id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17671 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.3-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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: { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""89899d2f53ae54f79a95ce4e2faa9b03fb28a5ca"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000032 }, { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""6647f0f7b6a75d3dc32993e7"" }, ""deploymentId"" : 240000042 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet > camera ortho > cofr centerOfView > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136; > movie encode ~/Desktop/rock_movie.mp4; stop > alias roll_movie cofr showpivot false; movie record; roll y 1 360; wait 420; > movie encode ~/Desktop/roll_movie.mp4; stop 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/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > alignment-with-VAVC.cxs Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 opened ChimeraX session > hide #!42 models > hide #!43 models > hide #!44 models > hide #!45 models > show #!36 models > hide #!36 models > show #!36 models > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- > sure.pdb Summary of feedback from opening /Users/hemaozhou/Library/CloudStorage/OneDrive- 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- sure.pdb --- warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0 Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a 180 0 Chain information for A35R-17H1_local_Final_renumber-sure.pdb #46 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide #46#!36 atoms > show #46#!36 cartoons > hide #!36 models > hide #46 models > show #46 models > hide #46 models > show #46 models > show #35 models > hide #46 models > show #46 models > hide #46 models > show #46 models > hide #46 models > hide #35 models > show #34 models > hide #34 models > show #35 models > show #34 models > hide #35 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > hide #34 models > show #34 models > show #35 models > hide #34 models > close #46#37-45 > combine #35 > rename #37 HCDR1 > rename #38 HCDR2 > rename #39 HCDR3 > rename #40 LCDR1 > rename #41 LCDR2 > rename #42 LCDR3 > hide #37-42 target m > hide #35 models > show #37 models > select #37/H:45-52 67 atoms, 69 bonds, 8 residues, 1 model selected > select ~sel & ## selected 2318 atoms, 2374 bonds, 297 residues, 1 model selected > delete sel > show #37 > hide #!37 cartoons > color byhetero > hide #37 atoms > show #37 atoms > style #37 stick Changed 67 atom styles > show #38 models > select #38/H:70-77 58 atoms, 59 bonds, 8 residues, 1 model selected > select ~sel & ## selected 2327 atoms, 2384 bonds, 297 residues, 1 model selected > delete sel > show #38 > hide #!38 cartoons > color byhetero > style #37-38 stick Changed 125 atom styles > select #39/H:116-123 66 atoms, 66 bonds, 8 residues, 1 model selected > select ~sel & ## selected 2319 atoms, 2377 bonds, 297 residues, 1 model selected > delete sel > show #39 > hide #!39 cartoons > color byhetero > style #37-38 stick Changed 125 atom styles > show #39 models > style #37-39 stick Changed 191 atom styles > select #40/L:46-51 51 atoms, 51 bonds, 6 residues, 1 model selected > select ~sel & ## selected 2334 atoms, 2392 bonds, 299 residues, 1 model selected > delete sel > show #40 > hide #!40 cartoons > color byhetero > select #40/L:46-51 51 atoms, 51 bonds, 6 residues, 1 model selected > select ~sel & ## selected Nothing selected > delete sel > show #40 > hide #!40 cartoons > color byhetero > show #40 models > hide #39 models > hide #38 models > hide #37 models > style #40 stick Changed 51 atom styles > show #41 models > hide #40 models > select #41/L:69-71 24 atoms, 23 bonds, 3 residues, 1 model selected > select ~sel & ## selected 2361 atoms, 2420 bonds, 302 residues, 1 model selected > delete sel > show #41 > hide #!41 cartoons > color byhetero > style #41 stick Changed 24 atom styles > hide #41 models > show #42 models > select #42/L:108-116 83 atoms, 86 bonds, 9 residues, 1 model selected > select ~sel & ## selected 2302 atoms, 2357 bonds, 296 residues, 1 model selected > delete sel > show #42 > hide #!42 cartoons > color byhetero > style #42 stick Changed 83 atom styles > hide #42 models > show #37 models > hide #37 models > show #35 models > combine #35 > hide #35 models > select #43/A:118-128 77 atoms, 77 bonds, 11 residues, 1 model selected > select ~sel & ##selected 2308 atoms, 2366 bonds, 294 residues, 1 model selected > delete sel > show #43 atoms > hide #43 cartoons > style #43 stick Changed 77 atom styles > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #44, grid size 300,300,300, pixel 1.2, shown at level 0.0147, step 1, values float32 > volume #44 level 6.911 > volume zone #44 nearAtoms #37 range 2.5 > hide #43 models > show #37 models > volume #44 style mesh > volume #44 level 6.762 > volume #44 level 6.194 > volume #44 level 6.493 > view name HCDR1-map > save /Users/hemaozhou/Desktop/HCDR1-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > hide #!44 models > show #!44 models > show #38 models > hide #37 models > volume zone #44 nearAtoms #38 range 2.5 > hide #38 models > show #38 models > combine #35 > close #38 > combine #35 > rename #38 HCDR2 > close #45 > select #38/H:69-77 70 atoms, 72 bonds, 9 residues, 1 model selected > select ~sel & ## selected 2315 atoms, 2371 bonds, 296 residues, 1 model selected > delete sel > show #38 > hide #!38 cartoons > color byhetero > style #38 stick Changed 70 atom styles > volume zone #44 nearAtoms #38 range 2.5 > volume #44 level 6.075 > volume #44 level 6.433 > volume #44 level 6.612 > volume #44 level 6.2 > view name HCDR2-map > save /Users/hemaozhou/Desktop/HCDR2-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > hide #38 models > show #39 models > volume zone #44 nearAtoms #39 range 2.5 > volume #44 level 3.931 > volume #44 level 5.722 > volume #44 level 6.021 > volume #44 level 6.319 > volume #44 level 6.2 > view name HCDR3-map > save /Users/hemaozhou/Desktop/HCDR3-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > volume zone #44 nearAtoms #40 range 2.5 > show #40 models > hide #39 models > volume #44 level 6.1 > save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > view name LCDR1-map > save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > hide #40 models > show #41 models > volume zone #44 nearAtoms #41 range 2.5 > volume #44 level 5.8 > volume #44 level 5.5 > volume #44 level 5.8 > view name LCDR2-map > save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > close #41 > combine #35 > select #41/L:69-71 24 atoms, 23 bonds, 3 residues, 1 model selected > select ~sel & ## selected 2361 atoms, 2420 bonds, 302 residues, 1 model selected > delete sel > show #41 > hide #!41 cartoons > color byhetero > style #41 stick Changed 24 atom styles > close #41 > combine #35 > select #41/L:68-72 47 atoms, 47 bonds, 5 residues, 1 model selected > select ~sel & ## selected 2338 atoms, 2396 bonds, 300 residues, 1 model selected > delete sel > show #41 > hide #!41 cartoons > color byhetero > style #41 stick Changed 47 atom styles > volume zone #44 nearAtoms #41 range 2.5 > volume #44 level 6.039 > volume #44 level 5.8 > save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > view name LCDR2-map > hide #41 models > show #42 models > volume zone #44 nearAtoms #42 range 2.5 > volume #44 level 6.2 > view name LCDR3-map > save /Users/hemaozhou/Desktop/LCDR3-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Density- > map.cxs > hide #42 models > show #43 models > volume zone #44 nearAtoms #43 range 2.5 > combine #35 > select #45/A:115-127 101 atoms, 102 bonds, 13 residues, 1 model selected > hide #43 models > show #43 models > hide #45 models > show #45 models > hide #43 models > select #45/A:116-127 93 atoms, 94 bonds, 12 residues, 1 model selected > select #45/A:116-128 98 atoms, 99 bonds, 13 residues, 1 model selected > select ~sel & ##selected 2287 atoms, 2344 bonds, 292 residues, 1 model selected > delete sel > hide #45 atoms > show #45 atoms > style #45 stick Changed 98 atom styles > hide #45 cartoons > volume zone #44 nearAtoms #45 range 2.5 > ui tool show ""Side View"" > save /Users/hemaozhou/Desktop/A35R-116-128-map-new.tiff width 2794 height > 2576 supersample 4 transparentBackground true > volume #44 level 6.5 > volume #44 level 6.4 > volume #44 level 6.3 > save /Users/hemaozhou/Desktop/A35R-116-128-map-new.tiff width 2794 height > 2576 supersample 4 transparentBackground true > close #43 > rename #45 A35R-116-128 > combine #35 > hide #45 models > select #43/A:168 8 atoms, 7 bonds, 1 residue, 1 model selected > show #29 models > hide #29 models > show #28 models > hide #28 models > show #28 models > hide #28 models > show #28 models > hide #28 models > show #28 models > hide #28 models > show #40 models > hide #40 models > show #25 models > show #!26 models > show #27 models > show #28 models > hide #!44 models > hide #43 models > hide #28 models > show #!24 models > hide #27 models > hide #!26 models > show #!26 models > show #43 models > hide #43 models > show #43 models > hide #!26 models > show #!26 models > hide #25 models > show #25 models > hide #!24 models > show #!24 models > hide #!26 models > show #!26 models > hide #25 models > show #25 models > hide #25 models > show #25 models > hide #25 models > select #43/A:170 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #43/A:173 17 atoms, 15 bonds, 2 residues, 1 model selected > hide #43 models > show #43 models > hide #!24 models > hide #!26 models > select #43/A:169-174 45 atoms, 44 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 45 atom styles > hide sel cartoons > select ~sel & ##selected 2340 atoms, 2399 bonds, 299 residues, 1 model selected > delete sel > volume zone #44 nearAtoms #43 range 2.5 > show #!44 models > volume #44 level 4.748 > volume #44 level 4.807 > select #43/A:169@N 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > delete sel > volume zone #44 nearAtoms #43 range 2.5 > volume #44 level 5.046 > volume #44 level 4.986 > volume #44 level 4.927 > view name Missing or invalid ""name"" argument: Expected a text string > view list Named views: HCDR1, HCDR1-2, HCDR1-map, HCDR2, HCDR2-map, HCDR3, HCDR3-map, LCDR, LCDR1-map, LCDR2-map, LCDR3-map, Light-footprint, global-rotate90, global-view > view HCDR1-map > save /Users/hemaozhou/Desktop/A35R-170-174-map-new.tiff width 2794 height > 2576 supersample 4 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Density- > map.cxs Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #44, grid size 300,300,300, pixel 1.2, shown at level 6.2, step 1, values float32 Log from Wed May 14 15:05:00 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > alignment-with-VAVC.cxs Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Log from Tue May 13 23:18:00 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > align-analysis.cxs Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Log from Wed Apr 30 15:18:22 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Light- > footprint.cxs format session Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Log from Tue Apr 22 15:10:46 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/LCDR.cxs > format session Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Log from Tue Apr 22 09:51:42 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR3.cxs Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Log from Mon Apr 21 09:13:57 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > global.cxs format session Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #13, grid size 300,300,300, pixel 1.2, shown at level 6.91, step 1, values float32 Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #14, grid size 300,300,300, pixel 1.2, shown at level 4.14, step 1, values float32 Log from Thu Apr 17 14:20:34 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > global.cxs Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32 Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #13, grid size 300,300,300, pixel 1.2, shown at level 6.91, step 1, values float32 Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #14, grid size 300,300,300, pixel 1.2, shown at level 4.14, step 1, values float32 Opened cryosparc_P23_J197_003_volume_map_sharp (1).mrc as #15, grid size 300,300,300, pixel 1.2, shown at level 0.287, step 1, values float32 Log from Wed Apr 16 23:10:21 2025 Startup Messages --- note | available bundle cache has not been initialized yet > camera ortho > cofr centerOfView > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136; > movie encode ~/Desktop/rock_movie.mp4; stop > alias roll_movie cofr showpivot false; movie record; roll y 1 360; wait 420; > movie encode ~/Desktop/roll_movie.mp4; stop 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/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 0.0231, step 1, values float32 > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final.pdb Chain information for A35R-17H1_global_Final.pdb #2 --- Chain | Description A a | No description available H h | No description available L l | No description available > volume #1 level 1.575 > set bgColor white > hide atoms > show cartoons > hide #!1 models > show #!1 models > hide #!1 models > color #2/A rgb (245, 204, 114) > color #2/H rgb (232, 111, 151) > color #2/L rgb (182, 219, 227) > lighting soft > color #2/l,L rgb (245, 204, 114) > select #2/A 657 atoms, 674 bonds, 1 pseudobond, 83 residues, 2 models selected > select #2/A,a 1314 atoms, 1348 bonds, 2 pseudobonds, 166 residues, 2 models selected > ui tool show ""Color Actions"" > color sel deep sky blue > color sel dodger blue > color sel cornflower blue > color sel dark cyan > color sel orchid > color sel slate blue > color sel dodger blue > color sel dark turquoise > color sel dodger blue > color sel medium spring green > color sel dodger blue > color sel cornflower blue > color sel dodger blue > select #2/A,a Dodger Blue Expected a keyword > select #2/A,a DodgerBlue Expected a keyword > color #2/H,h rgb (232, 111, 151) > select clear > select add #2 7760 atoms, 7952 bonds, 4 pseudobonds, 1010 residues, 2 models selected > show #!1 models > ui tool show ""Color Zone"" > color zone #1 near #2 distance 7.2 > volume #1 level 3.541 > select subtract #2 Nothing selected > color zone #1 near #2 distance 4 > color zone #1 near #2 distance 6 > hide #!1 models > show #!1 models > hide #!2 models > ui mousemode right zoom > lighting soft > open 4LQF 4lqf title: Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at the resolution of 2.3 Angstroms [more info...] Chain information for 4lqf #3 --- Chain | Description | UniProt A | A33R | Q71TT1_9POXV 89-185 H | Murine IgG2b A2C7 Heavy chain Fab domain | L | Murine IgG2b A2C7 Light chain Fab domain | Non-standard residues in 4lqf #3 --- ZN — zinc ion 4lqf mmCIF Assemblies --- 1| author_defined_assembly > mmaker #3 to #2 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final.pdb, chain L (#2) with 4lqf, chain L (#3), sequence alignment score = 645.2 RMSD between 179 pruned atom pairs is 1.260 angstroms; (across all 211 pairs: 1.611) > hide #!1 models > show #!2 models > mmaker #3/A to #2 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final.pdb, chain A (#2) with 4lqf, chain A (#3), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > show #!1 models > hide #!3 models > show #!3 models > sym #3 4lqf mmCIF Assemblies --- 1| author_defined_assembly| 2 copies of chains A,H,L > hide #!2 models > hide #!1 models Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. > hide #!3 models > show #!3 models > hide #3.2 models > hide #3.1 models > show #3.1 models > show #3.2 models > sym #3 4lqf mmCIF Assemblies --- 1| author_defined_assembly| 2 copies of chains A,H,L > sym #3 axis y 4lqf mmCIF Assemblies --- 1| author_defined_assembly| 2 copies of chains A,H,L > sym #3 axis x 4lqf mmCIF Assemblies --- 1| author_defined_assembly| 2 copies of chains A,H,L > show #!1 models > hide #!1 models > show #!1 models > sym #3,C2 Missing or invalid ""structures"" argument: only initial part ""#3"" of atom specifier valid > sym #3 assembly Missing ""assembly"" keyword's argument > sym #3 assembly identifer Assembly ""identifer"" not found, have 1 > sym #3 assembly identifer copies true Assembly ""identifer"" not found, have 1 > open 4lqf maxAssemblies 2 'maxAssemblies' has no suffix > open 4lqf maxAssemblies 'maxAssemblies' has no suffix > open /Users/hemaozhou/Downloads/4lqf.pdb1 4lqf.pdb1 title: Structure of murine IGG2B A2C7-fab In complex with vaccinia antigen A33R At the resolution of 2.3 angstroms [more info...] Chain information for 4lqf.pdb1 --- Chain | Description 4.1/A | No description available 4.2/A | No description available 4.1/H | No description available 4.2/H | No description available 4.1/L 4.2/L | No description available > hide #!3 models > mmaker #4 to #3 Computing secondary structure [Repeated 2 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4lqf, chain L (#3) with 4lqf.pdb1, chain L (#4.1), sequence alignment score = 1139.3 RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs: 0.000) Matchmaker 4lqf, chain L (#3) with 4lqf.pdb1, chain L (#4.2), sequence alignment score = 1139.3 RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs: 0.000) > hide #3.1 models > hide #!1 models > hide #3.2 models > hide #!4 models > hide #!4.1 models > hide #!4.2 models > show #!4.2 models > show #!4.1 models Cell requested for row 6 is out of bounds for table with 9 rows! Resizing table model. > undo [Repeated 9 time(s)] > show #!1 models > hide #!4.1 models > show #!4.1 models > close #4 > open /Users/hemaozhou/Downloads/4lqf.pdb1 4lqf.pdb1 title: Structure of murine IGG2B A2C7-fab In complex with vaccinia antigen A33R At the resolution of 2.3 angstroms [more info...] Chain information for 4lqf.pdb1 --- Chain | Description 4.1/A | No description available 4.2/A | No description available 4.1/H | No description available 4.2/H | No description available 4.1/L 4.2/L | No description available > mmaker #4.1 to #3 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4lqf, chain L (#3) with 4lqf.pdb1, chain L (#4.1), sequence alignment score = 1139.3 RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs: 0.000) > mmaker #4.2/A to #2 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final.pdb, chain A (#2) with 4lqf.pdb1, chain A (#4.2), sequence alignment score = 319.5 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > hide #!3 models > show #!3 models > hide #!4.2 models > show #!4.2 models > hide #!4.1 models > hide #!4 models > hide #3.2 models > hide #3.1 models > hide #!3 models > hide #!1 models > show #!2 models > hide #!4.2 models > show #!4.2 models > show #!4.1 models > hide #!4.2 models > hide #!4.1 models > show #!4.1 models > hide #!4.1 models > show #!4.2 models > hide #!4.2 models > open /Users/hemaozhou/Downloads/4lqf.pdb1 4lqf.pdb1 title: Structure of murine IGG2B A2C7-fab In complex with vaccinia antigen A33R At the resolution of 2.3 angstroms [more info...] Chain information for 4lqf.pdb1 --- Chain | Description 5.1/A | No description available 5.2/A | No description available 5.1/H | No description available 5.2/H | No description available 5.1/L 5.2/L | No description available > show #!4.1 models > show #!4.2 models > hide #!5.1 models > close #5.1 > hide #!5.2 models > show #!5.2 models > mmaker #5.2/A to #2/a Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final.pdb, chain a (#2) with 4lqf.pdb1, chain A (#5.2), sequence alignment score = 319.5 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > hide #!4.2 models > close #4.2 > show #!1 models > view #1 clip false > hide #!2 models > hide #!4 models > hide #!5 models > color zone #1 near #2 distance 7 > graphics silhouettes true > view #1 clip false > view orient > ui tool show ""Volume Viewer"" > volume #1 level 4.004 > save /Users/hemaozhou/Desktop/A35R-17H1-global.tiff width 2794 height 2576 > supersample 4 transparentBackground true > view name global-view > roll y 1 90 > roll x 1 90 > roll x -1 90 > save /Users/hemaozhou/Desktop/A35R-17H1-global-rotate90.tiff width 2794 > height 2576 supersample 4 transparentBackground true > view name global-rotate90 > hide #!1 models > show #!2 models > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Global- > structure.pdb Cell requested for row 5 is out of bounds for table with 9 rows! Resizing table model. Cell requested for row 2 is out of bounds for table with 8 rows! Resizing table model. Cell requested for row 0 is out of bounds for table with 7 rows! Resizing table model. > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final.pdb Chain information for A35R-17H1_local_Final.pdb #6 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide #!2,6 atoms > show #!2,6 cartoons Computing secondary structure > hide #!2 models > color #6/A,a Dodger Blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select #6/A,a 1314 atoms, 1348 bonds, 2 pseudobonds, 166 residues, 2 models selected > color sel dodger blue > color #6/l,L rgb (245, 204, 114) > color #6/H,h rgb (232, 111, 151) > select clear > combine #6 > hide #!6 models Drag select of 282 residues > select up 2323 atoms, 2377 bonds, 299 residues, 1 model selected > delete sel Drag select of 2 residues > select up 32 atoms, 33 bonds, 3 residues, 1 model selected > select up 62 atoms, 64 bonds, 6 residues, 1 model selected > delete sel > combine #7 > hide #!8 models > select #7/A:61,62,64,65,68 37 atoms, 34 bonds, 5 residues, 1 model selected > view sel > select #7/A:61,62,64,65,68 #7/H:50,52,118,52,69,71 84 atoms, 77 bonds, 10 residues, 1 model selected > view sel > show sel atoms > style sel stick Changed 84 atom styles > color sel byhetero > select #8/A:67,117,114 #8/L:72,68,110 61 atoms, 57 bonds, 6 residues, 1 model selected > view sel No displayed objects specified. > hide #!7 models > show #!8 models > view sel > show sel atoms > style sel stick Changed 61 atom styles > color sel byhetero > show #!7 models > hide #!8 models > show #!6 models > hide #!6 models > hide #!7 models > show #!8 models > view sel > combine #6 > hide #!8 models > select add #8 2385 atoms, 2445 bonds, 1 pseudobond, 305 residues, 2 models selected > show #!6 models > hide #!6 models > select subtract #8 Nothing selected > interfaces #!9 & ~solvent 7 buried areas: H L 741, h l 741, H A 524, h a 524, A a 440, L A 307, l a 307 > color #9 byhetero > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models Drag select of 74 residues > show sel atoms > style sel stick Changed 588 atom styles > color sel byhetero > select clear > show #!4 models > hide #!4 models > show #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A Alignment identifier is 9/A > open > /Users/hemaozhou/Downloads/fold_2025_03_21_15_41_a35r_dimer/fold_2025_03_21_15_41_a35r_dimer_model_0.cif Chain information for fold_2025_03_21_15_41_a35r_dimer_model_0.cif #10 --- Chain | Description A B | . Computing secondary structure > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A Alignment identifier is 10/A > hide #!3 models > hide #10#!9 atoms > hide #!9 models > show #!9 models > hide #10 models > show #10 models > hide #10 models > show #10 models > close #10 > show #!9 atoms > hide #!9 atoms > show #!8 models > hide #!8 models > show #!8 models > hide #!9 models > show #!7 models > hide #!7 models > show #!7 models > ui tool show ""Side View"" > ui tool show ""Show Sequence Viewer"" > sequence chain #7/A Alignment identifier is 7/A Populating font family aliases took 126 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > close #7-9 > show #!2 models > hide #!2 models > show #!2 models > show #!6 models > hide #!2 models > ui tool show ""Renumber Residues"" > renumber #6/A seqStart 99 83 residues renumbered > renumber #6/a seqStart 99 83 residues renumbered > renumber #6/a seqStart 99 0 residues renumbered > ui tool show ""Renumber Residues"" > renumber #2/A seqStart 99 83 residues renumbered > renumber #2/a seqStart 99 83 residues renumbered > renumber #2/a seqStart 99 0 residues renumbered > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > combine #6 > rename #7 A35R-Heavy > combine #7 > rename #8 A35R-Light > combine #6 > rename #9 A35R-17H1_local_Final.pdb > hide #!9 models > hide #!6 models > hide #!8 models Drag select of 215 residues, 1 pseudobonds > select up 2021 atoms, 2068 bonds, 1 pseudobond, 257 residues, 2 models selected > select up 2385 atoms, 2445 bonds, 1 pseudobond, 305 residues, 2 models selected > delete sel > select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71 84 atoms, 77 bonds, 10 residues, 1 model selected Drag select of 26 residues > select ~sel & ##selected 2186 atoms, 2247 bonds, 1 pseudobond, 279 residues, 2 models selected > select ~sel & ##selected 199 atoms, 198 bonds, 26 residues, 1 model selected > select up 272 atoms, 272 bonds, 36 residues, 1 model selected > select up 837 atoms, 857 bonds, 107 residues, 1 model selected > delete sel > select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71 84 atoms, 77 bonds, 10 residues, 1 model selected > view sel > show sel atoms > style sel stick Changed 84 atom styles > color sel byhetero > hide sel atoms > combine #7 [Repeated 2 time(s)] > hide #!7 models > select add #7 1548 atoms, 1588 bonds, 1 pseudobond, 198 residues, 2 models selected > select subtract #7 Nothing selected > rename #10 ""copy of A35R-Heavy CDR1"" > rename #11 ""copy of A35R-Heavy CDR2"" > rename #12 ""copy of A35R-Heavy CDR3"" > hide #!12 models > hide #!11 models > rename #11 ""copy of A35R-Heavy CDR2-3"" > select #10/A:118, 121 #10/H:50,51,52 42 atoms, 40 bonds, 5 residues, 1 model selected > show sel atoms > style sel stick Changed 42 atom styles > color sel byhetero Drag select of 27 atoms, 57 residues, 23 bonds > show sel atoms > style sel stick Changed 465 atom styles > show #!1 models > combine #1 No structures specified > hide #!1 models > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #13, grid size 300,300,300, pixel 1.2, shown at level 0.0147, step 1, values float32 > volume #13 level 7.728 > volume #13 style mesh > volume #13 level 6.965 > volume #13 level 5.909 > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #14, grid size 300,300,300, pixel 1.2, shown at level 0.0231, step 1, values float32 > volume #14 level 6.746 > volume #14 style mesh > volume #14 level 5.01 > open ""/Users/hemaozhou/Downloads/cryosparc_P23_J197_003_volume_map_sharp > (1).mrc"" Opened cryosparc_P23_J197_003_volume_map_sharp (1).mrc as #15, grid size 300,300,300, pixel 1.2, shown at level 0.0238, step 1, values float32 > volume #15 level 0.5002 > volume #15 level 0.4362 > volume #15 level 0.3793 > volume #14 level 3.245 > volume #14 style surface > volume #14 level 4.141 > transparency #13 20 > volume #13 style surface > volume #13 level 4.099 > volume #15 level 0.2869 > volume #13 level 6.905 > hide sel atoms > select #10/A:118, 121 #10/H:50,51,52 42 atoms, 40 bonds, 5 residues, 1 model selected > show sel atoms > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #10 to IUPAC-IUB standards. > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > global.cxs ——— End of log from Wed Apr 16 23:10:21 2025 ——— opened ChimeraX session > select clear Cell requested for row 9 is out of bounds for table with 18 rows! Resizing table model. > close #10 > combine #11 > hide #!13 models > clipper off > mousemode leftMode select control > mousemode leftMode none control shift > mousemode middleMode none control > mousemode wheelMode zoom > mousemode rightMode none shift > mousemode wheelMode none control > mousemode wheelMode none alt > mousemode wheelMode none shift > cofr frontCenter showPivot false > camera mono > clip off > lighting soft > select #10/A:118, 121 #10/H:50,51,52 42 atoms, 40 bonds, 5 residues, 1 model selected > show sel atoms > style sel stick Changed 42 atom styles > color sel byhetero > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > global.cxs > hide #!10 models > select add #10 1548 atoms, 1588 bonds, 1 pseudobond, 198 residues, 2 models selected > select subtract #10 Nothing selected > show #!1 models > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/09.KP.3.1.1/Deposited_structure/KP311_S_global_J668_007_volume_map_Masked_Decon_emready_inte.mrc Opened KP311_S_global_J668_007_volume_map_Masked_Decon_emready_inte.mrc as #16, grid size 400,400,400, pixel 0.76, shown at level 1.33, step 1, values float32 > hide #!1 models > view #16 clip false > color #16 darkgrey models > color #16 silver models > save /Users/hemaozhou/Desktop/KP311-trimer.tiff width 2794 height 2576 > supersample 4 transparentBackground false > close #16 > show #!15 models > hide #!15 models > show #!15 models > close #15 > show #!14 models > hide #!14 models > show #!10 models > view list Named views: global-rotate90, global-view > view global-view > view #10 clip false > show #!11 models > hide #!11 models > select #10/A:118, 121 #10/H:50,51,52 42 atoms, 40 bonds, 5 residues, 1 model selected > ui mousemode right zoom > select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71 84 atoms, 77 bonds, 10 residues, 1 model selected > hide #!10 models > show #!7 models > show sel atoms > style sel stick Changed 84 atom styles > select clear > view list Named views: global-rotate90, global-view > view global-view > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > ui tool show ""Render/Select by Attribute"" > select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71 84 atoms, 77 bonds, 10 residues, 1 model selected > ui tool show ""Basic Actions"" > ui tool show Toolbar > nucleotides sel tube/slab shape box > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > cartoon style helix width 1.5 thickness 0.5 > cartoon style strand xsection rectangle width 1.5 > hide sel cartoons > show sel cartoons > combine #7 > hide sel cartoons > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > hide #7.1 models > show #7.1 models > show #!15 models > cartoon style strand xsection rectangle width 1.5 [Repeated 1 time(s)] > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > cartoon style strand xsection rectangle width 1.5 > cartoon style helix width 1.5 thickness 0.5 > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > transparency #7,15 50 target 50 Invalid ""target"" argument: Character '5' is not an allowed target, must be one of acrsbmpfl > transparency #7,15 50 target c > hide #!15 models > show #!15 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > select #7/H:70-77 58 atoms, 59 bonds, 8 residues, 1 model selected > cartoon style width 1.5 thickness 0.5 sel Expected a keyword > cartoon style sel width 1.5 thickness 0.5 > cartoon style sel width 3 thickness 0.5 > undo [Repeated 1 time(s)] > cartoon style #7/H:70-77 width 3 thickness 0.5 > ribbon style #7/H:70-77 width 3 thick 0.5 > hide #!15 models > ribbon style #7/H:70-77 width 3 thick 0.5 > ribbon style #7/H:70-77 width 1 thick 0.5 > ribbon tether #7/H:70-77 width 1 thick 0.5 > cartoon tether #7/H:70-77 width 1 thick 0.5 Expected a keyword > ribbon tether #7/H:70-77 shape cone > ribbon tether #7/H:70-77 shape steeple > ribbon tether #7/H:70-77 shape cylinder > ribbon tether #7/H:70-77 scale 2 > cartoon tether #7/H:70-77 scale 2 Invalid ""scale"" argument: Must be less than or equal to 1.0 > ribbon tether #7/H:70-77 scale 1 > ribbon tether #7/H:70-77 scale 0.1 > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > global.cxs ——— End of log from Thu Apr 17 14:20:34 2025 ——— opened ChimeraX session > close #13-14 > rename #1 17H1_global_J192.mrc > hide #!7 models > show #!7 models > show #!8 models > hide #!7 models > select add #7 1548 atoms, 1588 bonds, 1 pseudobond, 198 residues, 2 models selected > select subtract #7 Nothing selected > hide #!8 models > show #!10 models > cartoon style coil thickness 0.25 > select #10/H:42-53 95 atoms, 97 bonds, 12 residues, 1 model selected > cartoon style coil thickness 0.25 sel Expected a keyword > cartoon style sel coil thickness 0.25 Expected a keyword > cartoon style coil sel thickness 0.25 Expected a keyword > cartoon style coil #10/H:42-53 l thickness 0.25 Expected a keyword > cartoon style coil #10/H:42-53 thickness 0.25 Expected a keyword > cartoon style coil thickness 0.5 > combine #10 > rename #13 ""A35R-Heavy CDR2-3"" > hide #!10 models > show #!10 models > select #13/H:42-53 95 atoms, 97 bonds, 12 residues, 1 model selected > select #13/H:43-53 86 atoms, 88 bonds, 11 residues, 1 model selected > select #13/H:43-52 78 atoms, 80 bonds, 10 residues, 1 model selected > select ~sel & ##selected 1470 atoms, 1508 bonds, 1 pseudobond, 188 residues, 2 models selected > delete sel > hide #!10 models > show #!10 models > hide #!10 models > hide #!13 atoms > show #!10 models > hide #!10 models > cartoon style coil thickness 1 > show #!10 models [Repeated 1 time(s)] > cartoon style coil thickness 0.5 #13 Expected a keyword > cartoon style #13 thickness 0.5 > cartoon style #13 thickness 1 > cartoon style #13 thickness 0.8 > combine #10 > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > select #14/H:41-54 113 atoms, 116 bonds, 14 residues, 1 model selected > select ~sel & ##selected 1435 atoms, 1472 bonds, 1 pseudobond, 184 residues, 2 models selected > delete sel > hide #!13 models > cartoon style #14 thickness 0.8 > cartoon style strand xsection rectangle width 1.5 > hide #!14 models > close #13-14 > combine #10 > cartoon style helix width 1.5 thickness 0.5 > cartoon style strand xsection rectangle width 1.5 > hide #!13 models > show #!13 models > cartoon style #13 thickness 0.8 > hide #!10 models > show #!10 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > cartoon style (#13 & coil) thickness 0.8 > show #!13 models > hide #!13 models > show #!13 models > cartoon style (#13 & coil) thickness 0.1 > cartoon style (#13 & coil) thickness 0.8 > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > cartoon style (#13 & coil) thickness 0.1 > cartoon style (#13 & coil) thickness 0.9 > hide #!13 models > show #!13 models > hide #!13 models > close #13 > combine #10 > cartoon style (#13 & coil) thickness 0.9 > hide #!13 models > show #!13 models > cartoon style strand xsection rectangle width 1.5 > cartoon style (#13 & coil) thickness 0.6 > cartoon style (#13 & coil) thickness 0.1 > cartoon style (#13 & coil) thickness 0.2 > cartoon style (#13 & coil) thickness 0.1 > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > cartoon style helix width 1.5 thickness 0.5 > show #!13 models > hide #!13 models > show #!13 models > cartoon style strand xsection rectangle width 1.5 > hide #!13 models > show #!13 models > cartoon style (#13/H:42-53 & coil) thickness 0.1 > cartoon style (#13/H:42-53 & coil) thickness 0.9 > cartoon style (#13/H:42-53 & coil) thickness 0.5 > cartoon style (#13/H:42-53) thickness 0.5 [Repeated 1 time(s)] > cartoon style (#13/H:42-53) thickness 0.9 > cartoon style (#13/H:42-53 & coil) thickness 0.5 > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > select #13/H:35-61 212 atoms, 218 bonds, 27 residues, 1 model selected > select ~sel & ##selected 1336 atoms, 1370 bonds, 1 pseudobond, 171 residues, 2 models selected > delete sel > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > cartoon style (#13/H:42-53 & coil) thickness 0.5 > show #!13 models > hide #!13 models > show #!13 models > cartoon style (#13/H:42-53 & coil) thickness 0.9 > color #13 magenta > hide #!13 models > show #!13 models > hide #!13 models > undo [Repeated 3 time(s)] > ui tool show ""Side View"" > select #13/H:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #13/H:52 20 atoms, 19 bonds, 2 residues, 1 model selected > select add #10/A:118 26 atoms, 25 bonds, 3 residues, 2 models selected > view sel > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > select clear > graphics silhouettes true > graphics silhouettes false > select #13/H:51 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel target a > hide #!13 models > show #!13 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!13 models > show #!13 models > show #!10 models > hide #!10 models > show #!10 models > hide #!13 models > select #10/H:51 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > select clear > hide #!13 models > hide #!10 models > show #!13 models > hide #!13 atoms > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > select #13/H:50 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #13/H:52 16 atoms, 14 bonds, 2 residues, 1 model selected > hide sel cartoons > undo > hide #!13 models > select clear > select #10/H:50 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/H:52 16 atoms, 14 bonds, 2 residues, 1 model selected > hide sel cartoons > show #!13 models > hide #!13 models > show #!13 models > select #10/A:118 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel cartoons > select clear > combine #10/A > cartoon style helix width 1.5 thickness 0.5 > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!13 models > hide #!10 models > hide #!14 atoms > show #!14 cartoons > delete #14/H > show #!13 models > show #!10 models > transparency 50 target s > transparency 50 target c > transparency 10 target c > transparency 20 target c > graphics silhouettes true > view name HCDR1 > ui tool show Distances > select #10/H:52@N 1 atom, 1 residue, 1 model selected > select add #10/A:121@OD2 2 atoms, 2 residues, 1 model selected > distance #10/H:52@N #10/A:121@OD2 Distance between copy of copy of A35R-Heavy CDR2-3 #10/H ASN 52 N and /A ASP 121 OD2: 2.815Å > distance style symbol false [Repeated 2 time(s)] > distance #10/H:52@N #10/A:121@OD2 Distance already exists; modify distance properties with 'distance style' > hide #16.1 models > view list Named views: HCDR1, global-rotate90, global-view > view HCDR1 > select clear > hide #!14 models > select #10/A:118@N 1 atom, 1 residue, 1 model selected > select add #10/H:50@O 2 atoms, 2 residues, 1 model selected > distance #10/A:118@N #10/H:50@O Distance between copy of copy of A35R-Heavy CDR2-3 #10/A SER 118 N and /H ASN 50 O: 3.846 > show #!14 models > select clear > view HCDR1 > save /Users/hemaozhou/Desktop/HCDR1.tiff width 2794 height 2576 supersample > 4 transparentBackground false > view name HCDR1 > graphics silhouettes true depthJump 0.2 > graphics silhouettes true depthJump 0.5 > graphics silhouettes true depthJump 0.6 > graphics silhouettes true depthJump 0.3 > graphics silhouettes true depthJump 0 > graphics silhouettes true depthJump Missing ""depthJump"" keyword's argument > graphics silhouettes true depthJump 0.1 > graphics selection color black > graphics selection color black width 3 > select #13/H:42-53 95 atoms, 97 bonds, 12 residues, 1 model selected > select #13/H:42-52 87 atoms, 89 bonds, 11 residues, 1 model selected > graphics selection color black width 5 > graphics selection color rgb (232, 111, 151) width 4 > graphics selection color rgb (232, 111, 151) width 6 > select #13/H:42-52 87 atoms, 89 bonds, 11 residues, 1 model selected > graphics selection color rgb (232, 111, 151) width 10 > select #13/H:42-53 95 atoms, 97 bonds, 12 residues, 1 model selected > graphics silhouettes true depthJump 0.5 > graphics silhouettes true depthJump 0.2 > graphics silhouettes true depthJump 0.1 > save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576 > supersample 4 transparentBackground false > graphics silhouettes false > save /Users/hemaozhou/Desktop/HCDR1-3.tiff width 2794 height 2576 > supersample 4 transparentBackground false > graphics silhouettes true > hide #!16 models > rename #16 CDR1 Cell requested for row 15 is out of bounds for table with 17 rows! Resizing table model. > show #!16 models > rename #16 HCDR1 > rename #10 ""copy of copy of A35R-Heavy CDR1"" > rename #13 ""copy of copy of copy of A35R-Heavy CDR1"" > rename #14 ""copy of copy of copy of A35R-Heavy CDR1"" > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR1.cxs > hide #!10 models > hide #!13 models > hide #!14 models > hide #!16 models > select add #13 212 atoms, 218 bonds, 27 residues, 1 model selected > show #!11 models > show #!12 models > select subtract #13 Nothing selected > ui tool show ""Side View"" > hide #!12 models > rename #11 ""copy of A35R-Heavy CDR2"" > combine #11 > rename #17 ""A35R-Heavy CDR2"" > combine #17 > rename #18 ""A35R-Heavy CDR2"" > combine #17 > rename #19 ""Heavy CDR2"" > 1\. cartoon style helix width 1.5 thick 0.5 Unknown command: 1. cartoon style helix width 1.5 thick 0.5 > cartoon style helix width 1.5 thickness 0.5 > cartoon style strand xsection rectangle width 1.5 > hide #!19 models > hide #!18 models > select #17/H:69,71 #17/A:117,124 34 atoms, 31 bonds, 4 residues, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > show #!18 models > select #11/A:124 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > hide #!17 models > show #!17 models > hide #!18 models > show #!18 models > hide #!18 models > select #17/A:124 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > show #!18 models > select clear > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > ui tool show Distances > select #17/A:124@O 1 atom, 1 residue, 1 model selected > select add #17/H:69@OH 2 atoms, 2 residues, 1 model selected > distance #17/A:124@O #17/H:69@OH Distance between A35R-Heavy CDR2 #17/A ALA 124 O and /H TYR 69 OH: 3.365 > select #17/H:71@OD1 1 atom, 1 residue, 1 model selected > select add #17/A:117@NZ 2 atoms, 2 residues, 1 model selected > distance #17/H:71@OD1 #17/A:117@NZ Distance between A35R-Heavy CDR2 #17/H ASP 71 OD1 and /A LYS 117 NZ: 2.995 > distance style color #00f900 [Repeated 2 time(s)] > undo [Repeated 1 time(s)] > distance style color #fffb00 [Repeated 2 time(s)] > undo [Repeated 2 time(s)] > select clear > color sel green > select clear > hide #20.1 models > select #17/H:69,71 #17/A:117,124 34 atoms, 31 bonds, 2 pseudobonds, 4 residues, 2 models selected > view sel > select clear > view name HCDR2 > show #!19 models > hide #!18 models > hide #!17 models > select #19/H:65-85 173 atoms, 179 bonds, 21 residues, 1 model selected > select ~sel & ##selected 1375 atoms, 1409 bonds, 1 pseudobond, 177 residues, 2 models selected > delete sel > hide #!19 models > show #!19 models > hide #!11 models > cartoon style (#19/H:42-53 & coil) thickness 0.9 > cartoon style (#19/H:70-77 & coil) thickness 0.9 [Repeated 1 time(s)] > show #!18 models > show #!17 models > transparency 50 target c > transparency 20 target c > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > save /Users/hemaozhou/Desktop/HCDR2.tiff width 2794 height 2576 supersample > 4 transparentBackground false > rename #20 HCDR2 > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > show #!16 models > show #!15 models > show #!12 models > hide #!12 models > show #!13 models > show #!14 models > show #!10 models > hide #!15 models > select #13/H:42-52 87 atoms, 89 bonds, 11 residues, 1 model selected > show #!17 models > show #!18 models > show #!19 models > show #!20 models > show #20.1 models > hide #20.1 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!18 models > show #!18 models > graphics selection color red width 10 > select clear > graphics selection color rgb (232, 111, 190) width 10 > select #13/H:42-52 87 atoms, 89 bonds, 11 residues, 1 model selected > color violet #13/H:42-52 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #13/H:42-52 87 atoms, 89 bonds, 11 residues, 1 model selected > ui tool show ""Color Actions"" > color sel violet > select clear > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > select #19/H:70-77 58 atoms, 59 bonds, 8 residues, 1 model selected > color sel violet > undo > select #19/H:71-76 43 atoms, 44 bonds, 6 residues, 1 model selected > color sel violet > select clear > hide #!18 models > hide #!17 models > show #!17 models > hide #!16 models > show #!16 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > select #19/H:79 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #19/H:80 20 atoms, 19 bonds, 2 residues, 1 model selected > select add #19/H:81 29 atoms, 27 bonds, 3 residues, 1 model selected > select add #10/H:82 38 atoms, 35 bonds, 4 residues, 2 models selected > hide sel cartoons > select add #19/H:82 47 atoms, 43 bonds, 5 residues, 2 models selected > hide sel cartoons > select add #17/H:82 56 atoms, 51 bonds, 6 residues, 3 models selected > hide sel cartoons > hide #!17 models > show #!17 models > select clear > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > select #19/H:70 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > undo [Repeated 1 time(s)] > select #19/H:71 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > hide sel atoms > hide #!19 models > show #!19 models > show #!17 models > hide #!17 models > show #!17 models > select #19/H:71 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > hide #!17 models > show #!17 models > hide #!19 models > show #!19 models > hide sel atoms > select clear > hide #!17 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > view name HCDR1-2 > save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576 > supersample 4 transparentBackground false > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR1-2.cxs > select #10/H:118 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #10/A:120 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > undo Cell requested for row 19 is out of bounds for table with 21 rows! Resizing table model. > hide #!20 models > hide #!19 models > hide #!17 models > hide #!16 models > hide #!14 models > hide #!13 models > hide #!10 models > show #!11 models > select add #10 1548 atoms, 1588 bonds, 3 pseudobonds, 198 residues, 3 models selected > select subtract #10 Nothing selected > hide #!11 models > show #!12 models > combine #12 > rename #21 ""A35R-Heavy CDR3"" > rename #12 ""A35R-Heavy CDR3"" > combine #21 [Repeated 1 time(s)] > rename #22 ""A35R-Heavy CDR3"" > rename #23 ""A35R-Heavy CDR3"" > cartoon style helix width 1.5 thickness 0.5 > cartoon style strand xsection rectangle width 1.5 > hide #!23 models > hide #!22 models > select add #12/H:118 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #12/A:120 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > hide sel cartoons > show #!22 models > select clear > select #23/H:110-130 167 atoms, 171 bonds, 21 residues, 1 model selected > show #!23 models > select ~sel & ##selected 1381 atoms, 1417 bonds, 1 pseudobond, 177 residues, 2 models selected > delete sel > hide #!22 models > show #!22 models > hide #!21 models > show #!21 models > cartoon style (#23 & coil) thickness 0.9 > hide #!21 models > hide #!22 models > hide #!12 models Drag select of 16 residues > select subtract #23/H:117 118 atoms, 15 residues, 1 model selected > hide sel cartoons > show #!22 models > show #!21 models > hide #!22 models > hide #!21 models > select add #23/H:117 129 atoms, 10 bonds, 16 residues, 1 model selected > hide sel cartoons > show #!22 models > show #!21 models > hide #!21 models > hide #!22 models > show #!22 models > show #!21 models > select #21/H:118 #21/A:120 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > hide sel cartoons > view list Named views: HCDR1, HCDR1-2, HCDR2, global-rotate90, global-view > view HCDR1-2 > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > select clear > graphics silhouettes true depthJump 0.1 > graphics silhouettes true depthJump 0.01 > graphics silhouettes true depthJump 0.1 > select #23/H:118-122 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel violet > select clear > ui tool show Distances > select #21/H:118@NH2 1 atom, 1 residue, 1 model selected > select add #21/A:120@OE2 2 atoms, 2 residues, 1 model selected > distance #21/H:118@NH2 #21/A:120@OE2 Distance between A35R-Heavy CDR3 #21/H ARG 118 NH2 and /A GLU 120 OE2: 2.985 > select #21/H:118@NH2 1 atom, 1 residue, 1 model selected > select add #21/A:120@OE1 2 atoms, 2 residues, 1 model selected > distance #21/H:118@NH2 #21/A:120@OE1 Distance between A35R-Heavy CDR3 #21/H ARG 118 NH2 and /A GLU 120 OE1: 2.859 > select #21/H:118@NE 1 atom, 1 residue, 1 model selected > select add #21/A:120@OE1 2 atoms, 2 residues, 1 model selected > distance #21/H:118@NE #21/A:120@OE1 Distance between A35R-Heavy CDR3 #21/H ARG 118 NE and /A GLU 120 OE1: 3.581 > distance style color #8efa00 [Repeated 2 time(s)] > distance style color #00f900 [Repeated 2 time(s)] > hide #24.1 models > select clear > view list Named views: HCDR1, HCDR1-2, HCDR2, global-rotate90, global-view > view HCDR1-2 > ui tool show ""Side View"" > view HCDR1-2 > hide #!23 models > show #!23 models > hide #!22 models > show #!22 models > hide #!22 models > hide #!23 models > show #!22 models > hide #!21 models > show #!21 models > hide #!24 models > show #!24 models > show #!23 models > select #23/H:118 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #22/A:120 20 atoms, 18 bonds, 2 residues, 2 models selected > view sel > select clear > graphics silhouettes false > graphics silhouettes true > select #23/H:119 5 atoms, 4 bonds, 1 residue, 1 model selected > select #23/H:117 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel cartoons > select clear > select #23/H:117 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel violet > select clear > view name HCDR3 > save /Users/hemaozhou/Desktop/HCDR3.tiff width 2794 height 2576 supersample > 4 transparentBackground false > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > color #20 #00f900ff models > show #!20 models > show #20.1 models > show #!19 models > show #!18 models > show #!17 models > show #!10 models > show #!13 models > show #!14 models > show #!16 models > hide #!18 models > view list Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, global-rotate90, global-view > view HCDR1-2 > hide #20.1 models > color #20.1 #fffb00ff models > show #20.1 models > hide #20.1 models > show #20.1 models > hide #20.1 models > color lemonchiffon sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel lomon Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lemonchiffon > select clear > color sel yellow > select clear > color sel orange > select clear > color sel yellow [Repeated 1 time(s)] > select clear > save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576 > supersample 4 transparentBackground false > select clear > save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576 > supersample 4 transparentBackground false > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR3.cxs ——— End of log from Mon Apr 21 09:13:57 2025 ——— opened ChimeraX session > show #!1 models > hide #!1 models > ui mousemode right zoom Cell requested for row 17 is out of bounds for table with 26 rows! Resizing table model. > hide #!17 models > hide #!19 models > hide #!20 models Cell requested for row 15 is out of bounds for table with 25 rows! Resizing table model. > hide #!16 models > hide #!14 models > hide #!13 models > hide #!10 models > show #!9 models > show #!7 models > hide #!9 models > show #!8 models > hide #!7 models > combine #8 [Repeated 3 time(s)] > cartoon style helix width 1.5 thickness 0.5 > cartoon style strand xsection rectangle width 1.5 > hide #!28 models > hide #!27 models > hide #!26 models > select #25/L: 68,72,110 #25/A:123,170,167 52 atoms, 49 bonds, 5 residues, 1 model selected > show sel atoms > style sel stick Changed 52 atom styles > color sel byhetero > hide #!8 models > delete #25/H > show #!26 models > hide #!26 models > delete #26/H > select #26/L:60-76 132 atoms, 133 bonds, 17 residues, 1 model selected > show #!26 models > select #26/L:60-78 146 atoms, 148 bonds, 19 residues, 1 model selected > select #26/L:60-80 163 atoms, 165 bonds, 21 residues, 1 model selected > select #26/L:60-80, 106-120 287 atoms, 294 bonds, 36 residues, 1 model selected > select ~sel & ##selected 3592 atoms, 3682 bonds, 2 pseudobonds, 459 residues, 2 models selected > delete sel > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > delete sel > cartoon style (#26 & coil) thickness 0.9 > hide #!25 models > select #26/L:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #26/L:65 15 atoms, 13 bonds, 2 residues, 1 model selected > select add #26/L:64 24 atoms, 21 bonds, 3 residues, 1 model selected > select add #26/L:63 31 atoms, 28 bonds, 4 residues, 1 model selected > select add #26/L:76 35 atoms, 31 bonds, 5 residues, 1 model selected > select add #26/L:77 42 atoms, 37 bonds, 6 residues, 1 model selected > select add #26/L:79 48 atoms, 42 bonds, 7 residues, 1 model selected > select add #26/L:78 55 atoms, 49 bonds, 8 residues, 1 model selected > select add #26/L:80 66 atoms, 59 bonds, 9 residues, 1 model selected > hide sel cartoons > select add #26/L:106 78 atoms, 71 bonds, 10 residues, 1 model selected > select add #26/L:107 84 atoms, 76 bonds, 11 residues, 1 model selected > select add #26/L:108 92 atoms, 83 bonds, 12 residues, 1 model selected > select add #26/L:119 96 atoms, 86 bonds, 13 residues, 1 model selected > select add #26/L:118 100 atoms, 89 bonds, 14 residues, 1 model selected > select add #26/L:117 111 atoms, 100 bonds, 15 residues, 1 model selected > select add #26/L:116 118 atoms, 106 bonds, 16 residues, 1 model selected > select add #26/L:120 122 atoms, 109 bonds, 17 residues, 1 model selected > select add #26/L:62 128 atoms, 114 bonds, 18 residues, 1 model selected > select add #26/L:61 137 atoms, 122 bonds, 19 residues, 1 model selected > select add #26/L:60 141 atoms, 125 bonds, 20 residues, 1 model selected > hide sel cartoons > show #!25 models > trasn 50 target r Unknown command: trasn 50 target r > transparency 50 target r > select #25/L:110 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > transparency 20 target r > select #25/A:170@OD2 1 atom, 1 residue, 1 model selected > select add #25/L:72@NE 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #25/A:170@OD2 #25/L:72@NE Distance between copy of A35R-Light #25/A ASP 170 OD2 and /L ARG 72 NE: 2.916 > show #!24 models > distance style color #00f900 [Repeated 2 time(s)] > select #25/L:72@NH1 1 atom, 1 residue, 1 model selected > select add #25/A:170@OD2 2 atoms, 2 residues, 1 model selected > distance #25/L:72@NH1 #25/A:170@OD2 Distance between copy of A35R-Light #25/L ARG 72 NH1 and /A ASP 170 OD2: 4.493 > show #24.1 models > hide #24.1 models > show #24.1 models > distance style color #8efa00 [Repeated 2 time(s)] > distance style color #00f900 [Repeated 2 time(s)] > hide #24.1 models > show #24.1 models > hide #24.1 models > delete sel > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > select add #24 5 pseudobonds, 2 models selected > hide #!24 models > select #25/L:72@NE 1 atom, 1 residue, 1 model selected > select add #25/A:170@OD2 2 atoms, 2 residues, 1 model selected > distance #25/L:72@NE #25/A:170@OD2 Distance already exists; modify distance properties with 'distance style' > show #!24 models > close #24 > select #25/L:72@NE 1 atom, 1 residue, 1 model selected > select add #25/A:170@OD2 2 atoms, 2 residues, 1 model selected > distance #25/L:72@NE #25/A:170@OD2 Distance between copy of A35R-Light #25/L ARG 72 NE and /A ASP 170 OD2: 2.916 > select #25/L:72@NH2 1 atom, 1 residue, 1 model selected > select add #25/A:170@OD2 2 atoms, 2 residues, 1 model selected > distance #25/L:72@NH2 #25/A:170@OD2 Distance between copy of A35R-Light #25/L ARG 72 NH2 and /A ASP 170 OD2: 3.112 > hide #24.1 models > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber.pdb Chain information for A35R-17H1_local_Final_renumber.pdb #29 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide #!25 models > hide #!26 models > select add #25 3879 atoms, 3976 bonds, 4 pseudobonds, 495 residues, 3 models selected > select subtract #25 Nothing selected > style #29 stick Changed 4770 atom styles > hide #29 atoms > show #29 cartoons > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #29 models > show #29 models Drag select of 268 residues > select up 2265 atoms, 2318 bonds, 292 residues, 1 model selected > select up 2385 atoms, 2446 bonds, 305 residues, 1 model selected > delete sel > hide #29 models > show #29 models > show #!26 models > hide #!26 models > show #!26 models > show #!27 models > hide #!27 models > show #!25 models > hide #29 models > show #29 models > hide #29 models > show #29 models > hide #29 models > close #25 > close #27-28 > rename #29 A35R-17H1_local_Light.pdb > combine #29 > hide #!26 models > show #!26 models > show #29 models > hide #29 models > hide #!26 models > show #!26 models > hide #25 models > show #25 models > hide #25 models > show #25 models > hide #24 models > select subtract #24 Nothing selected > rename #25 A35R-17H1_local_Light.pdb > combine #29 [Repeated 1 time(s)] > rename #27 A35R-17H1_local_Light.pdb > rename #28 A35R-17H1_local_Light.pdb > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > cartoon style helix width 1.5 thickness 0.5 > cartoon style strand xsection rectangle width 1.5 > show #29 models > color #25,27-29/l,L rgb (245, 204, 114) > color #25,27-29/A,a Dodger Blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select #25,27-29/A 2628 atoms, 2700 bonds, 332 residues, 4 models selected > ui tool show ""Color Actions"" > color sel dodger blue > select clear > hide #28 models > hide #29 models > hide #27 models > hide #25 models > show #25 models > delete #25/H > view list Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, global-rotate90, global-view > view HCDR3 > select #25/L: 68,72,110 #25/A:123,170,167 61 atoms, 57 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 61 atom styles > color sel byhetero > show #!26 models > select clear > transparency 20 target r > show #24 models > hide #24 models > show #24 models > ui tool show Distances > select #26/L:110 12 atoms, 12 bonds, 1 residue, 1 model selected > hide #!26 models > select #25/L:110 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel cartoons > show #!26 models > select clear > select #25/A:167@OD2 1 atom, 1 residue, 1 model selected > select add #25/L:72@NE 2 atoms, 2 residues, 1 model selected > distance #25/A:167@OD2 #25/L:72@NE Distance between A35R-17H1_local_Light.pdb #25/A ASP 167 OD2 and /L ARG 72 NE: 2.916 > select #25/L:72@NH2 1 atom, 1 residue, 1 model selected > select add #25/A:167@OD2 2 atoms, 2 residues, 1 model selected > distance #25/L:72@NH2 #25/A:167@OD2 Distance between A35R-17H1_local_Light.pdb #25/L ARG 72 NH2 and /A ASP 167 OD2: 3.112 > select #25/L:68@OH 1 atom, 1 residue, 1 model selected > select add #25/A:170@NE2 2 atoms, 2 residues, 1 model selected > distance #25/L:68@OH #25/A:170@NE2 Distance between A35R-17H1_local_Light.pdb #25/L TYR 68 OH and /A GLN 170 NE2: 3.318 > select add #25/A:123@NZ 3 atoms, 3 residues, 1 model selected > select add #25/L:110@O 4 atoms, 4 residues, 1 model selected Exactly two atoms must be selected! > select clear > select #25/L:110@O 1 atom, 1 residue, 1 model selected > select add #25/A:123@NZ 2 atoms, 2 residues, 1 model selected > distance #25/L:110@O #25/A:123@NZ Distance between A35R-17H1_local_Light.pdb #25/L TYR 110 O and /A LYS 123 NZ: 3.206 > select clear > hide #24.1 models > distance style color #fffb00 [Repeated 2 time(s)] > undo [Repeated 3 time(s)] > hide #24.1 models > distance style color #00f900 [Repeated 2 time(s)] > color sel orange > color sel yellow > color sel orange > select clear > graphics silhouettes false > graphics silhouettes width 2 > graphics silhouettes true > graphics silhouettes width 3 > graphics silhouettes width 2 > save /Users/hemaozhou/Desktop/LCDR.tiff width 2794 height 2576 supersample 4 > transparentBackground false [Repeated 1 time(s)] > view name LCDR > hide #25 models > show #25 models > hide #!26 models > show #!26 models > color #26 #ff7e79ff > color #26 #ffd479ff > color #26 #ff9300ff > transparency 20 target r > select clear > color sel cyan > select clear > save /Users/hemaozhou/Desktop/LCDR.tiff width 2794 height 2576 supersample 4 > transparentBackground false > hide #!24 models > hide #25 models > hide #!26 models > show #!10 models > show #!13 models > show #!14 models > show #!16 models > show #!17 models > show #!19 models > show #!20 models > viee list Unknown command: viee list > viee listview list Unknown command: viee listview list > view list Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, LCDR, global-rotate90, global-view > view HCDR1-2 [Repeated 1 time(s)] > transparency 20 target r > hide #!16 models > show #!16 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!16 models > show #!16 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!20 models > show #!20 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!13 models > show #!13 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > hide #!16 models > show #!16 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > show #!14 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > transparency 20 target r,c Invalid ""target"" argument: Character ',' is not an allowed target, must be one of acrsbmpfl > transparency 20 target c > color sel cyan > select clear > save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576 > supersample 4 transparentBackground false > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/LCDR.cxs ——— End of log from Tue Apr 22 09:51:42 2025 ——— opened ChimeraX session > open 1HZH Summary of feedback from opening 1HZH fetched from pdb --- notes | Fetching compressed mmCIF 1hzh from http://files.rcsb.org/download/1hzh.cif Fetching CCD FUC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/FUC/FUC.cif Fetching CCD GAL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GAL/GAL.cif 1hzh title: Crystal structure of the intact human igg B12 with broad and potent activity against primary hiv-1 isolates: A template for hiv vaccine design [more info...] Chain information for 1hzh #30 --- Chain | Description | UniProt H K | IMMUNOGLOBULIN HEAVY CHAIN | IGG1_HUMAN 111-478 L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein | Q8TCD0_HUMAN 107-214 Non-standard residues in 1hzh #30 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > mmaker 20 to #19 > matchmaker 20 to #19 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > mmaker #20 to #19 No molecules/chains to match specified > mmaker #20 to #17 No molecules/chains to match specified > mmaker #30 to #17 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-Heavy CDR2, chain H (#17) with 1hzh, chain K (#30), sequence alignment score = 345.1 RMSD between 112 pruned atom pairs is 0.851 angstroms; (across all 115 pairs: 1.054) > show #25 models > hide #25 models > show #25 models > show #27 models > hide #27 models > show #27 models > hide #27 models > show #!21 models > hide #!21 models > show #!21 models > show #!2 models > mmaker #30 to #2 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final.pdb, chain H (#2) with 1hzh, chain H (#30), sequence alignment score = 737.4 RMSD between 188 pruned atom pairs is 1.145 angstroms; (across all 211 pairs: 1.712) > hide #!2 models > hide #!30 models > hide #25 models > show #25 models > hide #25 models > show #27 models > hide #27 models > show #27 models > hide #27 models > show #29 models > combine #29 > hide #29 models > hide #31 models > show #31 models > hide #31 models > show #31 models > hide #!10 models > hide #!13 models > hide #!14 models > hide #!16 models > hide #!17 models > hide #!19 models > hide #!20 models > hide #!21 models Drag select of 116 residues > select up 1311 atoms, 1339 bonds, 164 residues, 1 model selected > select up 1728 atoms, 1771 bonds, 222 residues, 1 model selected > delete sel > surface #32 No atoms specified by #32 > surface #31 > transparency 0 target s > show #29 models > select #31/A:119-120,123-124,127-128,154,167,169-170 73 atoms, 68 bonds, 10 residues, 1 model selected > hide #29 models > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for copy of A35R-17H1_local_Light.pdb_A SES surface #31.1: minimum, -16.74, mean -3.85, maximum 7.71 To also show corresponding color key, enter the above coulombic command and add key true > undo > coulombic #31 Coulombic values for copy of A35R-17H1_local_Light.pdb_A SES surface #31.1: minimum, -16.74, mean -3.85, maximum 7.71 > transparency 20 sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 20 target s sel Expected a keyword > transparency sel 20 target s > show #29 models > hide #29 models > show #25 models > hide #25 models > show #!26 models > hide #!26 models > show #!23 models > hide #!23 models > show #!22 models > hide #!22 models > show #29 models > transparency sel 50 target s > hide #31.1 models > show #31.1 models > hide #29 models > transparency sel 100 target s > transparency sel 0 target s > combine #32 No structures specified > combine #31 > hide #31.1 models > show #31.1 models > coulombic #31 offset Missing ""offset"" keyword's argument > ~coulombic #31 Unknown command: ~coulombic #31 > hide #31.1 models > show #31.1 models > surface #31 > hide #31.1 models > close #31.1 > surface #31 > transparency 0 target s > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #31.1 models > show #31.1 models > hide #31.1 models > hide #!31 models > surface #32 > hide #!32 models > show #!2 models > surface #2 > hide #!2 models > show #!2 models > hide #2.1 models > hide #2.2 models > hide #!2 models > show #!31 models > show #31.1 models > hide #31.1 models > select clear > style #!31 stick Changed 657 atom styles > select clear > style #!31 stick Changed 657 atom styles > select clear Drag select of 83 residues > style sel stick Changed 657 atom styles > show sel atoms > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- > sure.pdb Summary of feedback from opening /Users/hemaozhou/Library/CloudStorage/OneDrive- 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- sure.pdb --- warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0 Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a 180 0 Chain information for A35R-17H1_local_Final_renumber-sure.pdb #33 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide sel atoms > select clear > hide #33#!31 atoms > show #33#!31 atoms > hide #33#!31 atoms > show #33#!31 cartoons > hide #!31 models > hide #33 models > show #33 models > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final- > renumber-sure_副本.pdb Chain information for A35R-17H1_global_Final-renumber-sure_副本.pdb #34 --- Chain | Description A a | No description available H h | No description available L l | No description available > show #33#!34 cartoons Computing secondary structure > hide #33#!34 atoms > hide #33 models > hide #2.3 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > hide #2.7 models > hide #!34 models > show #!34 models > show #33 models > hide #!34 models > show #!34 models > hide #!34 models > hide #33 models > show #33 models > hide #33 models > show #33 models > hide #33 models > show #33 models > show #!32 models > hide #!32 models > show #!32 models > hide #33 models > hide #!32 models > show #!32 models > show #33 models > hide #!32 models > close #33#34 > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- > sure.pdb Summary of feedback from opening /Users/hemaozhou/Library/CloudStorage/OneDrive- 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- sure.pdb --- warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0 Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a 180 0 Chain information for A35R-17H1_local_Final_renumber-sure.pdb #33 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide #33 atoms > show #33 cartoons > surface #33/A > hide #!33 cartoons > select #33/A 657 atoms, 674 bonds, 83 residues, 1 model selected > color sel dodger blue > select clear > combine #33 > show #!32 models > select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118, > 120-121,123-125,128,172-173,175,178 196 atoms, 186 bonds, 25 residues, 2 models selected > hide #!32 models > show #!32 models > hide #!33 models > show #!33 models > hide #!32 models > select add #32 776 atoms, 789 bonds, 98 residues, 4 models selected > select subtract #32 119 atoms, 114 bonds, 15 residues, 3 models selected > show #!32 models > select add #32 776 atoms, 789 bonds, 98 residues, 3 models selected > select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118, > 120-121,123-125,128,172-173,175,178 196 atoms, 186 bonds, 25 residues, 2 models selected > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > trasns 0 Unknown command: trasns 0 > transparency 0 > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > show #29 models > hide #!32 models > hide #!33 models > hide #34 models > show #34 models > show #!33 models > select add #34 4966 atoms, 5072 bonds, 635 residues, 5 models selected > hide #!33 models > select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118, > 120-121,123-125,128,172-173,175,178 196 atoms, 186 bonds, 25 residues, 2 models selected > hide #34 models > show #!33 models > show #!32 models > hide #!33 models > hide #!32 models > show #!32 models > show sel & #!32 atoms > hide #!32 models > select #29/A:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 50 atoms, 52 bonds, 5 residues, 1 model selected > select up 657 atoms, 675 bonds, 83 residues, 1 model selected > show sel atoms > select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118, > 120-121,123-125,128,172-173,175,178 196 atoms, 186 bonds, 25 residues, 2 models selected > show #!32 models > hide #!32 models > show #!32 models > select add #33 4847 atoms, 4958 bonds, 620 residues, 4 models selected > select subtract #33 77 atoms, 72 bonds, 10 residues, 3 models selected > hide #29 models > hide #!32 models > show #!32 models > show #29 models > select #32/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > combine #29 > hide #29 models > hide #!32 models > hide #35 models > show #35 models Drag select of 127 atoms, 107 bonds, 32 residues > select up 272 atoms, 269 bonds, 38 residues, 1 model selected > select up 310 atoms, 313 bonds, 38 residues, 1 model selected > select up 519 atoms, 532 bonds, 65 residues, 1 model selected > select up 657 atoms, 675 bonds, 83 residues, 1 model selected > delete sel > select #35/H:54 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 59 atoms, 61 bonds, 6 residues, 1 model selected > select up 891 atoms, 914 bonds, 115 residues, 1 model selected > delete sel > show #!32 models > select #32/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > show #29 models > hide #29 models > show sel atoms > hide #!32 models > show #!32 models > combine #32 > select #36/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > show sel atoms > select #32/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > transparency sel 20 target s > transparency sel 40 target s > select #36/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > show sel cartoons > hide #35 models > hide #!32 models > show #!32 models > hide #!32 models > transparency 0 target r > show #!32 models > color sel byhetero > select clear > select #36/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > select #32/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > show #35 models > hide #35 models > show #35 models > hide #36 models > show #36 models > show #28 models > hide #28 models > hide #35 models > show #35 models > hide #35 models > show #35 models > hide #35 models > show #35 models > hide #35 models > show #35 models > hide #35 models > show #35 models > select #35/L:109-116, 66-74 153 atoms, 156 bonds, 17 residues, 1 model selected > select #35/L:109-116, 66-74,45-52 218 atoms, 221 bonds, 25 residues, 1 model selected > combine #35 > hide #37 models > select ~sel & ##selected 619 atoms, 636 bonds, 82 residues, 1 model selected > delete sel > select #32/A:164@C 1 atom, 1 residue, 1 model selected > delete sel > hide sel > cartoon style (#35 & coil) thickness 0.9 > cartoon style (#35 & coil) thickness 1.5 > cartoon style (#35 & coil) thickness 1 > hide #36 models > show #36 models > hide #36 models > hide #!32 models > show #!32 models > show #36 models > hide #36 models > show #36 models > hide #!35 models > show #!35 models > select #32/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > transparency sel 50 target s > select clear > select #32/A:119-120,123-124,127-128,154,170,172-173 77 atoms, 72 bonds, 10 residues, 1 model selected > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!35 models > show #37 models > select #37/L:75 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #35/L:72 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #34 models > hide #34 models > hide #37 models > show #34 models > hide #!32 models > hide #!35 models > hide #36 models > hide #34 models > show #34 models > show #34 cartoons > show #36 models > hide #36 models > close #36-37#35 > undo > show #!33 models > show #!32 models > hide #!33 models > hide #34 models > hide #!32 models > show #!32 models > close #32 Cell requested for row 39 is out of bounds for table with 43 rows! Resizing table model. > close #31 > show #!33 models > select #33/A:119-120,123-124,127-128,154,170,172-173 73 atoms, 68 bonds, 10 residues, 1 model selected > show #25 models > show #34 models > hide #!33 models Drag select of 262 residues > select up 2266 atoms, 2318 bonds, 291 residues, 1 model selected > select up 2385 atoms, 2443 bonds, 305 residues, 1 model selected > delete sel > hide #25 models > color #34/l,L rgb (245, 204, 114) > color #34/H,h rgb (232, 111, 151) > show #!33 models > hide #!33 models > hide #34 models > show #34 models > combine #34 [Repeated 2 time(s)] > rename #34 A35R-17H1_local_Final_renumber-sure.pdb > rename #35 A35R-17H1_local_Final_renumber-sure.pdb > rename #31 A35R-17H1_local_Final_renumber-sure.pdb > rename #32 A35R-17H1_local_Final_renumber-sure.pdb > show #!33 models > hide #32 models > hide #31 models > hide #34 models > hide #35 models > show #35 models > hide #35 models > select #33/A:119-120,123-124,127-128,154,170,172-173 73 atoms, 68 bonds, 10 residues, 1 model selected > show #31 models > hide #!33 models > show #!33 models > hide #31 models > show #31 models > hide #!33 models Drag select of 96 residues > select up 1245 atoms, 1272 bonds, 159 residues, 1 model selected > select up 1728 atoms, 1769 bonds, 222 residues, 1 model selected > delete sel > show #!33 models > select #33/A:119-120,123-124,127-128,154,170,172-173 73 atoms, 68 bonds, 10 residues, 1 model selected > transparency sel 50 target s > show sel atoms > style sel stick Changed 73 atom styles > color (#!33 & sel) byhetero > color #33 target s > color #33 blue target s > transparency sel 50 target s > color sel dodger blue > color (#!33 & sel) byhetero > color #33 dodger blue target s > transparency sel 50 target s > hide #31 models > show #31 models > hide #31 models > show #31 models > select #31/A:168 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #31/A:169 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel cartoons > show #32 models > rename #32 A35R-17H1_local_Final_renumber-sure-lightchain.pdb > hide #!33 models > hide #31 models Drag select of 4 residues Drag select of 2 residues > select up 68 atoms, 66 bonds, 10 residues, 1 model selected > select up 1548 atoms, 1587 bonds, 198 residues, 1 model selected > delete sel > show #!33 models > show #31 models > hide #31 models > show #31 models > hide #31 models > show #31 models > hide #31 models > show #31 models > hide #32 models > hide #!33 models > show #!33 models > hide #31 models > show #31 models > hide #!33 models > show #!33 models > hide #31 models > show #31 models > hide #31 models > show #31 models > hide #31 models > show #32 models > select #32/L:109-116, 66-74,45-52 218 atoms, 221 bonds, 25 residues, 1 model selected > select ~sel & ##selected 619 atoms, 635 bonds, 82 residues, 1 model selected > delete sel > hide sel > cartoon style (#32 & coil) thickness 1 > hide #!33 models > show #!33 models > select #33/A:119-120,123-124,127-128,154,170,172-173 73 atoms, 68 bonds, 10 residues, 1 model selected > show sel cartoons > hide sel cartoons > hide #!32 models > show #!32 models > hide #!33 models > show #!33 models > select clear > show #!32-33 cartoons > hide #!32 models > hide #!33 models > show #!33 models Drag select of 110 residues Drag select of 86 residues > select up 2503 atoms, 2558 bonds, 317 residues, 1 model selected > select up 4113 atoms, 4212 bonds, 527 residues, 1 model selected > delete sel > show #!32 models > hide #!33 models > show #!33 models > transparency 0 target r > select #33/A:119-120,123-124,127-128,154,170,172-173 73 atoms, 68 bonds, 10 residues, 1 model selected > transparency sel 80 target s > graphics silhouettes false > graphics silhouettes true > transparency sel 60 target s > transparency #32 50 target r > transparency #32 20 target r > graphics selection color rgb (245, 204, 114) width 10 > view name Light-footprint > save /Users/hemaozhou/Desktop/Light-footprint.tiff width 2794 height 2576 > supersample 4 transparentBackground false > graphics selection color rgb (245, 204, 114) width 20 > graphics selection color rgb (245, 204, 114) width 30 > graphics selection color rgb (245, 204, 114) width 20 > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > save /Users/hemaozhou/Desktop/Light-footprint-2.tiff width 2794 height 2576 > supersample 4 transparentBackground false > graphics selection color rgb (245, 204, 114) width 30 > save /Users/hemaozhou/Desktop/Light-footprint-3.tiff width 2794 height 2576 > supersample 4 transparentBackground false [Repeated 1 time(s)] > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Light- > footprint.cxs ——— End of log from Tue Apr 22 15:10:46 2025 ——— opened ChimeraX session > select add #33 657 atoms, 674 bonds, 83 residues, 3 models selected > hide #!33 models > hide #!32 models > show #!30 models > hide #!30 models > show #31 models > hide #31 models > show #31 models > hide #31 models > show #31 models > hide #31 models > show #!32 models > hide #!32 models > show #!33 models > hide #!33 models > show #34 models > show #35 models > hide #35 models > hide #34 models > select subtract #33 1 model selected > show #34 models > view #34 clip false > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final- > renumber-sure.pdb Summary of feedback from opening /Users/hemaozhou/Library/CloudStorage/OneDrive- 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final- renumber-sure.pdb --- warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0 Start residue of secondary structure not found: SHEET 37 3737 THR a 178 HIS a 180 0 Chain information for A35R-17H1_global_Final-renumber-sure.pdb #36 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide #34#!36 atoms > show #34#!36 cartoons > hide #34 models > select #236A,a Dodger Blue Expected an objects specifier or a keyword > select #36A,a Dodger Blue Expected an objects specifier or a keyword > ui tool show ""Color Actions"" > select #36/A,a 1314 atoms, 1348 bonds, 166 residues, 1 model selected > color sel dodger blue > color #36/l,L rgb (245, 204, 114) > color #36/H,h rgb (232, 111, 151) > select clear Drag select of 299 residues > select up 2937 atoms, 2996 bonds, 382 residues, 1 model selected > select up 3880 atoms, 3972 bonds, 505 residues, 1 model selected > delete sel > open 4LQF 4lqf title: Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at the resolution of 2.3 Angstroms [more info...] Chain information for 4lqf #37 --- Chain | Description | UniProt A | A33R | Q71TT1_9POXV 89-185 H | Murine IgG2b A2C7 Heavy chain Fab domain | L | Murine IgG2b A2C7 Light chain Fab domain | Non-standard residues in 4lqf #37 --- ZN — zinc ion 4lqf mmCIF Assemblies --- 1| author_defined_assembly > hide #!36 models > view #37 clip false > open 4LU5 Summary of feedback from opening 4LU5 fetched from pdb --- note | Fetching compressed mmCIF 4lu5 from http://files.rcsb.org/download/4lu5.cif 4lu5 title: Structure of murine IgG2a A20G2-Fab in complex with vaccinia antigen A33R at the resolution of 2.9 Angstroms [more info...] Chain information for 4lu5 #38 --- Chain | Description | UniProt A B | A33R | Q71TT1_9POXV 89-185 H I | Murine IgG2a A20G2 Heavy chain Fab domain | L M | Murine IgG2a A20G2 Light chain Fab domain | > undo [Repeated 2 time(s)]Undo failed, probably because structures have been modified. > close #36 > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final- > renumber-sure.pdb Summary of feedback from opening /Users/hemaozhou/Library/CloudStorage/OneDrive- 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final- renumber-sure.pdb --- warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0 Start residue of secondary structure not found: SHEET 37 3737 THR a 178 HIS a 180 0 Chain information for A35R-17H1_global_Final-renumber-sure.pdb #36 --- Chain | Description A a | No description available H h | No description available L l | No description available > show #!36-38 cartoons > hide #!36-38 atoms > select #36/A,a 1314 atoms, 1348 bonds, 166 residues, 1 model selected > open 4LQF 4lqf title: Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at the resolution of 2.3 Angstroms [more info...] Chain information for 4lqf #39 --- Chain | Description | UniProt A | A33R | Q71TT1_9POXV 89-185 H | Murine IgG2b A2C7 Heavy chain Fab domain | L | Murine IgG2b A2C7 Light chain Fab domain | Non-standard residues in 4lqf #39 --- ZN — zinc ion 4lqf mmCIF Assemblies --- 1| author_defined_assembly > color #36/H,h rgb (232, 111, 151) > color #36/l,L rgb (245, 204, 114) > select #36/A,a 1314 atoms, 1348 bonds, 166 residues, 1 model selected > color sel dodger blue > close #39 > select add #36 7760 atoms, 7944 bonds, 2 pseudobonds, 1010 residues, 2 models selected > select subtract #36 Nothing selected > mmaker #37 to #36 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain L (#36) with 4lqf, chain L (#37), sequence alignment score = 645.2 RMSD between 179 pruned atom pairs is 1.260 angstroms; (across all 211 pairs: 1.611) > mmaker #38 to #36 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain L (#36) with 4lu5, chain M (#38), sequence alignment score = 677.2 RMSD between 69 pruned atom pairs is 0.980 angstroms; (across all 211 pairs: 6.470) > view #36 clip false > mmaker #38 to #36/A Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lu5, chain A (#38), sequence alignment score = 332.4 RMSD between 77 pruned atom pairs is 0.667 angstroms; (across all 83 pairs: 1.746) > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > mmaker #37 to #36/A Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf, chain A (#37), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > open 4M1G Summary of feedback from opening 4M1G fetched from pdb --- note | Fetching compressed mmCIF 4m1g from http://files.rcsb.org/download/4m1g.cif 4m1g title: Structure of murine IgG2a A27D7-Fab in complex with vaccinia antigen A33R at the resolution of 1.6 Angstroms [more info...] Chain information for 4m1g #39 --- Chain | Description | UniProt A B | A33R | Q71TT1_9POXV 89-185 H | Murine IgG2a A27D7 Heavy chain Fab domain | L | Murine IgG2a A27D7 Light chain Fab domain | Non-standard residues in 4m1g #39 --- SO4 — sulfate ion > mmaker #39 to #36/A Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4m1g, chain A (#39), sequence alignment score = 346.8 RMSD between 71 pruned atom pairs is 0.786 angstroms; (across all 82 pairs: 1.630) > hide #!38 models > show #!38 models > hide #!36-39 atoms > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 58572 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 > undo > hide #!37 models > show #!37 models > sym #37 4lqf mmCIF Assemblies --- 1| author_defined_assembly| 2 copies of chains A,H,L > sym #37 assembly 1 Made 2 copies for 4lqf assembly 1 > view > mmaker #40 to #36/A Computing secondary structure [Repeated 2 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf, chain A (#40.1), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf, chain A (#40.2), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > undo > mmaker #40.1 to #36/A Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf, chain A (#40.1), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > mmaker #40.2 to #36/a Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain a (#36) with 4lqf, chain A (#40.2), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) > close #40 > sym #37 4lqf mmCIF Assemblies --- 1| author_defined_assembly| 2 copies of chains A,H,L > show #!37 models > sym #37 assembly 1 Made 2 copies for 4lqf assembly 1 > view > merge #40.1 #40.2 Unknown command: merge #40.1 #40.2 > combine #40.1 #40.2 Remapping chain ID 'A' in 4lqf #40.2 to 'B' Remapping chain ID 'H' in 4lqf #40.2 to 'I' Remapping chain ID 'L' in 4lqf #40.2 to 'M' > hide #!40.1 models > hide #!40 models > hide #!40.2 models > hide #!41 models > show #!41 models > mmaker #41 to #36/a Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain a (#36) with combination, chain A (#41), sequence alignment score = 339 RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs: 0.850) Cell requested for row 36 is out of bounds for table with 43 rows! Resizing table model. > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > align-analysis.cxs ——— End of log from Wed Apr 30 15:18:22 2025 ——— opened ChimeraX session > show #!40 models > hide #!40 models > hide #!38 models > show #!38 models > hide #!39 models > show #!39 models > hide #!41 models > show #!41 models > hide #!41 models > show #!41 models > hide #!41 models > show #!41 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > hide #!39 models > show #!39 models > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/4LU5.pdb > models #38 relModel #36 > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/4M1G.pdb > models #39 relModel #36 > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/4LQF.pdb > models #41 relModel #36 > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/A35R-17H1.pdb > models #36 relModel #36 > ui tool show ""Color Actions"" > hide #!36 models > show #!36 models > combine #38 > combine #39 > combine #41 > rename #44 ""copy of 4lqf"" > combine #36 > hide #!36 models > hide #!38 models > hide #!39 models > hide #!44 models > hide #!41 models > hide #!43 models > hide #!42 models > show #!44 models > hide #!45 models Drag select of 60 residues > select up 829 atoms, 850 bonds, 105 residues, 1 model selected > select up 1222 atoms, 1252 bonds, 156 residues, 1 model selected > delete sel > show #!43 models > hide #!44 models Drag select of 50 residues > select up 801 atoms, 819 bonds, 100 residues, 1 model selected > select up 1276 atoms, 1306 bonds, 163 residues, 1 model selected > delete sel > show #!42 models > hide #!43 models Drag select of 45 residues > select up 703 atoms, 719 bonds, 87 residues, 1 model selected > select up 1350 atoms, 1380 bonds, 173 residues, 1 model selected > delete sel > hide #!42 models > show #!42 models > show #!43 models > color #42 #73fdffff > color #43 #d783ffff > show #!44 models > color #44 #ff7e79ff > show #!45 models > surface #42-44 > lighting soft > surface #45/H,h,L,l > transparency #42-45 50 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes width 5 > graphics silhouettes width 3 > graphics silhouettes width 2 > graphics silhouettes #42 width 2 Expected true or false or a keyword > graphics silhouettes #42 width 5 Expected true or false or a keyword > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > graphics silhouettes width 5 > graphics silhouettes width 3 > graphics silhouettes width 2 > hide #!45 models > show #!45 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > transparency #42-45 10 > lighting flat > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting flat > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > lighting flat > graphics silhouettes true depthJump 0.2 > graphics silhouettes true depthJump 0.4 > graphics silhouettes true depthJump 0.2 > graphics silhouettes true depthJump 0.1 > graphics silhouettes true depthJump 0.2 > lighting soft > graphics silhouettes true depthJump 0.3 > graphics silhouettes width 4 > graphics silhouettes width 2 > graphics silhouettes width 3 > graphics silhouettes width 2 > select add #42 6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 2 models selected > select subtract #42 4 models selected > select add #42 6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 2 models selected > select subtract #42 4 models selected > select add #42 6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 2 models selected > select add #43 10397 atoms, 10100 bonds, 3 pseudobonds, 1831 residues, 8 models selected > select add #44 17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 13 models selected > select add #45 24915 atoms, 24804 bonds, 27 pseudobonds, 3873 residues, 19 models selected > select subtract #45 17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 21 models selected > select subtract #44 10397 atoms, 10100 bonds, 3 pseudobonds, 1831 residues, 14 models selected > select subtract #43 6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 8 models selected > select subtract #42 4 models selected > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > lighting full > lighting soft > lighting flat > graphics silhouettes true depthJump 0.2 > transparency #42-45 50 > transparency #42-45 0 > transparency #42-45 10 > transparency #42-45 20 > hide #!45 models > show #!45 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > select add #43 3739 atoms, 3336 bonds, 1 pseudobond, 915 residues, 2 models selected > select subtract #43 2 models selected > select add #43 3739 atoms, 3336 bonds, 1 pseudobond, 915 residues, 2 models selected > graphics silhouettes true depthJump 0.6 > graphics silhouettes true depthJump 0.2 > select subtract #43 2 models selected > select add #43 3739 atoms, 3336 bonds, 1 pseudobond, 915 residues, 2 models selected > select subtract #43 2 models selected > hide #!44 models > hide #!42 models > graphics silhouettes false > graphics silhouettes true > show #!44 models > show #!42 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > graphics silhouettes true depthJump 0.1 > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!44 models > show #!44 models > hide #!43 models > show #!43 models > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > color #42 #ff2f92ff > color #42 #ff7e79ff > color #42 #ffd479ff > color #42 #fffc79ff > color #42 #d4fb79ff > color #42 #fffc79ff > color #42 #d4fb79ff > color #42 #73fa79ff > hide #!43 models > show #!43 models > transparency #42-45 0 > hide #!44 models > hide #!43 models > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > show #!43 models > show #!44 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > graphics selection color black width 3 > select add #44 6758 atoms, 6760 bonds, 22 pseudobonds, 1032 residues, 3 models selected > select subtract #44 4 models selected > select add #44 6758 atoms, 6760 bonds, 22 pseudobonds, 1032 residues, 3 models selected > graphics silhouettes true depthJump 0.2 > graphics silhouettes true depthJump 0.3 > graphics silhouettes true depthJump 0.5 > graphics silhouettes true depthJump 0.8 > graphics silhouettes true depthJump 0.2 > select subtract #44 4 models selected > hide #!44 models > hide #!43 models > hide #!42 models > transparency #45 80 > show #!44 models > transparency #44-45 80 > show #!43 models > show #!42 models > transparency #42-45 80 > graphics silhouettes false > select add #44 6758 atoms, 6760 bonds, 22 pseudobonds, 1032 residues, 3 models selected > select add #43 10497 atoms, 10096 bonds, 23 pseudobonds, 1947 residues, 9 models selected > select add #42 17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 13 models selected > select add #45 24915 atoms, 24804 bonds, 27 pseudobonds, 3873 residues, 19 models selected > select subtract #45 17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 21 models selected > select #42-44, #45/H,h,L,l Expected an objects specifier or a keyword > select #42-44, sel #45/H,h,L,l Expected an objects specifier or a keyword > select #42-44 sel #45/H,h,L,l Expected a keyword > select #42-44 17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 7 models selected > select #45/H,h,L,l 6446 atoms, 6596 bonds, 2 pseudobonds, 844 residues, 2 models selected > select #42-44 17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 7 models selected > select #42-44, #45/H,h,L,l Expected an objects specifier or a keyword > select #42-44, 45/H,h,L,l 16733 atoms, 16693 bonds, 15 pseudobonds, 2573 residues, 9 models selected > select #42-44, 45/H,h,L,l,M 20181 atoms, 20172 bonds, 25 pseudobonds, 3061 residues, 9 models selected > select #42-44, 45/H,h,L,l,M,N 20181 atoms, 20172 bonds, 25 pseudobonds, 3061 residues, 9 models selected > select #42-44, 45/H,h,L,l,M,N,I 23413 atoms, 23456 bonds, 27 pseudobonds, 3519 residues, 9 models selected > transparency (#!42-45 & sel) 10 > graphics silhouettes true depthJump 0.1 > graphics silhouettes true depthJump 0.4 > graphics silhouettes true depthJump 0.6 > transparency (#!42-45 & sel) 0 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes true depthJump 0.2 > graphics silhouettes false > graphics silhouettes true > lighting soft > transparency (#!42-45 & sel) 10 > lighting soft > transparency (#!42-45 & sel) 0 Drag select of copy of 4lu5_L SES surface, 32351 of 197904 triangles, copy of 4lqf_H SES surface, 49873 of 184766 triangles, copy of 4lqf_L SES surface, 100098 of 200140 triangles, copy of A35R-17H1_global_Final-renumber-sure.pdb_h SES surface, 96576 of 199722 triangles, copy of A35R-17H1_global_Final- renumber-sure.pdb_l SES surface, 97071 of 206196 triangles, 423 residues, 2 pseudobonds > select up 3838 atoms, 3912 bonds, 2 pseudobonds, 506 residues, 10 models selected > select up 8215 atoms, 8415 bonds, 2 pseudobonds, 1072 residues, 10 models selected > select up 8291 atoms, 8415 bonds, 2 pseudobonds, 1148 residues, 10 models selected > select ~sel & ##selected 12885 atoms, 13053 bonds, 14 pseudobonds, 1810 residues, 7 models selected > select clear > view list Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, LCDR, Light-footprint, global- rotate90, global-view > view global-view > view Light-footprint > view global-view > graphics silhouettes true depthJump 0.2 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > hide #!44 models > show #!44 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > select clear > hide sel > select clear > hide #43.1 models > hide #43.2 models > hide #43.3 models > show #43.3 models > show #43.2 models > save /Users/hemaozhou/Desktop/structural-comparison.tiff width 2794 height > 2576 supersample 4 transparentBackground true > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure- > alignment-with-VAVC.cxs ——— End of log from Tue May 13 23:18:00 2025 ——— opened ChimeraX session > hide #!42 models > hide #!43 models > hide #!44 models > hide #!45 models > show #!36 models > hide #!36 models > show #!36 models > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- > sure.pdb Summary of feedback from opening /Users/hemaozhou/Library/CloudStorage/OneDrive- 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber- sure.pdb --- warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0 Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a 180 0 Chain information for A35R-17H1_local_Final_renumber-sure.pdb #46 --- Chain | Description A a | No description available H h | No description available L l | No description available > hide #46#!36 atoms > show #46#!36 cartoons > hide #!36 models > hide #46 models > show #46 models > hide #46 models > show #46 models > show #35 models > hide #46 models > show #46 models > hide #46 models > show #46 models > hide #46 models > hide #35 models > show #34 models > hide #34 models > show #35 models > show #34 models > hide #35 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > hide #34 models > show #34 models > show #35 models > hide #34 models > close #46#37-45 > combine #35 [Repeated 5 time(s)] > rename #37 HCDR1 > rename #38 HCDR2 > rename #39 HCDR3 > rename #40 LCDR1 > rename #41 LCDR2 > rename #42 LCDR3 > hide #37-42 target m > hide #35 models > show #37 models > select #37/H:45-52 67 atoms, 69 bonds, 8 residues, 1 model selected > select ~sel & ## selected 2318 atoms, 2374 bonds, 297 residues, 1 model selected > delete sel > show #37 > hide #!37 cartoons > color byhetero > hide #37 atoms > show #37 atoms > style #37 stick Changed 67 atom styles > show #38 models > select #38/H:70-77 58 atoms, 59 bonds, 8 residues, 1 model selected > select ~sel & ## selected 2327 atoms, 2384 bonds, 297 residues, 1 model selected > delete sel > show #38 > hide #!38 cartoons > color byhetero > style #37-38 stick Changed 125 atom styles > select #39/H:116-123 66 atoms, 66 bonds, 8 residues, 1 model selected > select ~sel & ## selected 2319 atoms, 2377 bonds, 297 residues, 1 model selected > delete sel > show #39 > hide #!39 cartoons > color byhetero > style #37-38 stick Changed 125 atom styles > show #39 models > style #37-39 stick Changed 191 atom styles > select #40/L:46-51 51 atoms, 51 bonds, 6 residues, 1 model selected > select ~sel & ## selected 2334 atoms, 2392 bonds, 299 residues, 1 model selected > delete sel > show #40 > hide #!40 cartoons > color byhetero > select #40/L:46-51 51 atoms, 51 bonds, 6 residues, 1 model selected > select ~sel & ## selected Nothing selected > delete sel > show #40 > hide #!40 cartoons > color byhetero > show #40 models > hide #39 models > hide #38 models > hide #37 models > style #40 stick Changed 51 atom styles > show #41 models > hide #40 models > select #41/L:69-71 24 atoms, 23 bonds, 3 residues, 1 model selected > select ~sel & ## selected 2361 atoms, 2420 bonds, 302 residues, 1 model selected > delete sel > show #41 > hide #!41 cartoons > color byhetero > style #41 stick Changed 24 atom styles > hide #41 models > show #42 models > select #42/L:108-116 83 atoms, 86 bonds, 9 residues, 1 model selected > select ~sel & ## selected 2302 atoms, 2357 bonds, 296 residues, 1 model selected > delete sel > show #42 > hide #!42 cartoons > color byhetero > style #42 stick Changed 83 atom styles > hide #42 models > show #37 models > hide #37 models > show #35 models > combine #35 > hide #35 models > select #43/A:118-128 77 atoms, 77 bonds, 11 residues, 1 model selected > select ~sel & ##selected 2308 atoms, 2366 bonds, 294 residues, 1 model selected > delete sel > show #43 atoms > hide #43 cartoons > style #43 stick Changed 77 atom styles > open /Users/hemaozhou/Library/CloudStorage/OneDrive- > 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #44, grid size 300,300,300, pixel 1.2, shown at level 0.0147, step 1, values float32 > volume #44 level 6.911 > volume zone #44 nearAtoms #37 range 2.5 > hide #43 models > show #37 models > volume #44 style mesh > volume #44 level 6.762 > volume #44 level 6.194 > volume #44 level 6.493 > view name HCDR1-map > save /Users/hemaozhou/Desktop/HCDR1-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > hide #!44 models > show #!44 models > show #38 models > hide #37 models > volume zone #44 nearAtoms #38 range 2.5 > hide #38 models > show #38 models > combine #35 > close #38 > combine #35 > rename #38 HCDR2 > close #45 > select #38/H:69-77 70 atoms, 72 bonds, 9 residues, 1 model selected > select ~sel & ## selected 2315 atoms, 2371 bonds, 296 residues, 1 model selected > delete sel > show #38 > hide #!38 cartoons > color byhetero > style #38 stick Changed 70 atom styles > volume zone #44 nearAtoms #38 range 2.5 > volume #44 level 6.075 > volume #44 level 6.433 > volume #44 level 6.612 > volume #44 level 6.2 > view name HCDR2-map > save /Users/hemaozhou/Desktop/HCDR2-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > hide #38 models > show #39 models > volume zone #44 nearAtoms #39 range 2.5 > volume #44 level 3.931 > volume #44 level 5.722 > volume #44 level 6.021 > volume #44 level 6.319 > volume #44 level 6.2 > view name HCDR3-map > save /Users/hemaozhou/Desktop/HCDR3-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > volume zone #44 nearAtoms #40 range 2.5 > show #40 models > hide #39 models > volume #44 level 6.1 > save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > view name LCDR1-map > save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > hide #40 models > show #41 models > volume zone #44 nearAtoms #41 range 2.5 > volume #44 level 5.8 > volume #44 level 5.5 > volume #44 level 5.8 > view name LCDR2-map > save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > close #41 > combine #35 > select #41/L:69-71 24 atoms, 23 bonds, 3 residues, 1 model selected > select ~sel & ## selected 2361 atoms, 2420 bonds, 302 residues, 1 model selected > delete sel > show #41 > hide #!41 cartoons > color byhetero > style #41 stick Changed 24 atom styles > close #41 > combine #35 > select #41/L:68-72 47 atoms, 47 bonds, 5 residues, 1 model selected > select ~sel & ## selected 2338 atoms, 2396 bonds, 300 residues, 1 model selected > delete sel > show #41 > hide #!41 cartoons > color byhetero > style #41 stick Changed 47 atom styles > volume zone #44 nearAtoms #41 range 2.5 > volume #44 level 6.039 > volume #44 level 5.8 > save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > view name LCDR2-map > hide #41 models > show #42 models > volume zone #44 nearAtoms #42 range 2.5 > volume #44 level 6.2 > view name LCDR3-map > save /Users/hemaozhou/Desktop/LCDR3-map-new.tiff width 2794 height 2576 > supersample 4 transparentBackground true > save > /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Density- > map.cxs ——— End of log from Wed May 14 15:05:00 2025 ——— opened ChimeraX session > rename #41 LCDR2 OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AV0005NCH/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 11881.81.2 OS Loader Version: 11881.81.2 Software: System Software Overview: System Version: macOS 15.3 (24D60) Kernel Version: Darwin 24.3.0 Time since boot: 35天30分钟 Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 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 Redmi 27 NU: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-clix: 0.2.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect new normal Unassigned