id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16781 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.5-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. 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""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""1979"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 6906789888, ""size"" : 3553361920, ""uuid"" : ""9c875b0a-d532-3933-b1f0-f1ea72cedde2"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 5440K 8 \nCG image 1264K 60 \nColorSync 592K 30 \nCoreAnimation 544K 34 \nCoreGraphics 144K 9 \nCoreUI image data 5648K 49 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.4G 431 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 640.0M 8 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 40 \nStack 200.8M 40 \nVM_ALLOCATE 305.4M 213 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 1930K 398 \n__AUTH_CONST 29.5M 636 \n__CTF 824 1 \n__DATA 20.9M 788 \n__DATA_CONST 40.5M 795 \n__DATA_DIRTY 2039K 247 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 832.6M 157 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 890.9M 814 \ndyld private memory 320K 4 \nmapped file 228.2M 58 \nshared memory 3200K 28 \n=========== ======= ======= \nTOTAL 4.8G 4880 \nTOTAL, minus reserved VM space 4.0G 4880 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""89ffc6da225233b246bd7954fb6dafde7d7db9d1"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62fe74515312cd4599bd3c80"", ""factorPackIds"" : { ""MYRIAD_BOOSTS"" : ""62fe74805312cd4599bd3c81"" }, ""deploymentId"" : 240000006 }, { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000032 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/local_res.cxs"" Opened P2_J174_map_flipped_nosharp.mrc as #6, grid size 224,224,224, pixel 0.832, shown at level 0.0255, step 1, values float32 Opened cryosparc_P2_J178_map_locres.mrc z flip as #9, grid size 224,224,224, pixel 0.832, shown at level 2.77, step 1, values float32 Log from Mon Feb 3 16:57:41 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/local_res.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0526, step 1, values float32 Opened cryosparc_P2_J77_004_volume_map.mrc as #3, grid size 224,224,224, pixel 0.832, shown at level 0.0661, step 1, values float32 Opened cryosparc_P2_J135_map_locres.mrc as #4, grid size 224,224,224, pixel 0.832, shown at level 3.23, step 1, values float32 Map values for surface ""surface"": minimum 0, mean 2.002, maximum 3.728 Log from Wed Jan 29 13:58:14 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0526, step 1, values float32 Log from Mon Jan 27 14:41:44 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0526, step 1, values float32 Log from Sun Jan 26 23:19:58 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0526, step 1, values float32 Log from Sun Jan 26 22:49:43 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0623, step 1, values float32 Log from Sun Jan 26 22:19:26 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/side_view_1.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0623, step 1, values float32 Log from Sun Jan 26 22:02:04 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview_mrc.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0914, step 1, values float32 Log from Mon Jan 13 14:04:48 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview_Helix_fixed.cxs"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0599, step 1, values float32 Log from Sun Jan 12 22:11:30 2025 Startup Messages --- note | available bundle cache has not been initialized yet 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/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J74_map_flipped_nosharp.mrc"" Opened P2_J74_map_flipped_nosharp.mrc as #1, grid size 224,224,224, pixel 0.832, shown at level 0.0599, step 1, values float32 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-16.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-16.pdb #2 --- Chain | Description A | No description available B C D | No description available > set bgColor white Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > lighting soft > lighting full > lighting soft > color #1 #b2b2b280 models > color #1 #b2b2b252 models > ui mousemode right zoom > ui tool show ""Side View"" > hide #!1 models Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > select #2/C:24 Nothing selected > select #2/C:240 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > select H 9145 atoms, 1108 residues, 1 model selected > ~select Nothing selected > select H 9145 atoms, 1108 residues, 1 model selected > delete sel > select #2/C:240 11 atoms, 10 bonds, 1 residue, 1 model selected > hbonds sel reveal true 2 hydrogen bonds found > select #2/C:240|#2/B:298 19 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected > show #!1 models > view #2/C:240|#2/B:298 > graphis selection color black Unknown command: graphis selection color black > graphics selection color black > color #1 #d6d6d6ff models > color #1 #d6d6d646 models > color #1 #76d6ffff models > color #1 #76d6ff0f models > color sel bychain > select add #2 8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 2 models selected > color sel bychain > color sel byhetero > view #2/C:240|#2/B:298 > select subtract #2 Nothing selected > view #2/C:240|#2/B:298 > select #2/C:240|#2/B:298 19 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected > color #1 #76d6ff31 models > color #1 #76d6ff49 models > color #1 darkgrey models > color #1 #a9a9a9de models > color #1 #a9a9a93e models > color #1 #a9a9a936 models > color #1 #a9a9a935 models > color #1 #a9a9a936 models > lighting flat [Repeated 1 time(s)] > lighting soft > hide #!1 models > setattr #2/B:348-357 res ss_type 1 Assigning ss_type attribute to 10 items > show #!1 models > view #2/C:240|#2/B:298 > save ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/240-298_SaltBridge.cxs"" > save ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/240-298_SaltBridge.png"" width 1020 height 778 > supersample 3 > lighting soft [Repeated 1 time(s)] > lighting flat > lighting soft > view #2 > hide #!1 models > setattr #2/C:89-103res ss_type 1 Missing or invalid ""attrValue"" argument: Expected a text string > setattr #2/C:89-103 res ss_type 1 Assigning ss_type attribute to 15 items > setattr #2/C:108-120 res ss_type 1 Assigning ss_type attribute to 13 items > show #!1 models > select up 284 atoms, 284 bonds, 1 pseudobond, 35 residues, 2 models selected > select up 4460 atoms, 4536 bonds, 1 pseudobond, 554 residues, 2 models selected > select up 8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 2 models selected > select up 8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 2 models selected > select up 8922 atoms, 9075 bonds, 2 pseudobonds, 1108 residues, 4 models selected > view #2 > save ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Chimera-Image/Overview_Helix_fixed.cxs"" ——— End of log from Sun Jan 12 22:11:30 2025 ——— opened ChimeraX session > close #2 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-18.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-18.pdb #2 --- Chain | Description A | No description available B C D | No description available > color bychain > setattr #5:90-101|#5:108-120|#5:293-310|#5:341-357|#5:313-331 res ss_type 1 Assigning ss_type attribute to 0 items > setattr #2:90-101|#2:108-120|#2:293-310|#2:341-357|#2:313-331 res ss_type 1 Assigning ss_type attribute to 316 items > hide #!1 models > setattr #2:310-316|#2:293-312 res ss_type 0 Assigning ss_type attribute to 96 items > setattr #2:297-304 res ss_type 0 Assigning ss_type attribute to 32 items > setattr #2:297-304 res ss_type 1 Assigning ss_type attribute to 32 items > setattr #2:297-304 res ss_type 0 Assigning ss_type attribute to 32 items > setattr #2:297-303 res ss_type 1 Assigning ss_type attribute to 28 items > setattr #2:329 res ss_type 1 Assigning ss_type attribute to 4 items > setattr #2:329 res ss_type 1 Assigning ss_type attribute to 4 items > setattr #2:330-331 res ss_type 0 Assigning ss_type attribute to 8 items > setattr #2:330-334 res ss_type 0 Assigning ss_type attribute to 20 items > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/model and maps from Emily/InvEd79CL_C1.pdb"" Chain information for InvEd79CL_C1.pdb #3 --- Chain | Description A C | No description available B D | No description available Computing secondary structure > tile 2 models tiled > select add #3 18446 atoms, 18608 bonds, 1124 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.48089,-0.4225,0.76827,61.224,-0.67867,0.37541,0.63125,-28.025,-0.55512,-0.82496,-0.10621,208.16 > view matrix models > #3,-0.71647,-0.33539,-0.61171,301.29,0.39514,0.52754,-0.75204,-22.962,0.57493,-0.78052,-0.24544,102.8 > view matrix models > #3,-0.75359,-0.60534,-0.25625,295.6,0.051562,0.3342,-0.94109,45.663,0.65532,-0.72241,-0.22064,87.416 > view matrix models > #3,-0.75628,-0.63923,-0.13934,288.06,-0.059577,0.27938,-0.95833,63.177,0.65153,-0.71647,-0.24938,89.923 > view matrix models > #3,0.30717,0.10181,0.94619,17.611,0.81457,0.48597,-0.31672,-101.71,-0.49207,0.86803,0.066344,41.029 > view matrix models > #3,0.4214,0.16776,0.89122,5.4443,0.74905,0.4896,-0.44634,-83.517,-0.51122,0.85565,0.080661,42.714 > view matrix models > #3,0.46047,0.25973,0.84882,-2.4988,0.6976,0.48544,-0.52698,-70.569,-0.54892,0.8348,0.042339,51.824 > view matrix models > #3,0.35127,0.36487,0.86225,-1.6834,0.83813,0.28794,-0.46328,-73.71,-0.41732,0.88541,-0.20467,56.803 > view matrix models > #3,0.59118,0.50311,0.63039,-16.548,0.61842,0.21898,-0.75472,-18.886,-0.51775,0.83602,-0.18168,69.086 > view matrix models > #3,0.6299,0.38635,0.67377,-14.442,0.52605,0.42599,-0.73607,-28.974,-0.5714,0.81809,0.065093,53.444 > view matrix models > #3,0.39001,0.14428,0.90944,8.961,0.79636,0.44299,-0.4118,-87.475,-0.46228,0.88484,0.057871,37.352 > view matrix models > #3,0.35766,0.23924,0.90269,4.722,0.75911,0.48851,-0.43024,-85.915,-0.54391,0.83912,-0.0068889,55.456 > view matrix models > #3,0.24448,0.32778,0.91257,7.685,0.68388,0.60891,-0.40192,-91.207,-0.68741,0.72235,-0.075295,86.235 > view matrix models > #3,0.23012,0.36364,0.90267,6.9748,0.7258,0.55376,-0.40811,-90.16,-0.64827,0.74907,-0.1365,85.595 > color sel bychain > setattr #2:82-84|#2:118-119 res ss_type 0 Assigning ss_type attribute to 20 items > view matrix models > #3,0.44735,0.67801,-0.58325,94.196,-0.053756,-0.63058,-0.77426,123.63,-0.89274,0.37772,-0.24565,152.12 > view matrix models > #3,0.39568,0.84702,-0.35495,64.041,0.0047469,-0.38838,-0.92149,110.47,-0.91837,0.36293,-0.15769,147.92 > setattr #2:108-120 res ss_type 1 Assigning ss_type attribute to 52 items > setattr #2:118 res ss_type 1 Assigning ss_type attribute to 4 items > setattr #2:120 res ss_type 0 Assigning ss_type attribute to 4 items > select subtract #3 Nothing selected > hide #3 models > setattr #2:341 res ss_type 0 Assigning ss_type attribute to 4 items > show #3 models > setattr #2:330 res ss_type 1 Assigning ss_type attribute to 4 items > hide #3 models > view #2 > close #3 > show #!1 models > hide #!1 models > show #!1 models > select add #2 17967 atoms, 18121 bonds, 1108 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.79303,-0.59721,-0.12018,234.34,-0.60352,0.79706,0.021628,69.88,0.082877,0.089685,-0.99252,155.71 > view matrix models > #2,-0.7841,-0.61773,-0.059968,262.12,-0.61213,0.78568,-0.089479,19.264,0.10239,-0.033453,-0.99418,156.55 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.87348,0.36279,0.32468,-15.966,-0.40507,0.9115,0.071283,-25.477,-0.27009,-0.19378,0.94313,39.423 > view matrix models > #2,0.6866,0.68476,0.2443,-21.42,-0.71396,0.69849,0.048727,24.92,-0.13727,-0.20787,0.96848,26.179 > view matrix models > #2,0.65914,0.68984,0.29944,-24.074,-0.70888,0.70287,-0.058842,33.294,-0.25106,-0.17348,0.9523,34.985 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.65914,0.68984,0.29944,-55.58,-0.70888,0.70287,-0.058842,94.601,-0.25106,-0.17348,0.9523,43.834 > view matrix models > #2,-0.92993,-0.31103,0.1962,190.88,0.284,-0.94635,-0.15413,168.23,0.23362,-0.087606,0.96837,-10.543 > view matrix models > #2,-0.69836,-0.69612,0.16648,210.81,0.68819,-0.71697,-0.11107,99.941,0.19668,0.037005,0.97977,-18.676 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.4353,0.87727,0.20226,-43.306,-0.8943,0.44722,-0.015047,131.4,-0.10365,-0.17433,0.97922,28.877 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.4353,0.87727,0.20226,-46.161,-0.8943,0.44722,-0.015047,136.54,-0.10365,-0.17433,0.97922,28.628 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.89932,0.21352,0.38161,124.06,-0.24576,-0.96862,-0.037207,208.96,0.36169,-0.12724,0.92357,-14.27 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.75647,-0.098997,-0.64649,87.199,-0.45219,0.63499,-0.62635,130.59,0.47252,0.76615,0.43559,-65.221 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09697, steps = 124 shifted from previous position = 1.24 rotated from previous position = 12.3 degrees atoms outside contour = 6623, contour level = 0.059907 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999996 0.00014108 0.00025768 186.33283726 -0.00014111 -0.99999998 -0.00013184 186.38559753 0.00025766 -0.00013188 0.99999998 -0.01152858 Axis -0.00015165 0.00008216 -0.99999999 Axis point 93.17299394 93.18622572 0.00000000 Rotation angle (degrees) 179.99191595 Shift along axis -0.00141580 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_Helix_fixed.cxs"" > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_Helix_fixed.png"" width 923 height 778 supersample 3 > set view z Expected a keyword > set view Expected a keyword > select subtract #2 Nothing selected > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_Helix_fixed.png"" width 923 height 778 supersample 3 > view orient [Repeated 2 time(s)] > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > view name p1 > view p1 > rainbow polymers palette pubugn > undo [Repeated 1 time(s)] > color bychain > preset ""molecular surfaces"" ""chain id coloring (opaque)"" Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color bychain targ s trans 0 > hide #!2 models > show #!2 models > volume #1 level 0.05506 > color bychain > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide surfaces > show atoms [Repeated 1 time(s)] > hide atoms > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09696, steps = 88 shifted from previous position = 2.01 rotated from previous position = 9.62 degrees atoms outside contour = 6092, contour level = 0.055057 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999995 0.00004038 0.00030409 186.33580992 -0.00004044 -0.99999998 -0.00019307 186.38795964 0.00030408 -0.00019309 0.99999995 -0.02269610 Axis -0.00023177 0.00015318 -0.99999996 Axis point 93.16979056 93.19209564 0.00000000 Rotation angle (degrees) 179.99768469 Shift along axis 0.00805974 > hide #!1 models > show #!1 models > select #2/B 4517 atoms, 4555 bonds, 277 residues, 1 model selected > hbonds sel reveal true 245 hydrogen bonds found > hide #!1 models > view matrix models > #2,0.59349,-0.78929,-0.15744,125.06,-0.0088879,-0.20203,0.97934,28.362,-0.8048,-0.57982,-0.12692,225.89 > view matrix models > #2,0.57657,-0.8013,-0.15966,127.93,0.019451,-0.18189,0.98313,23.535,-0.81682,-0.56995,-0.089287,222.86 > show #!1 models > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09697, steps = 136 shifted from previous position = 0.742 rotated from previous position = 16.3 degrees atoms outside contour = 6090, contour level = 0.055057 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999996 0.00013771 0.00023680 186.33626316 -0.00013773 -0.99999998 -0.00011738 186.38540532 0.00023678 -0.00011742 0.99999998 -0.01543045 Axis -0.00014211 0.00007568 -0.99999999 Axis point 93.17454990 93.18628654 0.00000000 Rotation angle (degrees) 179.99210925 Shift along axis 0.00305471 > select add #2 17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 3 models selected > select subtract #2 4 models selected > ui tool show ""Side View"" > style stick Changed 17967 atom styles > color bypolymer [Repeated 1 time(s)] > color bychain > style stick Changed 17967 atom styles > style stick Changed 17967 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style sphere Changed 17967 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 17967 atom styles > style stick Changed 17967 atom styles > color bychain > color bfactor 17967 atoms, 1108 residues, 4 surfaces, atom bfactor range 30 to 262 > undo > color zone #1 near #2 distance 4.99 [Repeated 1 time(s)] > hide #!2 models > hide #!1 models > show #!1 models > volume #1 level 0.08011 > volume #1 level 0.1019 > show #!2 models > hide #!2 models > volume #1 level 0.1076 > lighting flat > lighting full > lighting soft > lighting full > lighting soft > volume #1 level 0.11 > volume #1 level 0.09224 > show #!2 models > ui mousemode right ""translate selected models"" > select add #2 17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 2 models selected > view matrix models > #2,0.86091,-0.5002,0.09295,118.47,0.28124,0.31566,-0.90623,109.43,0.42396,0.80633,0.41243,-54.339 > view p1 > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09697, steps = 48 shifted from previous position = 0.776 rotated from previous position = 0.00678 degrees atoms outside contour = 9832, contour level = 0.092237 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999996 0.00013094 0.00023673 186.33597857 -0.00013100 -0.99999996 -0.00024792 186.40323872 0.00023669 -0.00024796 0.99999996 -0.00201516 Axis -0.00014291 0.00014145 -0.99999998 Axis point 93.17409266 93.19551819 0.00000000 Rotation angle (degrees) 179.99249607 Shift along axis 0.00175156 > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09696, steps = 28 shifted from previous position = 0.00609 rotated from previous position = 0.0118 degrees atoms outside contour = 9832, contour level = 0.092237 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999991 0.00013328 0.00040667 186.32680752 -0.00013342 -0.99999993 -0.00036541 186.41549141 0.00040662 -0.00036547 0.99999987 -0.00684003 Axis -0.00022742 0.00019991 -0.99999995 Axis point 93.16961923 93.20153329 0.00000000 Rotation angle (degrees) 179.99235953 Shift along axis 0.00173211 > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09697, steps = 40 shifted from previous position = 0.0161 rotated from previous position = 0.0153 degrees atoms outside contour = 9819, contour level = 0.092237 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999995 0.00014329 0.00027422 186.32188104 -0.00014332 -0.99999998 -0.00013440 186.39201925 0.00027419 -0.00013444 0.99999997 -0.01654028 Axis -0.00015957 0.00008319 -0.99999998 Axis point 93.16761954 93.18933375 0.00000000 Rotation angle (degrees) 179.99178926 Shift along axis 0.00231578 > hide #!2 models > show #!2 models > hide #!2 models > view p1 > select add #1 17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 8 models selected > show #!2 models > view p1 > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09697, steps = 52 shifted from previous position = 0.726 rotated from previous position = 0.0123 degrees atoms outside contour = 9816, contour level = 0.092237 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999989 0.00014690 0.00043305 186.30481430 -0.00014701 -0.99999996 -0.00025432 186.40234758 0.00043301 -0.00025439 0.99999989 -0.01954564 Axis -0.00023840 0.00014279 -0.99999996 Axis point 93.15925756 93.19432790 0.00000000 Rotation angle (degrees) 179.99158024 Shift along axis 0.00174627 > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09697, steps = 40 shifted from previous position = 0.0142 rotated from previous position = 0.00931 degrees atoms outside contour = 9833, contour level = 0.092237 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999995 0.00014052 0.00029053 186.33155559 -0.00014057 -0.99999998 -0.00017639 186.39851600 0.00029050 -0.00017644 0.99999996 -0.01392357 Axis -0.00016815 0.00010450 -0.99999998 Axis point 93.17232811 93.19271049 0.00000000 Rotation angle (degrees) 179.99194762 Shift along axis 0.00207069 > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09696, steps = 28 shifted from previous position = 0.00582 rotated from previous position = 0.0119 degrees atoms outside contour = 9834, contour level = 0.092237 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999991 0.00013421 0.00040367 186.32795998 -0.00013435 -0.99999993 -0.00035125 186.41449296 0.00040361 -0.00035131 0.99999988 -0.00786976 Axis -0.00022575 0.00019272 -0.99999996 Axis point 93.17023895 93.20099055 0.00000000 Rotation angle (degrees) 179.99230615 Shift along axis 0.00173094 > select subtract #2 6 models selected > select subtract #1 Nothing selected > hide #!2 models > volume #1 level 0.09143 > view p1 > view name p1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.png"" width 923 height 778 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > surface dust #1 size 8.32 [Repeated 3 time(s)] > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > view p1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" ——— End of log from Mon Jan 13 14:04:48 2025 ——— opened ChimeraX session > view name p1 > view > lighting shadows false > volume #1 level 0.09143 > volume #1 level 0.06675 > volume #1 level 0.06011 > volume #1 level 0.08573 > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > select add #2 17967 atoms, 18121 bonds, 245 pseudobonds, 1108 residues, 2 models selected > hide sel atoms > ~hbonds > show #!1 models > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule P2_J73_map_flipped_nosharp-coot-18.pdb (#2) to map P2_J74_map_flipped_nosharp.mrc (#1) using 17967 atoms average map value = 0.09696, steps = 156 shifted from previous position = 0.633 rotated from previous position = 23.7 degrees atoms outside contour = 9212, contour level = 0.085735 Position of P2_J73_map_flipped_nosharp-coot-18.pdb (#2) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.99999996 0.00013775 0.00023762 186.33969735 -0.00013778 -0.99999998 -0.00015605 186.39740178 0.00023760 -0.00015609 0.99999998 -0.01109390 Axis -0.00014227 0.00009354 -0.99999999 Axis point 93.17626917 93.19228265 0.00000000 Rotation angle (degrees) 179.99210671 Shift along axis 0.00201851 > color zone #1 near sel & #2 distance 4.99 > volume #1 level 0.06553 > volume #1 level 0.06391 > volume #1 level 0.0728 > volume #1 level 0.0623 > ui mousemode right zoom > select subtract #2 4 models selected > view name p1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" > view p1 > turn y 60 > view p1 > hide #!1 models > turn y 90 > turn y -90 > show #!1 models > hide #!1 models > show #!1 models > view p1 > turn y 60 > hide #!1 models > select > #1/b:270|#1/b:261-262|#1/b:217-218|#1/b:179|#1/a:270|#1/a:261-262|#1/a:217-218|#1/a:179|#1/a:175 Nothing selected > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 246 atoms, 240 bonds, 13 residues, 1 model selected > show sel cartoons > show sel atoms > view sel > select H 9034 atoms, 1093 residues, 1 model selected > delete sel > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > show atoms > hide atoms > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 113 atoms, 107 bonds, 13 residues, 1 model selected > show sel atoms > transparency #2 50 cartoons/ Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #2 50 cartoons > view sel > transparency #2 0 cartoons > view sel > ui tool show ""Side View"" > show #!1 models > turn y -60 > view p1 > turn y 60 > view p1 > turn y 50 > view sel > hide #!1 models > show #!1 models > view p1 > turn y 45 > view sel > hide #!1 models > view p1 > turn y 40 > view sel > view p1 > view name p1 > turn y 40 > view name p2 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > view sel [Repeated 4 time(s)] > view name p3 > transparency #2 80 cartoons > view name p3 > transparency #2 60 cartoons > transparency #2 75cartoons Missing or invalid ""percent"" argument: Expected a number > transparency #2 75 cartoons > view name p3 > hide #2/c|#2/d > select #2/c|#2/d 4460 atoms, 4536 bonds, 554 residues, 1 model selected > hide sel cartoons > view name p3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic.cxs"" > size stickRadius +.1 Changed 9087 bond radii > size stickRadius +.1 Changed 9087 bond radii > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick.cxs"" > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick.png"" width 938 height 879 supersample 3 > undo [Repeated 1 time(s)] > redo > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-1.png"" width 938 height 879 supersample 3 > lighting flat [Repeated 3 time(s)] > lighting full > lighting flat > graphics silhouettes false > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 113 atoms, 107 bonds, 13 residues, 1 model selected > lighting soft > lighting simple > lighting full > lighting soft > lighting simple > lighting full > transparency #2 80 cartoons > transparency #2 90 cartoons > transparency #2 85 cartoons > transparency #2 60 cartoons > transparency #2 75 cartoons > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-1.cxs"" > size stickRadius +.1 Changed 9087 bond radii > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-1.cxs"" > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-1.png"" width 938 height 879 supersample 3 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > transparency #2 60 cartoons > view p3 [Repeated 1 time(s)] > show #!1 models > hide #!1 models > view p3 > show #!1 models > hide #!1 models > view name p3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-2.png"" width 938 height 879 supersample 3 > transparency #2 80 cartoons > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-2.png"" width 938 height 879 supersample 3 > show #!1 models > view p2 > view p3 [Repeated 1 time(s)] > turn y -40 > turn y 40 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/side_view_1.cxs"" ——— End of log from Sun Jan 26 22:02:04 2025 ——— opened ChimeraX session > view p2 > view p1 > view p4 Expected an objects specifier or a view name or a keyword > view p4 Expected an objects specifier or a view name or a keyword > view p3 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > view name p4 [Repeated 1 time(s)] > turn y -30 > view p1 > undo > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > view p1 > undo > lighting shadows false > view p1 > undo > view p4 [Repeated 2 time(s)] > view p1 > view p3 > view p1 > turn y -15 > view p1 > undo > view p1-1 Expected an objects specifier or a view name or a keyword > view name p1-1 > view p4 > turn y -45 > view p1-1 > undo > view p1-1 > turn y 40 > view p4 > undo [Repeated 1 time(s)] > redo > view p4 > undo > view name p4-2 > view p4 > view p4-2 > view p3 > view p4 > view p3 > view p4 > view p1 > view p1-1 > turn y 45 > view p3 > view p4 > view p3 > view p4-1 Expected an objects specifier or a view name or a keyword > view p4-2 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p4-2.png"" width 938 height 879 supersample 3 > turn y -45 > turn y 40 > view p4 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p4.png"" width 938 height 879 supersample 3 > view p1 > view p1-1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p1-1.png"" width 938 height 879 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" ——— End of log from Sun Jan 26 22:19:26 2025 ——— opened ChimeraX session > volume #1 level 0.0526 > volume #1 level 0.06209 > volume #1 level 0.0526 > volume #1 level 0.04406 > volume #1 level 0.0526 > view p1-1 > undo > view p1-1 > undo > view p1-1 [Repeated 2 time(s)] > view p3 > ui tool show ""Side View"" > view p3 > hide #!1 models > show #!1 models > show #!2 models > select add #2 8933 atoms, 9087 bonds, 1108 residues, 1 model selected > select subtract #2 4 models selected > select add #2 8933 atoms, 9087 bonds, 1108 residues, 1 model selected > select subtract #2 4 models selected > hide #!1 models > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 113 atoms, 107 bonds, 13 residues, 1 model selected > graphics selection color black > graphics selection color green > graphics selection color black > view p4 > show #!1 models > hide #!2 models > show #!2 models > volume #1 level 0.0526 > volume #1 level 0.06311 > view p1-1 > volume #1 level 0.05341 > view p1-1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p1-1-2.png"" width 938 height 879 supersample 3 > view p4 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p4-2.png"" width 938 height 879 supersample 3 > hide #!2 models > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p4-2.png"" width 938 height 879 supersample 3 > view p1-1 > view p1 > view p1-1 > view p1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p1.png"" width 938 height 879 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" > view p5 Expected an objects specifier or a view name or a keyword > turn x 90 > view name p5 [Repeated 1 time(s)] > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/p5-top_view.png"" width 938 height 879 supersample 3 > volume #1 level 0.0526 [Repeated 1 time(s)] > view p5 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" ——— End of log from Sun Jan 26 22:49:43 2025 ——— opened ChimeraX session > lighting shadows true > lighting flat > lighting soft > graphics silhouettes false > graphics silhouettes true > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/p5-top_view-1.png"" width 1035 height 879 supersample 3 > view p4 > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p4-1.png"" width 1035 height 879 supersample 3 > view p1-1 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > lighting soft [Repeated 2 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > graphics silhouettes false > graphics silhouettes true > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p1-1_1.png"" width 1035 height 879 supersample 3 [Repeated 1 time(s)] > view p1 > lighting soft [Repeated 1 time(s)] > graphics silhouettes false > graphics silhouettes true > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p1.png"" width 1035 height 879 supersample 3 > view p4 > lighting soft [Repeated 2 time(s)] > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p4.png"" width 1035 height 879 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" > view p3 > show #!2 models > hide #!1 models > size stickRadius +.1 Changed 9087 bond radii > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-3.png"" width 1035 height 879 supersample 3 > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > transparency #2 0 cartoons > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 113 atoms, 107 bonds, 13 residues, 1 model selected > show sel atoms > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 113 atoms, 107 bonds, 13 residues, 1 model selected > show sel atoms > transparency #2 80 cartoons > graphics silhouettes false > lighting soft [Repeated 2 time(s)] > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic-stick-thick-3.png"" width 1035 height 879 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/interface-AB- > hydrophobic_1.cxs"" > view p5 > show #!1 models > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting flat > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > view p1-1 > lighting soft > view p5 > graphics silhouettes false > graphics silhouettes true > vew p1-1 Unknown command: vew p1-1 > view p1-1 > lighting soft [Repeated 2 time(s)] > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_mrc.cxs"" ——— End of log from Sun Jan 26 23:19:58 2025 ——— opened ChimeraX session > view p1-1 > view name p1 > turn y 45 > hide #!1 models > show #!1 models > hide #!2 models > view p1 > turn y 45 > view p3 > hide #!1 models > show #!2 models > show #!1 models > ui tool show ""Side View"" > hide #!2 models > view p3 > show #!2 models > hide #!1 models > view name p2-1 > view p2 > show #!1 models > hide #!1 models > show #!1 models > view name p2-2 > view p2 [Repeated 1 time(s)] > turn y -45 > view p1 > turn y 45 > select > #2/b:270|#2/b:261-262|#2/b:217-218|#2/b:179|#2/a:270|#2/a:261-262|#2/a:217-218|#2/a:179|#2/a:175 113 atoms, 107 bonds, 13 residues, 1 model selected > hide #!1 models > view > view sel > view p2 > show #!1 models > turn y -45 > view p1 > turn y 45 > hide #!1 models > view sel > view name p2-1 > show #!1 models > hide #!1 models > show #!1 models > turn y -45 > hide #!1 models > show #!1 models > hide #!2 models > view name p1 > turn y 45 > view name p2 > view p1 > turn x 90 > lighting soft [Repeated 2 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > view name p3 > view p2 > view sel > show #!2 models > hide #!1 models > view name p2-1 > show #!1 models > hide #!2 models > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/Overview.cxs"" > view p1 > lighting soft [Repeated 5 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > graphics silhouettes false > graphics silhouettes true > view name p1 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p1.png"" width 938 height 879 supersample 3 > turn y 45 > view name p2 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p2.png"" width 938 height 879 supersample 3 > view p3 > view name p3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera- > Image/Overview_p3-topview.png"" width 938 height 879 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/Overview.cxs"" ——— End of log from Mon Jan 27 14:41:44 2025 ——— opened ChimeraX session > view p1 > open /Users/liyanzhu/Downloads/cryosparc_P2_J77_004_volume_map.mrc Opened cryosparc_P2_J77_004_volume_map.mrc as #3, grid size 224,224,224, pixel 0.832, shown at level 0.0661, step 1, values float32 > open /Users/liyanzhu/Downloads/cryosparc_P2_J135_map_locres.mrc Opened cryosparc_P2_J135_map_locres.mrc as #4, grid size 224,224,224, pixel 0.832, shown at level 3.23, step 1, values float32 > hide #!1 models > hide #!4 models > ui tool show ""Surface Color"" > color sample #3.1 map #4 palette > 2,#0000ff:2.33,#00aaff:2.66,#00ffa9:3,#00ff00:3.33,#aaff00:3.66,#ffaa00:4,#ff0000 Map values for surface ""surface"": minimum 2.357, mean 2.615, maximum 3.303 > key blue:2.00 #00aaff:2.33 #00ffa9:2.66 lime:3.00 #aaff00:3.33 #ffaa00:3.66 > red:4.00 showTool true > ui mousemode right ""color key"" > key pos 0.77867,0.5034 size 0.0293152,0.253146 > show #!1 models > view p1 > select add #2 8933 atoms, 9087 bonds, 1108 residues, 1 model selected > select subtract #2 4 models selected > select add #3 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.96397,0.24652,0.099986,150.1,-0.064154,0.14934,-0.9867,183.29,-0.25817,-0.95756,-0.12814,225.38 > view matrix models > #3,-0.96602,0.23887,0.098691,151.14,-0.064051,0.14868,-0.98681,183.35,-0.2504,-0.9596,-0.12832,224.86 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.96602,0.23887,0.098691,145.11,-0.064051,0.14868,-0.98681,183.83,-0.2504,-0.9596,-0.12832,224.19 > view matrix models > #3,-0.96602,0.23887,0.098691,147.84,-0.064051,0.14868,-0.98681,183.67,-0.2504,-0.9596,-0.12832,222.34 > view matrix models > #3,-0.96602,0.23887,0.098691,157.82,-0.064051,0.14868,-0.98681,182.53,-0.2504,-0.9596,-0.12832,215.57 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.98553,0.065635,-0.15628,201.11,0.15561,-0.015247,-0.9877,177.42,-0.067211,-0.99773,0.0048132,188.82 > view matrix models > #3,-0.8518,0.52387,0.00075561,130.35,0.00788,0.014255,-0.99987,189.65,-0.52381,-0.85168,-0.01627,219.85 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.8518,0.52387,0.00075561,126.96,0.00788,0.014255,-0.99987,190.54,-0.52381,-0.85168,-0.01627,213.59 > view matrix models > #3,-0.8518,0.52387,0.00075561,122.41,0.00788,0.014255,-0.99987,190.63,-0.52381,-0.85168,-0.01627,213.93 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit map cryosparc_P2_J77_004_volume_map.mrc in map P2_J74_map_flipped_nosharp.mrc using 112355 points correlation = 0.999, correlation about mean = 0.9936, overlap = 2249 steps = 76, shift = 2.22, angle = 2.81 degrees Position of cryosparc_P2_J77_004_volume_map.mrc (#3) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation -0.46804955 0.88370223 -0.00005218 54.45417383 0.88370222 0.46804956 0.00012372 -32.78150145 0.00013375 0.00001180 -0.99999998 185.28762784 Axis -0.51572078 -0.85675672 -0.00004797 Axis point 37.08755750 0.00000000 92.64645560 Rotation angle (degrees) 179.99378296 Shift along axis -0.00626472 > view p1 > hide #!1 models > view matrix models > #3,-0.86002,0.50914,0.033906,114.11,-0.037083,0.0039095,-0.9993,194.77,-0.50892,-0.86068,0.015518,212.89 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.png"" > width 985 height 879 supersample 3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.cxs"" ——— End of log from Wed Jan 29 13:58:14 2025 ——— opened ChimeraX session > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J174_map_flipped_nosharp.mrc"" Opened P2_J174_map_flipped_nosharp.mrc as #6, grid size 224,224,224, pixel 0.832, shown at level 0.0255, step 1, values float32 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-36.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-36.pdb #7 --- Chain | Description A | No description available B C D | No description available 10 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/liyanzhu/Downloads/cryosparc_P2_J178_map_locres.mrc Opened cryosparc_P2_J178_map_locres.mrc as #8, grid size 224,224,224, pixel 0.832, shown at level 2.77, step 1, values float32 > hide #7 models > show #7 models > hide #7 models > view p1 > volume flip #8 Opened cryosparc_P2_J178_map_locres.mrc z flip as #9, grid size 224,224,224, pixel 0.832, shown at step 1, values float32 > close #8 > ui tool show ""Surface Color"" > color sample #6.1 map #9 palette > 2,#0000ff:2.33,#00aaff:2.66,#00ffa9:3,#00ff00:3.33,#aaff00:3.66,#ffaa00:4,#ff0000 Map values for surface ""surface"": minimum 0.1247, mean 2.481, maximum 3.159 Map values for surface ""cap near"": minimum 2.689, mean 2.761, maximum 2.922 > hide #!9 models > select add #6 3 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.99169,-0.086803,0.094912,0.68667,-0.10199,-0.081116,0.99147,24.839,-0.078364,-0.99292,-0.089295,193.66 > view matrix models > #6,0.93262,-0.34975,0.088862,31.215,-0.11896,-0.065481,0.99074,25.026,-0.34069,-0.93455,-0.10267,213.82 > view matrix models > #6,0.93792,-0.34345,-0.048382,41.956,0.013996,-0.1019,0.9947,15.69,-0.34656,-0.93363,-0.090768,213.25 > ui tool show ""Side View"" > view matrix models > #6,0.92429,-0.3662,0.10761,31.908,-0.10169,0.035484,0.99418,13.713,-0.36789,-0.92986,-0.0044427,207.45 > view matrix models > #6,0.82143,-0.57019,0.011748,68.76,-0.048041,-0.048654,0.99766,16.254,-0.56828,-0.82007,-0.067358,221.32 > view matrix models > #6,0.82588,-0.56302,0.030677,66.047,-0.049261,-0.017848,0.99863,13.414,-0.5617,-0.82625,-0.042475,219.14 > view matrix models > #6,0.83721,-0.54607,0.029765,63.49,-0.054485,-0.029131,0.99809,14.998,-0.54416,-0.83723,-0.054141,219.53 > view matrix models > #6,0.83839,-0.54453,0.024098,63.725,-0.047706,-0.029266,0.99843,14.35,-0.54297,-0.83823,-0.050513,219.2 > view matrix models > #6,0.84841,-0.52808,-0.036468,66.475,0.024323,-0.029929,0.99926,7.6286,-0.52877,-0.84867,-0.012547,215.58 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.84841,-0.52808,-0.036468,59.956,0.024323,-0.029929,0.99926,6.9834,-0.52877,-0.84867,-0.012547,219.46 > view matrix models > #6,0.84841,-0.52808,-0.036468,57.99,0.024323,-0.029929,0.99926,8.0521,-0.52877,-0.84867,-0.012547,216.59 > ui tool show ""Fit in Map"" > fitmap #6 inMap #1 Fit map P2_J174_map_flipped_nosharp.mrc in map P2_J74_map_flipped_nosharp.mrc using 112357 points correlation = 0.9985, correlation about mean = 0.9916, overlap = 949.3 steps = 120, shift = 8.58, angle = 0.565 degrees Position of P2_J174_map_flipped_nosharp.mrc (#6) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999862 0.00165371 -0.00017055 -0.12699015 -0.00165369 0.99999863 0.00011089 0.14531308 0.00017074 -0.00011060 0.99999997 -0.11813288 Axis -0.06646642 -0.10241739 -0.99251846 Axis point 94.67450911 72.41668611 0.00000000 Rotation angle (degrees) 0.09546420 Shift along axis 0.11080706 > fitmap #6 inMap #1 Fit map P2_J174_map_flipped_nosharp.mrc in map P2_J74_map_flipped_nosharp.mrc using 112357 points correlation = 0.9985, correlation about mean = 0.9917, overlap = 949.3 steps = 44, shift = 0.0224, angle = 0.00655 degrees Position of P2_J174_map_flipped_nosharp.mrc (#6) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999861 0.00166495 -0.00005916 -0.16008130 -0.00166494 0.99999861 0.00008806 0.14679624 0.00005931 -0.00008796 0.99999998 -0.10969143 Axis -0.05275353 -0.03550751 -0.99797609 Axis point 90.49523166 92.65251344 0.00000000 Rotation angle (degrees) 0.09558775 Shift along axis 0.11270191 > undo > view p1 > hide #!3 models > show #!1 models > view matrix models > #6,0.84841,-0.52808,-0.036468,66.787,0.024323,-0.029929,0.99926,7.6268,-0.52877,-0.84867,-0.012547,218.68 > view matrix models > #6,0.84841,-0.52808,-0.036468,65.694,0.024323,-0.029929,0.99926,7.6973,-0.52877,-0.84867,-0.012547,217.6 > fitmap #6 inMap #1 Fit map P2_J174_map_flipped_nosharp.mrc in map P2_J74_map_flipped_nosharp.mrc using 112357 points correlation = 0.9985, correlation about mean = 0.9917, overlap = 949.3 steps = 72, shift = 2.26, angle = 0.57 degrees Position of P2_J174_map_flipped_nosharp.mrc (#6) relative to P2_J74_map_flipped_nosharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999861 0.00166482 0.00007526 -0.16995416 -0.00166481 0.99999861 -0.00005945 0.15898106 -0.00007536 0.00005933 0.99999998 -0.11068197 Axis 0.03561515 0.04516166 -0.99834462 Axis point 92.37975471 104.55095468 0.00000000 Rotation angle (degrees) 0.09554496 Shift along axis 0.11162565 > hide #!1 models > view p1 > key blue:2.00 #00aaff:2.33 #00ffa9:2.66 lime:3.00 #aaff00:3.33 #ffaa00:3.66 > red:4.00 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > ui mousemode right 'color key' > key pos 0.795206,0.540049 size 0.0465094,0.267371 > key blue:2.00 #00aaff:2.33 #00ffa9:2.66 lime:3.00 #aaff00:3.33 #ffaa00:3.66 > red:4.00 showTool true > key fontSize 25 > key fontSize 26 > ui mousemode right ""color key"" > show #7 models > hide #7 models > close #7 > close #1 > close #2 > close #3 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.cxs"" > close #4 > save ""/Users/liyanzhu/Desktop/Galan Lab/InvE_SP/Chimera-Image/local_res.cxs"" ——— End of log from Mon Feb 3 16:57:41 2025 ——— opened ChimeraX session > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > ui tool show ""Surface Color"" > color single #6.1 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-36.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-36.pdb #1 --- Chain | Description A | No description available B C D | No description available 10 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui mousemode right ""rotate selected models"" > close #9 > close #5 > select add #6 3 models selected > view matrix models > #6,0.81695,-0.57576,-0.03297,73.543,0.0038903,-0.051667,0.99866,11.595,-0.57669,-0.81599,-0.039969,219.27 > undo > select subtract #6 Nothing selected > select add #1 9334 atoms, 9499 bonds, 1148 residues, 1 model selected > view matrix models > #1,0.91831,-0.38727,-0.082069,50.634,-0.017246,-0.24625,0.96905,33.887,-0.39549,-0.88847,-0.23281,225.48 > ui tool show ""Fit in Map"" > fitmap #1 inMap #6 Fit molecule P2_J73_map_flipped_nosharp-coot-36.pdb (#1) to map P2_J174_map_flipped_nosharp.mrc (#6) using 9334 atoms average map value = 0.05463, steps = 144 shifted from previous position = 0.604 rotated from previous position = 15.1 degrees atoms outside contour = 2140, contour level = 0.025469 Position of P2_J73_map_flipped_nosharp-coot-36.pdb (#1) relative to P2_J174_map_flipped_nosharp.mrc (#6) coordinates: Matrix rotation and translation 0.99999999 -0.00014252 -0.00005834 0.02670625 0.00014251 0.99999999 -0.00007736 -0.00783315 0.00005835 0.00007735 1.00000000 -0.01950950 Axis 0.44887923 -0.33857885 0.82696541 Axis point 58.53060814 192.08823093 0.00000000 Rotation angle (degrees) 0.00987411 Shift along axis -0.00149366 > color sel bychain > color zone #6 near sel & #1 distance 4.99 > lighting soft > select subtract #1 Nothing selected > select add #6 3 models selected > lighting soft > select subtract #6 Nothing selected > ui mousemode right zoom > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > view p1 > turn y 180 > ui tool show ""Side View"" > hide #1 models > show #1 models > hide #!6 models > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > show #!6 models > hide #1 models > show #1 models > hide #!6 models > lighting simple > graphics silhouettes false > lighting simple > lighting soft > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > show #!6 models > hide #!6 models > show #!6 models > hide #1 models > view #1 No displayed objects specified. > view #6 > turn y 180 > hide #!6 models > show #!6 models > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting simple > lighting soft > ui tool show ""Side View"" > show #1 models > hide #1 models > view name p1 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-32.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-32.pdb #2 --- Chain | Description A | No description available B C D | No description available 18 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #2 18910 atoms, 19075 bonds, 1148 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.78025,-0.60909,0.14217,64.817,0.15091,-0.037257,-0.98784,167.02,0.60699,0.79222,0.062849,-49.665 > close #2 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-30.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-30.pdb #2 --- Chain | Description A | No description available B C D | No description available 10 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #2 18438 atoms, 18603 bonds, 1148 residues, 1 model selected > view matrix models > #2,0.58535,-0.78332,-0.20923,129.11,-0.23243,0.085108,-0.96888,189.45,0.77675,0.61577,-0.13225,-32.323 > close #2 > open ""/Users/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-29.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-29.pdb #2 --- Chain | Description A | No description available B C D | No description available > select add #2 18090 atoms, 18251 bonds, 1108 residues, 1 model selected > view matrix models > #2,0.37087,-0.89771,0.23785,121.33,-0.27102,0.14034,0.95229,23.188,-0.88826,-0.41764,-0.19125,223.55 > view matrix models > #2,0.9576,0.14494,0.249,-30.811,-0.27797,0.23759,0.93074,16.681,0.075738,-0.96049,0.26781,144.62 > view matrix models > #2,0.88546,-0.30216,0.35307,8.3731,-0.22828,0.37895,0.89682,1.8743,-0.40477,-0.8747,0.26657,181.56 > view matrix models > #2,0.92256,0.14227,-0.35866,24.794,0.33634,0.15902,0.92822,-33.073,0.18909,-0.97697,0.09885,150.07 > view matrix models > #2,0.92004,0.16808,-0.35394,22.236,0.35263,0.038633,0.93497,-24.027,0.17083,-0.98502,-0.023727,163.02 > view matrix models > #2,0.93243,-0.061064,-0.35616,42.482,0.3491,0.40676,0.8442,-49.991,0.09332,-0.91149,0.40059,127.06 > view matrix models > #2,0.91515,0.11004,-0.38781,30.968,0.38697,0.02978,0.92161,-25.263,0.11297,-0.99348,-0.01533,168.48 > view matrix models > #2,0.92393,0.3579,-0.13512,-14.456,0.25944,-0.32663,0.90885,20.706,0.28114,-0.87477,-0.39464,174.33 > view matrix models > #2,0.91489,0.38729,0.11394,-37.686,0.071627,-0.43347,0.89831,49,0.3973,-0.8137,-0.42432,160.4 > view matrix models > #2,0.86353,0.2137,-0.45677,32.095,0.46825,-0.0035269,0.88359,-26.494,0.18721,-0.97689,-0.10311,167.55 > view matrix models > #2,0.91162,-0.37785,-0.16178,57.08,0.14549,-0.071496,0.98677,1.028,-0.38442,-0.9231,-0.010204,207.87 > ui tool show ""Fit in Map"" > fitmap #2 inMap #6 Fit molecule P2_J73_map_flipped_nosharp-coot-29.pdb (#2) to map P2_J174_map_flipped_nosharp.mrc (#6) using 18090 atoms average map value = 0.04209, steps = 108 shifted from previous position = 1.09 rotated from previous position = 11.6 degrees atoms outside contour = 6535, contour level = 0.025469 Position of P2_J73_map_flipped_nosharp-coot-29.pdb (#2) relative to P2_J174_map_flipped_nosharp.mrc (#6) coordinates: Matrix rotation and translation 0.99999838 -0.00179014 -0.00019667 0.16787808 0.00179023 0.99999831 0.00042909 -0.21809681 0.00019590 -0.00042944 0.99999989 0.12973477 Axis -0.23186240 -0.10602232 0.96695351 Axis point 115.43481350 107.87604664 0.00000000 Rotation angle (degrees) 0.10607560 Shift along axis 0.10964600 > view p1 > ui mousemode right zoom > select subtract #2 Nothing selected > hide #2 models > show #2 models > hide #!6 models > color #2 bychain > show #!6 models > hide #!6 models > save /Users/liyanzhu/Desktop/Screenshot-p1-cartoon-1.png width 973 height > 879 supersample 3 > show #!6 models > lighting soft > hide #!6 models > show #!6 models > hide #2 models > hide #!6 models > show #2 models > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting soft > show #!6 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > turn x 90 > hide #!6 models > show #!6 models > view p1 > turn x 90 > hide #2 models > ui tool show ""Side View"" > hide #!6 models > show #2 models > hide #2 models > show #!6 models > show #2 models > hide #!6 models > show #!6 models > volume zone #6 nearAtoms #2/B,A range 2.5 > hide #2 models > color zone #6 near #2/B,A distance 2.5 > volume zone #6 nearAtoms #2/B,A range 2.9 > select ~sel & ##selected Nothing selected > volume zone #6 nearAtoms #2/B,A range 3 > color zone #6 near #2/B,A distance 3 > view p2 > surface dust #6 size 8.32 > volume zone #6 nearAtoms #2/B,A range 3 > color zone #6 near #2/B,A distance 3 > color zone #6 near #2/B,A distance 3.5 > volume zone #6 nearAtoms #2/B,A range 3.5 > volume zone #6 nearAtoms #2/B,A range 3.2 > volume zone #6 nearAtoms #2/B,A range 3.3 > volume zone #6 nearAtoms #2/B,A range 3.2 > volume #6 level 0.02616 > volume zone #6 nearAtoms #2/B,A range 3 > volume zone #6 nearAtoms #2/B,A range 3.1 > volume #6 level 0.0272 > volume #6 level 0.02651 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet 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/liyanzhu/Library/CloudStorage/OneDrive-Personal/Desktop/Galan > Lab/InvE_SP/Model_building_Mac/P2_J73_map_flipped_nosharp-coot-36.pdb"" Chain information for P2_J73_map_flipped_nosharp-coot-36.pdb #1 --- Chain | Description A | No description available B C D | No description available 10 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 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 Air Model Identifier: Mac14,15 Model Number: Z18S000LPLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 13 days, 14 hours, 47 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 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 Display Resolution: 2880 x 1864 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 babel: 2.16.0 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-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-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 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 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 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 packaging: 23.2 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 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 tornado: 6.4.2 traitlets: 5.14.3 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-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX