,0.01165,0.61607,151.31,0.55865,0.43532,0.70598,160.64,-0.25996,0.9002,-0.34937,125.99 > undo > hide #8 models > view matrix models > #9,-0.32589,0.74048,0.58778,138.91,0.93922,0.18256,0.29076,156.2,0.108,0.64681,-0.75496,124.69 > view matrix models > #9,-0.32589,0.74048,0.58778,141.9,0.93922,0.18256,0.29076,161.3,0.108,0.64681,-0.75496,128.2 > view matrix models > #9,-0.2218,0.70839,0.67007,150.61,0.9496,0.00081365,0.31346,158.78,0.22151,0.70583,-0.67286,122.77 > view matrix models > #9,-0.3239,0.1945,0.92588,156.83,0.84327,0.50304,0.18933,155.25,-0.42893,0.84209,-0.32696,129.49 > view matrix models > #9,-0.40876,0.49605,0.76606,150.93,0.91102,0.17172,0.37492,161.88,0.054435,0.85114,-0.5221,126.39 > hide #9 models > show #!10 models > hide #!10 models > hide #!11 models > show #!6 models > hide #!6 models > show #!4 models > open /Users/aorta/Downloads/Refine5_coot1.pdb Summary of feedback from opening /Users/aorta/Downloads/Refine5_coot1.pdb --- warning | End residue of secondary structure not found: HELIX 28 28 THR A 375 TRP A 396 1 22 Chain information for Refine5_coot1.pdb #12 --- Chain | Description A | No description available > hide #!4 models > rainbow #!12 > dssp Computing secondary structure ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields > lighting soft UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,1 Model Number: MW2V3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 16 days, 5 hours, 9 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal SE2717H/HX: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX