id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17512 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-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. 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""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so"", ""name"" : ""_mmcif.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 12958515200, ""size"" : 32768, ""uuid"" : ""a55a4181-c446-3fa3-8fd6-27f845527eab"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so"", ""name"" : ""_psutil_osx.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 12962267136, ""size"" : 16384, ""uuid"" : ""a516c5bc-1157-318a-a306-5c9b350e0c09"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so"", ""name"" : ""_psutil_posix.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13017677824, ""size"" : 81920, ""uuid"" : ""d7bd530c-3353-37a6-b81f-ee3179d65811"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so"", ""name"" : ""_version.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13019103232, ""size"" : 180224, ""uuid"" : ""87eed069-25fc-30f6-aa30-1e54859d92e2"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so"", ""name"" : ""_frame.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13025984512, ""size"" : 131072, ""uuid"" : ""c1a3c2d3-b21b-3231-839d-fcbc83ca2028"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so"", ""name"" : ""_serialize.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13030309888, ""size"" : 131072, ""uuid"" : ""650aead6-ce16-39bb-9ba1-4bf9986b96d6"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so"", ""name"" : ""_cmsgpack.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 6160498688, ""size"" : 32768, ""uuid"" : ""8abbdcef-1901-3d4b-9e6b-a38214b79214"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so"", ""name"" : ""_imagingmath.cpython-311-darwin.so"" }, { 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""base"" : 6519222272, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 21564928, ""uuid"" : ""1d6df541-4a74-3a0e-8a8f-15aee6f93da9"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2575.50.27"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6451429376, ""size"" : 633476, ""uuid"" : ""aca43a8d-6369-3a2c-af92-3d4c458523d6"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6455705600, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5500928, ""uuid"" : ""39e0f63a-3ab8-39e9-97f8-333cde9a7ba4"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""3423"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6475669504, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14676544, ""uuid"" : ""5ab66e9b-19c0-3fe8-9793-d5156d1c7050"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3423"" } ], ""sharedCache"" : { ""base"" : 6450593792, ""size"" : 5020123136, ""uuid"" : ""bb86a9b4-8362-37b8-b028-212703af6f30"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=6.0G written=67.8M(1%) resident=3020K(0%) swapped_out=64.8M(1%) unallocated=5.9G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 1376K 62 \nColorSync 704K 38 \nCoreAnimation 3280K 177 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 6832K 59 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 5.2G 135 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 42 \nStack 194.4M 42 \nVM_ALLOCATE 348.6M 257 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 5486K 695 \n__AUTH_CONST 77.2M 942 \n__CTF 824 1 \n__DATA 34.0M 1081 \n__DATA_CONST 36.8M 1100 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 651.3M 153 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1117 \n__TEXT (graphics) 688K 3 \n__TPRO_CONST 128K 2 \ndyld private memory 2976K 26 \nmapped file 656.6M 125 \npage table in kernel 3020K 1 \nshared memory 3168K 26 \n=========== ======= ======= \nTOTAL 8.8G 6469 \nTOTAL, minus reserved VM space 8.6G 6469 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""2802c4ea3f497f76a06aa4827277de4f97bac481"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ { ""treatmentId"" : ""d7ff00dd-1c5a-4dbb-85d6-7a936d671384"", ""experimentId"" : ""67f46bbc84eaf455d73c6098"", ""deploymentId"" : 400000001 } ] } } Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/minggu/Library/CloudStorage/GoogleDrive- > mgumoon@gmail.com/.shortcut-targets-by- > id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaF.cxs Opened 20250417_qcr_caa3_composite.mrc as #2, grid size 360,360,360, pixel 0.825, shown at level 0.0799, step 1, values float32 Log from Tue Apr 29 10:13:06 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/minggu/Library/CloudStorage/GoogleDrive- > mgumoon@gmail.com/.shortcut-targets-by- > id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Composite/250424_qcrABC_Caa3_composite.pdb Chain information for 250424_qcrABC_Caa3_composite.pdb #1 --- Chain | Description A | No description available B b | No description available C c | No description available D d | No description available E e | No description available F f | No description available G g | No description available H h | No description available I i | No description available J | No description available K | No description available L | No description available M | No description available N | No description available a | No description available > open /Users/minggu/Library/CloudStorage/GoogleDrive- > mgumoon@gmail.com/.shortcut-targets-by- > id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Composite/20250417_qcr_caa3_composite.mrc Opened 20250417_qcr_caa3_composite.mrc as #2, grid size 360,360,360, pixel 0.825, shown at level 0.0799, step 2, values float32 > volume #2 step 1 > set bgColor white > open /Users/minggu/Library/CloudStorage/GoogleDrive- > mgumoon@gmail.com/.shortcut-targets-by- > id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Global/250424_qcrABC_Caa3_J190_G02.pdb Chain information for 250424_qcrABC_Caa3_J190_G02.pdb #3 --- Chain | Description A | No description available B b | No description available C | No description available D d | No description available E e | No description available F f | No description available G g | No description available H h | No description available I i | No description available J | No description available K | No description available L | No description available M | No description available N | No description available a | No description available c | No description available > open ""/Users/minggu/Library/CloudStorage/GoogleDrive- > mgumoon@gmail.com/.shortcut-targets-by- > id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Global/G02_P39_J190_BC1_Caa3_R > (1).mrc"" Opened G02_P39_J190_BC1_Caa3_R (1).mrc as #4, grid size 360,360,360, pixel 0.825, shown at level 0.0576, step 2, values float32 > volume #4 step 1 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > select #1/A,a 2593 atoms, 2665 bonds, 11 pseudobonds, 324 residues, 2 models selected > show #!1 models > hide sel atoms > show sel atoms > select add #1 27762 atoms, 28527 bonds, 76 pseudobonds, 3381 residues, 2 models selected > hide sel atoms > show sel cartoons > hide sel cartoons > show #!3 models > select add #3 55151 atoms, 56680 bonds, 153 pseudobonds, 6715 residues, 4 models selected > hide #!1 models > select subtract #1 27389 atoms, 28153 bonds, 77 pseudobonds, 3334 residues, 2 models selected > hide sel atoms > show #!1 models > hide #!3 models > select subtract #3 Nothing selected > select add #1 27762 atoms, 28527 bonds, 76 pseudobonds, 3381 residues, 2 models selected > select #1/A,a 2593 atoms, 2665 bonds, 11 pseudobonds, 324 residues, 2 models selected > show sel cartoons > volume #2 style mesh > ui tool show ""Surface Zone"" > show sel atoms > style sel stick Changed 2593 atom styles > color (#!1 & sel) byhetero > surface zone #2 nearAtoms sel distance 2 > show #!2 models > select add #1 27762 atoms, 28527 bonds, 76 pseudobonds, 3381 residues, 2 models selected > hide sel atoms > show cartoons > color /A/a orange > color /B/b forest green > color /C/c orange red > color /D/d blue > color /E/e yellow > color /G/g dark goldenrod > color /H/h medium slate blue > color /I/i olive > color /J teal > color /F/f dim gray > color /K cornflower blue > color /L light pink > color /M spring green > color /N salmon > select #1/A,a 2593 atoms, 2665 bonds, 11 pseudobonds, 324 residues, 2 models selected > select #1 & ~sel 25169 atoms, 25862 bonds, 65 pseudobonds, 3057 residues, 2 models selected > hide sel cartoons > ui mousemode right select Drag select of 321 residues, 2 20250417_qcr_caa3_composite.mrc > hide sel cartoons > undo > hide sel cartoons > select clear > select #1/A:9-37 227 atoms, 231 bonds, 29 residues, 1 model selected > show sel > show sel cartoons > surface zone #2 nearAtoms sel distance 2 > color sel byhetero > lighting soft [Repeated 1 time(s)] > lighting full > label sel text ""/{0.chain_id} {0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1.5 > label height 1 > hide #1.2 models > select clear > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrA.cxs"" > includeMaps true > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"" > width 936 height 739 supersample 4 > volume subdivideSurface true > volume surfaceSmoothing true > color #2 #d6d6d6ff models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"" > width 936 height 739 supersample 4 > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrA.cxs"" > includeMaps true > color #2 silver models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrA.cxs"" > includeMaps true > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"" > width 936 height 739 supersample 4 > lighting soft > lighting full > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA-2.png"" > width 936 height 739 supersample 4 > color #2 #d6d6d6ff models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"" > width 936 height 739 supersample 4 > lighting soft > color #2 darkgrey models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA_soft.png"" > width 936 height 739 supersample 4 > subdivideSurface true subdivisionLevels 2 Unknown command: subdivideSurface true subdivisionLevels 2 > volume subdivideSurface true subdivisionLevels 2 > volume subdivideSurface true subdivisionLevels 1 > volume subdivideSurface true subdivisionLevels 1.5 Invalid ""subdivisionLevels"" argument: Expected an integer > volume subdivideSurface true subdivisionLevels 0 > volume subdivideSurface true subdivisionLevels 1 > volume subdivideSurface true subdivisionLevels 2 > volume subdivideSurface true subdivisionLevels 1 [Repeated 1 time(s)] > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA_soft-2.png"" > width 936 height 739 supersample 4 > show #1.2 models > lighting simple > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting soft Drag select of 138 atoms, 29 residues, 117 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel cartoons > hide sel atoms > select clear > close #3 > close #4 > select #1/B,b 4058 atoms, 4200 bonds, 28 pseudobonds, 458 residues, 2 models selected > show sel > hide sel atoms > show sel cartoons > surface zone #2 nearAtoms sel distance 2 > surface zone #2 nearAtoms sel distance 1.84 > surface zone #2 nearAtoms sel distance 1.49 [Repeated 1 time(s)] > surface zone #2 nearAtoms sel distance 1.39 > surface zone #2 nearAtoms sel distance 1.49 > surface zone #2 nearAtoms sel distance 1.59 > surface zone #2 nearAtoms sel distance 1.69 > show sel atoms > style sel stick Changed 4058 atom styles > color (#!1 & sel) byhetero > select clear > select #1/B,b 4058 atoms, 4200 bonds, 28 pseudobonds, 458 residues, 2 models selected > hide sel cartoons > hide sel atoms > undo > hide sel atoms > select #1/B:23-64 331 atoms, 343 bonds, 42 residues, 1 model selected > show sel cartoons > show sel atoms > select #1/B:23 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > hide sel atoms > select #1/B:24-64 326 atoms, 338 bonds, 41 residues, 1 model selected > surface zone #2 nearAtoms sel distance 1.69 > surface zone #2 nearAtoms sel distance 1.79 > surface zone #2 nearAtoms sel distance 1.89 > surface zone #2 nearAtoms sel distance 1.99 > surface zone #2 nearAtoms sel distance 2.09 > surface zone #2 nearAtoms sel distance 2.19 > surface zone #2 nearAtoms sel distance 2.29 > surface zone #2 nearAtoms sel distance 2.19 > surface zone #2 nearAtoms sel distance 2.09 > surface zone #2 nearAtoms sel distance 1.99 > surface zone #2 nearAtoms sel distance 1.89 > surface zone #2 nearAtoms sel distance 2 [Repeated 1 time(s)] > select clear > lighting full > lighting soft > color #2 #d6d6d6ff models > color #2 #ebebebff models > color #2 #d6d6d6ff models > color #2 #ebebebff models > color #2 silver models > select #2 2 models selected > select clear > color #2 #d6d6d6ff models > color #2 white models > color #2 #ebebebff models > color #2 #d6d6d6ff models > hide #!2 models > show #!2 models > hide #!2 models Drag select of 202 atoms, 41 residues, 177 bonds > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > label height 1 > show #!2 models > color #2 silver models > select clear > color #2 #76d6ffff models > color #2 #00fdffff models > color #2 #00f900ff models > color #2 #00fa92ff models > color #2 #7a81ffff models > color #2 #919191ff models > color #2 #929292ff models > color #2 silver models > color #2 darkgrey models > color #2 silver models > hide #1.2 models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrB.png"" > width 936 height 739 supersample 4 > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrB.cxs"" > includeMaps true > volume #2 showOutlineBox true > show #1.2 models Drag select of 202 atoms, 41 residues, 177 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel cartoons > hide sel atoms > select clear > select #1/C,c 4232 atoms, 4345 bonds, 9 pseudobonds, 516 residues, 2 models selected > show sel cartoons > show sel atoms > style sel stick Changed 4232 atom styles > color (#!1 & sel) byhetero > surface zone #2 nearAtoms sel distance 2 > hide sel cartoons > hide sel atoms > select #1/C:36-65 248 atoms, 258 bonds, 30 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #2 nearAtoms sel distance 2 > select clear > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrC.cxs"" > includeMaps true Drag select of 158 atoms, 30 residues, 141 bonds, 2 20250417_qcr_caa3_composite.mrc > show sel atoms > color (#!1 & sel) byhetero > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1 > select clear > hide #1.2 models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrC.png"" > width 936 height 739 supersample 4 > show #1.2 models Drag select of 158 atoms, 30 residues, 141 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel atoms > hide sel cartoons > select clear > select #1/N 2694 atoms, 2752 bonds, 7 pseudobonds, 337 residues, 2 models selected > show sel > hide sel atoms > show sel cartoons > show sel atoms > style sel stick Changed 2694 atom styles > color (#!1 & sel) byhetero > surface zone #2 nearAtoms sel distance 2 > hide sel cartoons > hide sel atoms > select #1/N:85-116 260 atoms, 265 bonds, 32 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #2 nearAtoms sel distance 2 > select clear Drag select of 166 atoms, 32 residues, 140 bonds, 2 20250417_qcr_caa3_composite.mrc > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1 > select clear > hide #1.2 models > select #1/N:85-116 260 atoms, 265 bonds, 32 residues, 1 model selected > surface zone #2 nearAtoms sel distance 1 > surface zone #2 nearAtoms sel distance 1.9 [Repeated 1 time(s)] > surface zone #2 nearAtoms sel distance 1 > surface zone #2 nearAtoms sel distance 1.8 [Repeated 1 time(s)] > surface zone #2 nearAtoms sel distance 1 > surface zone #2 nearAtoms sel distance 1.7 > surface zone #2 nearAtoms sel distance 1 > surface zone #2 nearAtoms sel distance 2 [Repeated 1 time(s)] > select clear No atoms selected for zoning [Repeated 1 time(s)] > select #1/N:85-116 260 atoms, 265 bonds, 32 residues, 1 model selected > surface zone #2 nearAtoms sel distance 1.9 > surface zone #2 nearAtoms sel distance 1.8 > surface zone #2 nearAtoms sel distance 1.7 > surface zone #2 nearAtoms sel distance 1.8 > surface zone #2 nearAtoms sel distance 1.9 > surface zone #2 nearAtoms sel distance 2 > surface zone #2 nearAtoms sel distance 2.1 > surface zone #2 nearAtoms sel distance 2.2 > select clear > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_CtaC.png"" > width 936 height 739 supersample 4 > select clear > ui mousemode right ""translate selected models"" > ui mousemode right zoom > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaC.cxs"" > includeMaps true > show #1.2 models > select #1/M 4965 atoms, 5133 bonds, 15 pseudobonds, 608 residues, 2 models selected > ui mousemode right select Drag select of 166 atoms, 32 residues, 140 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel atoms > hide sel cartoons > select clear > select #1/M 4965 atoms, 5133 bonds, 15 pseudobonds, 608 residues, 2 models selected > show sel cartoons > ui mousemode right zoom > show sel atoms > style sel stick Changed 4965 atom styles > color (#!1 & sel) byhetero > surface zone #2 nearAtoms sel distance 2.2 > select clear > ui tool show ""Side View"" > ui mousemode right select Drag select of 3124 atoms, 603 residues, 15 pseudobonds, 2752 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel atoms > hide sel cartoons > select clear > select #1/M:25-52 220 atoms, 224 bonds, 28 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #2 nearAtoms sel distance 2.2 Drag select of 47 atoms, 13 residues, 40 bonds, 2 20250417_qcr_caa3_composite.mrc > select clear > ui mousemode right zoom No atoms selected for zoning [Repeated 3 time(s)] > select #1/M:25-52 220 atoms, 224 bonds, 28 residues, 1 model selected > surface zone #2 nearAtoms sel distance 2 > select clear > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaD.cxs"" > includeMaps true > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_CtaD.png"" > width 936 height 739 supersample 4 > ui mousemode right select Drag select of 132 atoms, 28 residues, 113 bonds, 2 20250417_qcr_caa3_composite.mrc > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1 > select clear > ui mousemode right zoom > ui mousemode right select Drag select of 132 atoms, 28 residues, 113 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel atoms > hide sel cartoons > select clear [Repeated 1 time(s)] > select #1/L 1845 atoms, 1894 bonds, 209 residues, 1 model selected > show sel cartoons > select clear > select #1/L 1845 atoms, 1894 bonds, 209 residues, 1 model selected > show sel atoms > style sel stick Changed 1845 atom styles > color sel byhetero > ui mousemode right zoom > surface zone #2 nearAtoms sel distance 2 > select clear > select #1/L:175-206 273 atoms, 285 bonds, 32 residues, 1 model selected > select #1/L 1845 atoms, 1894 bonds, 209 residues, 1 model selected > hide sel atoms > show sel cartoons > hide sel cartoons > select #1/L:175-206 273 atoms, 285 bonds, 32 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #2 nearAtoms sel distance 2 > select clear > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_CtaE.png"" > width 936 height 739 supersample 4 > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaE.cxs"" > includeMaps true > ui mousemode right select Drag select of 177 atoms, 32 residues, 159 bonds, 2 20250417_qcr_caa3_composite.mrc > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1 > select clear Drag select of 177 atoms, 32 residues, 159 bonds, 2 20250417_qcr_caa3_composite.mrc > hide sel atoms > hide sel cartoons > select clear > select #1/K 1045 atoms, 1069 bonds, 112 residues, 1 model selected > show sel cartoons > ui mousemode right zoom > show sel atoms > style sel stick Changed 1045 atom styles > color sel byhetero > surface zone #2 nearAtoms sel distance 2 > hide sel atoms > hide sel cartoons > select #1/K:52-101 409 atoms, 424 bonds, 50 residues, 1 model selected > surface zone #2 nearAtoms sel distance 2 > show sel cartoons > show sel atoms > undo [Repeated 3 time(s)] > hide sel atoms > hide sel cartoons > select #1/K:52-110 492 atoms, 512 bonds, 59 residues, 1 model selected > surface zone #2 nearAtoms sel distance 2 > show sel cartoons > show sel atoms > select clear > select #1/K:83-110 231 atoms, 241 bonds, 28 residues, 1 model selected > undo [Repeated 4 time(s)] > redo > show sel atoms > undo [Repeated 1 time(s)] > select #1/K:83-110 231 atoms, 241 bonds, 28 residues, 1 model selected > surface zone #2 nearAtoms sel distance 2 > show sel cartoons > show sel atoms > select clear > select #1/K:83-110 231 atoms, 241 bonds, 28 residues, 1 model selected > surface zone #2 nearAtoms sel distance 1.9 > surface zone #2 nearAtoms sel distance 1.8 > surface zone #2 nearAtoms sel distance 1.9 > surface zone #2 nearAtoms sel distance 2 > surface zone #2 nearAtoms sel distance 2.1 > surface zone #2 nearAtoms sel distance 2.2 > surface zone #2 nearAtoms sel distance 2.3 > surface zone #2 nearAtoms sel distance 2 [Repeated 1 time(s)] > select clear > select #1/K:83-110 231 atoms, 241 bonds, 28 residues, 1 model selected > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > label height 1 > select clear > hide #1.2 models > save ""/Users/minggu/Google Drive/My > Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaF.cxs"" > includeMaps true ——— End of log from Tue Apr 29 10:13:06 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: Mac14,9 Model Number: MPHF3LL/A Chip: Apple M2 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 11 days, 16 hours, 41 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 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 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: 3.10.0 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: 2.2.1 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 plotly: 5.24.1 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 pyKVFinder: 0.7.2 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 tenacity: 9.0.0 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 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