id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19808 ChimeraX bug report submission chengtao.xu@… "{{{ The following bug report has been submitted: Platform: macOS-15.7.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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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""82c56b840f6684891fa68812616e7f0450124f05"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"" Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512, pixel 1.07, shown at level 0.142, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 Log from Tue Feb 3 15:37:02 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"" Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512, pixel 1.07, shown at level 0.142, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 Log from Tue Feb 3 13:26:30 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_2_movie1.cxs"" Log from Mon Feb 2 10:29:38 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM2.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.227, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384, pixel 1.07, shown at level 0.248, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel 1.07, shown at level 0.153, step 1, values float32 Log from Sun Feb 1 21:27:29 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 1.07, shown at level 0.145, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384, pixel 1.07, shown at level 0.143, step 1, values float32 Log from Thu Jan 15 09:33:23 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 1.07, shown at level 0.145, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384, pixel 1.07, shown at level 0.138, step 1, values float32 Log from Tue Jan 13 14:05:11 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 1.07, shown at level 0.145, step 1, values float32 Log from Tue Jan 13 12:34:22 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/merged_real_space_refined_007.pdb"" Chain information for merged_real_space_refined_007.pdb #2 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > hide atoms > show cartoons > set bgColor white > surface dust #1 size 10.7 > volume #1 step 1 > volume #1 level 0.1467 > hide #!1 models > select #2/D 2438 atoms, 2496 bonds, 297 residues, 1 model selected > ui tool show ""Color Actions"" > color sel hot pink > ui tool show ""Color Actions"" > color sel pink > select #2/A 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > select #2/S,R,Q,P,O,N 5281 atoms, 5363 bonds, 1 pseudobond, 664 residues, 2 models selected > ui tool show ""Color Actions"" > color sel gold > color sel orange > color sel gold > color sel orange > select #2/M,L,K,J,I,H,C, Expected an objects specifier or a keyword > select #2/M,L,K,J,I,H,C 16170 atoms, 16420 bonds, 1 pseudobond, 2079 residues, 2 models selected > ui tool show ""Color Actions"" > color sel medium sea green > color sel light green > color sel pale green > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_color1.cxs"" > select add #2 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #2 Nothing selected > lighting soft > lighting simple > lighting soft > lighting flat > open /Volumes/CHENGTAO/cryosparc_P6_J96_005_volume_map.mrc Opened cryosparc_P6_J96_005_volume_map.mrc as #3, grid size 256,256,256, pixel 1.61, shown at level 0.107, step 1, values float32 > surface dust #3 size 16.1 > lighting full > lighting soft > hide #!2 models > open /Volumes/CHENGTAO/cryosparc_P6_J97_004_volume_map.mrc Opened cryosparc_P6_J97_004_volume_map.mrc as #4, grid size 256,256,256, pixel 1.61, shown at level 0.11, step 1, values float32 > open /Volumes/CHENGTAO/cryosparc_P6_J98_004_volume_map.mrc Opened cryosparc_P6_J98_004_volume_map.mrc as #5, grid size 256,256,256, pixel 1.61, shown at level 0.103, step 1, values float32 > open /Volumes/CHENGTAO/cryosparc_P6_J99_004_volume_map.mrc Opened cryosparc_P6_J99_004_volume_map.mrc as #6, grid size 256,256,256, pixel 1.61, shown at level 0.107, step 1, values float32 > surface dust #3 size 16.1 > surface dust #4 size 16.1 > surface dust #5 size 16.1 > surface dust #6 size 16.1 > volume #3 level 0.2172 > volume #4 level 0.1954 > volume #4 level 0.2116 > volume #4 level 0.2035 > volume #5 level 0.2178 > volume #6 level 0.225 > volume #6 level 0.2054 > hide #!3 models > show #!2 models > show #!3 models > select add #2 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.86578,-0.49991,0.022818,486.88,0.49898,-0.86584,-0.036613,283.9,0.03806,-0.020313,0.99907,-3.613 > undo > select subtract #2 Nothing selected > hide #!2 models > show #!4 models > show #!5 models > show #!6 models > hide #!3 models > hide #!4 models > open ""/Users/xuchengtao/Documents/Building models undergoing/20251222 IVC > intermediate/20260112 IVC > intermediate/merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb"" Chain information for merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb #7 --- Chain | Description A | No description available B E G | No description available C | No description available D | No description available F H | No description available I | No description available J | No description available K L M O | No description available N | No description available P | No description available Q | No description available > show #!7 cartoons > hide #!7 atoms > show #!4 models > show #!3 models > hide #!7 models > volume #3 level 0.2008 > open ""/Users/xuchengtao/Documents/Building models undergoing/20251222 IVC > intermediate/flipped_cryosparc_P6_J90_004_volume_map.mrc"" Opened flipped_cryosparc_P6_J90_004_volume_map.mrc as #8, grid size 384,384,384, pixel 1.07, shown at level 0.0589, step 2, values float32 > surface dust #4 size 16.1 > surface dust #5 size 16.1 > surface dust #6 size 16.1 > surface dust #8 size 10.7 > ui tool show ""Fit in Map"" > ui mousemode right ""translate selected models"" > select add #8 2 models selected > view matrix models > #8,-0.71372,-0.49135,0.49917,334.98,-0.54393,0.83781,0.046962,132.29,-0.44129,-0.238,-0.86523,550.67 > view matrix models > #8,0.97257,0.03667,-0.2297,35.228,0.058924,-0.99413,0.090782,387.87,-0.22503,-0.10183,-0.96902,451.87 > volume #8 step 1 > volume #8 level 0.09502 > fitmap #8 inMap #3 Fit map flipped_cryosparc_P6_J90_004_volume_map.mrc in map cryosparc_P6_J96_005_volume_map.mrc using 324674 points correlation = 0.9805, correlation about mean = 0.9142, overlap = 2.547e+04 steps = 216, shift = 16.2, angle = 21 degrees Position of flipped_cryosparc_P6_J90_004_volume_map.mrc (#8) relative to cryosparc_P6_J96_005_volume_map.mrc (#3) coordinates: Matrix rotation and translation 0.97292447 0.21705585 0.07940239 -51.11804392 0.21669675 -0.97614950 0.01321611 360.31959015 0.08037724 0.00434796 -0.99675503 373.34043768 Axis -0.99320802 -0.10918025 -0.04021824 Axis point 0.00000000 183.38879293 187.30072229 Rotation angle (degrees) 179.74420803 Shift along axis -3.58402524 > select subtract #8 Nothing selected > show #!7 models > hide #!7 models > volume #8 level 0.1269 > hide #!6 models > show #!6 models > hide #!8 models > show #!8 models > hide #!6 models > volume #8 level 0.1181 > hide #!8 models > show #!6 models > volume #6 level 0.2054 > show #!7 models > volume #3 level 0.2069 > volume #4 level 0.2577 > volume #5 level 0.2147 > volume #6 level 0.2229 > hide #!6 models > show #!8 models > hide #!7 models > volume #8 level 0.134 > volume #6 level 0.2142 > volume #6 level 0.2287 [Repeated 1 time(s)] > volume #5 level 0.2392 > volume #5 level 0.2178 > volume #6 level 0.2083 > volume #6 level 0.2025 > volume #4 level 0.1914 > volume #5 level 0.2055 > volume #5 level 0.1872 > volume #4 level 0.2095 > show #!7 models > volume #3 level 0.1826 > volume #4 showOutlineBox true > volume #4 level 0.1945 > volume #4 showOutlineBox false > volume #4 level 0.1824 > volume #3 level 0.1673 > volume #5 level 0.1903 > hide #!7 models > volume #5 level 0.1658 > volume #4 level 0.1794 > volume #5 level 0.1933 > volume #5 level 0.2269 > volume #4 level 0.2246 > show #!7 models > volume #3 level 0.216 > volume #3 level 0.1978 > volume #5 level 0.2086 > hide #!7 models > show #!5 models > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > hide #!6 models > hide #!5 models > show #!4 models > volume #4 level 0.1794 > volume #5 level 0.1719 > volume #6 level 0.1734 > volume #5 level 0.1475 > volume #4 level 0.2095 > volume #6 level 0.22 > volume #3 level 0.213 > volume #4 level 0.2155 > show #!7 models > color #4 #b2ffffb0 models > color #4 #f4fcfeb1 models > color #4 #9a9fa0b1 models > color #4 #8e9293b1 models > color #4 #6c7070b1 models > color #4 #9ca1a2b1 models > color #4 #9ca1a2b0 models > color #3 #909071ff models > color #3 #867f90ff models > color #3 #867f90b3 models > hide #!4 models > show #!5 models > color #5 #b2b2ffba models > color #5 #f3ecfaba models > color #5 #95919aba models > color #6 #faf3fbff models > color #6 #817d82ff models > color #6 #817d82a5 models > color #6 #817d82a6 models > volume #5 level 0.2422 > volume #5 level 0.1994 > hide #!5 models > show #!6 models > volume #6 level 0.2038 > volume #6 level 0.2394 > volume #6 level 0.2167 > volume #6 level 0.2135 > volume #4 level 0.2357 > volume #3 level 0.2333 > volume #6 level 0.233 > copy #2 Unknown command: copy #2 > duplicate #2 Unknown command: duplicate #2 > mcopy #2 Missing required ""to_atoms"" argument > combine #2 > hide #!7 models > show #!2 models > hide #!2 models > show #!7 models > select add #9 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > view matrix models > #9,-0.78485,0.6147,-0.07848,262.35,-0.61967,-0.77759,0.10659,471.23,0.0044959,0.13229,0.9912,-26.215 > mmaker #9 to #7 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 merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb, chain A (#7) with copy of merged_real_space_refined_007.pdb, chain A (#9), sequence alignment score = 2382.1 RMSD between 256 pruned atom pairs is 1.157 angstroms; (across all 517 pairs: 3.343) > select subtract #9 Nothing selected > hide #!9 models > show #!9 models > hide #!7 models > show #!7 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!7 models > show #!2 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_2_states_compare.cxs"" > color zone #1 Missing required ""near"" argument > color zone #1 near #2 > color zone #1 near #2 range 3 Expected a keyword > open ""/Users/xuchengtao/Documents/Building models undergoing/20251030 > 8mut_ssDNA/DNA-RNA/IscB_8mut_ssDNA_DNA_model_coloring.cxc"" > hide #!4-13 models > select #1/A:1-54 Nothing selected > color sel hotpink > select #1/A:55-85,161-196,297-374 Nothing selected > color sel royalblue > select #1/A:86-122 Nothing selected > color sel mediumslateblue > select #1/A:123-160 Nothing selected > color sel yellow > select #1/A:197-296 Nothing selected > color sel orange > select #1/A:375-429 Nothing selected > color sel lightsalmon > select #1/A:430-496 Nothing selected > color sel blueviolet > select #1/D Nothing selected > color sel dodgerblue > select #1/B:1-16 Nothing selected > color sel firebrick > select #1/B:17-256 Nothing selected > color sel silver executed IscB_8mut_ssDNA_DNA_model_coloring.cxc > color zone #1 near #2 range 3 Expected a keyword > color zone #1 near #2 distance 3 > color zone #1 near #2 distance 3.5 > hide #!2 models > show #!2 models > hide #!1 models > select @2/G 4324 atoms, 4594 bonds, 395 residues, 3 models selected > select #2/G 983 atoms, 1100 bonds, 46 residues, 1 model selected > ui tool show ""Color Actions"" > color sel wheat > color sel khaki > select #2/F 972 atoms, 1090 bonds, 47 residues, 1 model selected > ui tool show ""Color Actions"" > color sel deep sky blue > color sel dodger blue > color sel cornflower blue > color sel dodger blue > select #2/E 200 atoms, 222 bonds, 10 residues, 1 model selected > ui tool show ""Color Actions"" > color sel tomato > color sel dark salmon > color sel hot pink > color sel pale violet red > color sel deep pink > color sel hot pink > select add #2 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #2 Nothing selected > color zone #1 near #2 distance 3.5 > show #!1 models > volume #1 level 0.1611 > hide #!2 models > volume #1 level 0.17 > volume #1 level 0.16 > color zone #1 near #2 distance 4 > volume #1 level 0.12 > volume #1 level 0.13 > volume #1 level 0.14 > volume #1 level 0.145 > save /Users/xuchengtao/Desktop/image166.png supersample 3 > color zone #1 near #2 distance 4.5 > save /Users/xuchengtao/Desktop/image167.png supersample 3 > hide #!1 models > show #!7 models > show #!9 models > hide #!7 models > hide #!9 models > show #!2 models > save /Users/xuchengtao/Desktop/image168.png supersample 3 > save /Users/xuchengtao/Desktop/image169.png supersample 3 > select add #2 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > cartoon style (#!2 & sel) modeHelix tube sides 20 > select subtract #2 Nothing selected > save /Users/xuchengtao/Desktop/image170.png supersample 3 > save /Users/xuchengtao/Desktop/image171.png supersample 3 > show #!1 models > hide #!2 models > save /Users/xuchengtao/Desktop/image172.png supersample 3 > hide #!1 models > show #!3 models > show #!4 models > show #!5 models > close #3-6,8 > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_color1.cxs"" ——— End of log from Tue Jan 13 12:34:22 2026 ——— > view name session-start opened ChimeraX session > show #!7 models > show #!9 models > hide #!7 models > hide #!9 models > close #7,9 > show #!2 models > combine #2 > hide #!1 models > hide #!2 models > combine #1 No structures specified > copy #1 Unknown command: copy #1 > duplicate #1 Unknown command: duplicate #1 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > close #4 > select #3/S,R,q,p,o,n 5281 atoms, 5363 bonds, 1 pseudobond, 664 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light gray > color sel gray > color sel light gray > color sel dark gray > color sel light gray > select #3/m,l,k,j,i,H,C 16170 atoms, 16420 bonds, 1 pseudobond, 2079 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light gray > volume copy #1 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384, pixel 1.07, shown at step 1, values float32 > color #4 #b2b2b299 models > color zone #4 near #3 distance 4 > color #4 #b2b2b280 models > color #4 #b2b2b299 models > transparency Missing or invalid ""percent"" argument: Expected a number > transparency #3 60 > hide #!3 models > show #!3 models > transparency #4 60 > color zone #4 near #3 distance 4 > transparency #4 60 > surface dust #4 size 10.7 > hide #!3 models > transparency #4 80 > color zone #4 near #3 distance 4 > transparency #4 90 > color zone #4 near #3 distance 4 > transparency #4 10 > lighting soft > lighting simple > lighting flat > lighting soft > lighting flat > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > lighting full > lighting simple [Repeated 1 time(s)] > lighting full > save /Users/xuchengtao/Desktop/image186.png supersample 3 > save /Users/xuchengtao/Desktop/image187.png supersample 3 > select add #3 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #3 Nothing selected > show #!3 models > hide #!4 models > hide #3 cartoons > show #3/A cartoons > ui mousemode right select > style #!3 stick Changed 30522 atom styles > show #!3 atoms > color #!3 byhetero > show #!4 models > hide #!4 models > transparency #4 20 > show #!4 models > hide #!3 models > show #!3 models > transparency #4.1 0 > transparency #4 20 > transparency #4 50 > volume #4 level 0.1208 > color zone #4 near #3 distance 4 > hide #!3 atoms > color zone #4 near #3 distance 4 > select #3/A 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > color zone #4 near #3 distance 4 > select add #3 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #3 Nothing selected > hide #!4 models > style #!3 stick Changed 30522 atom styles > show #!3 atoms > style #!3 stick Changed 30522 atom styles > color #!3 byhetero > hide #3/A > hide #!3 models > show #!3 models > hide #!3 models > select #3/A:115,147,146,159,94,93,70,97,54 87 atoms, 85 bonds, 9 residues, 1 model selected > show sel atoms > show #!3 models > hide #3/A cartoons > select add #3 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #3 Nothing selected > hide #3 cartoons > hide #3 atoms > show sel atoms > select #3/A:115,147,146,159,94,93,70,97,54 87 atoms, 85 bonds, 9 residues, 1 model selected > show sel atoms > show #!4 models > combine #3 > hide #!3 models > hide #!4 models > select add #3 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > show #!1 models > select subtract #3 Nothing selected > color zone #4 near #1 distance 5 color zone: No atoms specified. > show #!4 models > hide #!1 models > color #4 #b8bfbb66 models > color zone #4 near #1 distance 5 color zone: No atoms specified. > color zone #4 near #2 distance 5 > volume #4 level 0.13 > volume #4 level 0.135 > lighting soft > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!4 models > show #!4 models > volume #4 level 0.14 > transparency #4 20 > ui tool show ""Side View"" > transparency #4 50 > volume #4 level 0.138 > color zone #4 near #2 distance 5 > transparency #4 50 [Repeated 1 time(s)] > transparency #4 70 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs"" ——— End of log from Tue Jan 13 14:05:11 2026 ——— > view name session-start opened ChimeraX session > hide #!4 models > hide #!5 models > show #!3 models > show #!4 models > hide #!3 models > show #!1 models > hide #!4 models > hide #!1 models > show #!4 models > show #!5 models > hide #!4 models > show #!4 models > hide #!5 models > show #!3 models > hide #!4 models > show #!5 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > show #5 cartoons > show #5 atoms > hide #5 atoms > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > color zone #4 near #5 distance 5 > hide #!5 atoms > color zone #4 near #5 distance 5 > volume #4 level 0.09687 > volume #4 style mesh > volume #4 style surface > volume #4 level 0.1428 > color #!5 bychain > undo > hide #!4 models > show #!1 models > hide #!1 models > show #!5 atoms > select #5/E,F,A,D 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected > hide #5 cartoons > hide #5 atoms > select #5/E,F,A,D 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected > show sel cartoons > select #5/A 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > select #5/F 972 atoms, 1090 bonds, 47 residues, 1 model selected > ui tool show ""Color Actions"" > color sel deep sky blue > undo > color sel dodger blue [Repeated 3 time(s)] > select #5/D 2438 atoms, 2496 bonds, 297 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light pink > select #5/E 200 atoms, 222 bonds, 10 residues, 1 model selected > ui tool show ""Color Actions"" > color sel hot pink [Repeated 3 time(s)] > select add #5 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #5 Nothing selected > show #!5 atoms > hide #!5 atoms > select #5/A,D,E,F 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected > show #!4 models > hide #!4 models > show #!4 models > volume zone #4 nearAtoms 5 dist 4.5 Invalid ""nearAtoms"" argument: invalid atoms specifier > volume zone #4 nearAtoms #5 dist 4.5 Expected a keyword > volume zone #4 nearAtoms #5 > volume zone #4 nearAtoms sel > show #!4 models > volume zone #4 nearAtoms sel dist 5 Expected a keyword > volume zone #4 nearAtoms sel dis4 Expected a keyword > volume zone #4 nearAtoms sel dis 4 Expected a keyword > volume zone #4 nearAtoms sel range 4 > volume zone #4 nearAtoms sel range 3 > volume zone #4 nearAtoms sel range 2 > volume zone #4 nearAtoms sel range 2.5 > color zone #4 near sel distance 4 > select add #5 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #5 Nothing selected > hide #!5 models > volume zone #4 nearAtoms sel range 3 no atoms specified for zone > select #5/A,D,E,F 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected > volume zone #4 nearAtoms sel range 3 > transparency #4 50 > show #!5 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs"" Drag select of 4 cryosparc_P6_J91_004_volume_map.mrc copy , 10 residues > select clear > open ""/Users/xuchengtao/Documents/Building models > undergoing/20251003IVC/20251222 Xiaomeng AI > IVC/merged_real_space_refined_009.pdb"" Chain information for merged_real_space_refined_009.pdb #6 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > hide #!4 models > hide #!5 models > select add #6 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > hide sel atoms > show sel cartoons > select subtract #6 Nothing selected > hide #!6 models > show #!5 models > show #!4 models > hide #!5 models > hide #!4 models > show #!5 models > select #5/E:8 19 atoms, 20 bonds, 1 residue, 1 model selected > hide #5/F:1-36 > hide #5/F:1-36 cartoons > show #5/F:34-37 cartoons Drag select of 9 residues > select #5/E:6 22 atoms, 24 bonds, 1 residue, 1 model selected Drag select of 9 residues > select add #5/E:6 209 atoms, 24 bonds, 10 residues, 1 model selected > select add #5/E:7 228 atoms, 44 bonds, 11 residues, 1 model selected > select subtract #5/E:7 209 atoms, 24 bonds, 10 residues, 1 model selected > select add #5/E:7 228 atoms, 44 bonds, 11 residues, 1 model selected > select add #5/E:8 247 atoms, 64 bonds, 12 residues, 1 model selected > select subtract #5/E:8 228 atoms, 44 bonds, 11 residues, 1 model selected > select add #5/E:8 247 atoms, 64 bonds, 12 residues, 1 model selected > select subtract #5/E:8 228 atoms, 44 bonds, 11 residues, 1 model selected > select add #5/E:9 247 atoms, 64 bonds, 12 residues, 1 model selected > select add #5/E:8 266 atoms, 84 bonds, 13 residues, 1 model selected > select add #5/E:10 285 atoms, 104 bonds, 14 residues, 1 model selected > select add #5/F:43 304 atoms, 124 bonds, 15 residues, 1 model selected > select add #5/F:42 325 atoms, 147 bonds, 16 residues, 1 model selected > select add #5/F:41 344 atoms, 167 bonds, 17 residues, 1 model selected > select add #5/F:40 366 atoms, 191 bonds, 18 residues, 1 model selected > select add #5/F:39 388 atoms, 215 bonds, 19 residues, 1 model selected > select add #5/F:38 410 atoms, 239 bonds, 20 residues, 1 model selected > select add #5/F:37 432 atoms, 263 bonds, 21 residues, 1 model selected > select add #5/F:36 453 atoms, 286 bonds, 22 residues, 1 model selected > select add #5/F:35 472 atoms, 306 bonds, 23 residues, 1 model selected > select add #5/F:34 492 atoms, 327 bonds, 24 residues, 1 model selected > show sel atoms > color sel byhetero > color sel bychain > select add #5 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected > select subtract #5 Nothing selected > select #5/A:400,405,434,532,355 48 atoms, 43 bonds, 5 residues, 1 model selected > show sel atoms > color sel byhetero > hbonds sel reveal true 44 hydrogen bonds found > undo > color sel byhetero > hide #5/A:403 > select add #5 30522 atoms, 31271 bonds, 13 pseudobonds, 3693 residues, 3 models selected > select subtract #5 Nothing selected > lighting simple > lighting soft Drag select of 1 residues > select #5/D:159 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel byhetero > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs"" [Repeated 1 time(s)] ——— End of log from Thu Jan 15 09:33:23 2026 ——— > view name session-start opened ChimeraX session > close session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"" Chain information for merged_real_space_refined_011.pdb #2 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > style stick Changed 30524 atom styles > show cartoons > volume #1 step 1 > surface dust #1 size 10.7 > hide #!1 models > hide #2 > hide #2 cartoons > show #2/E:1-10 > show #2/F:37-47 > show #2/A > select #2/A 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > select #2/F 972 atoms, 1090 bonds, 47 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > ui tool show ""Color Actions"" > color sel deep sky blue > color sel royal blue > select #2/E 200 atoms, 222 bonds, 10 residues, 1 model selected > color sel hot pink > select #2/D 2438 atoms, 2496 bonds, 297 residues, 1 model selected > show > Hide Unknown command: Hide > hide > undo > show #2/D > color sel red > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #2 Nothing selected > color byhetero > undo > show #2/D [Repeated 1 time(s)] > select #2/D 2438 atoms, 2496 bonds, 297 residues, 1 model selected > ui tool show ""Color Actions"" > color sel violet > color sel light pink > volume copy #1 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #3, grid size 384,384,384, pixel 1.07, shown at step 1, values float32 > volume #3 level 0.1685 > volume #1 level 0.1879 > color #1 #b2b2b2ad models > color #3 #b2b2b2a9 models > color #3 #b2b2b2a8 models > volume #1 near #2/D range 3 Expected a keyword > volume zone #1 nearAtoms #2/D range 3 > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > hide #!1 models > hide #!3 models > select subtract #2 Nothing selected > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #2 Nothing selected > show #!1 models > volume #1 level 0.2145 > volume zone #3 nearAtoms #2/A range 3 > hide #!1 models > show #!3 models > hide #!3 models > select add #1 2 models selected > show #!1 models > ui tool show ""Color Actions"" > color sel light pink > color #1 #b2b2b29e models [Repeated 1 time(s)] > color #1 #b2b2b284 models > color #1 #b2b2b280 models > color #1 hotpink > color #1 lightpink > select ~sel & ##selected Nothing selected > color #1 hotpink transparency 20 > color #1 lightpink transparency Missing ""transparency"" keyword's argument > color #1 lightpink transparency 20 > color #1 lightpink transparency 60 > color #3 cornflowerblue transparency 60 > show #!3 models > ui tool show ""Color Actions"" > color #3 lightskyblue transparency 60 > volume #3 level 0.1491 > hide #2/F:42-47 > hide #2/F:37 > hide #!3 models > hide #!1 models > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > volume #4 step 1 > close #1,3 > volume copy #4 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384, pixel 1.07, shown at step 1, values float32 > volume #4 level 0.1491 > volume #1 level 0.154 > color #1 lightpink transparency 60 > color #4 lightskyblue transparency 60 > volume #4 level 0.2217 > volume #1 level 0.2217 > hide #2/E:1-5 > hide #2/E:10 > volume zone #1 nearAtoms #2/D range 4 > volume zone #4 nearAtoms #2/A range 4 > volume #4 level 0.1879 > volume #4 level 0.1927 > volume #4 level 0.212 > volume zone #4 nearAtoms #2/A range 2.5 > volume zone #1 nearAtoms #2/D range 2.5 > hide #2/A > hide #2/D > volume #4 level 0.1854 > volume #1 level 0.1951 > nucleotides fill > style nucleic stick Changed 2155 atom styles > color byhetero > nucleotides atoms > style nucleic stick Changed 2155 atom styles > volume #1 level 0.1612 > select #2/A:434 11 atoms, 10 bonds, 1 residue, 1 model selected > show (sel-residues & sidechain) target ab > volume #4 level 0.2 > volume #4 level 0.1927 > volume #4 level 0.1975 > select #2/A:405 9 atoms, 8 bonds, 1 residue, 1 model selected > show (sel-residues & sidechain) target ab > select #2/D:159 6 atoms, 5 bonds, 1 residue, 1 model selected > show (sel-residues & sidechain) target ab > volume zone #4 nearAtoms #2/A range 23 > volume zone #4 nearAtoms #2/A range 2.3 > volume zone #4 nearAtoms #2/A range 2 > volume zone #4 nearAtoms #2/A range 2.3 > volume zone #4 nearAtoms #2/A range 2 > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #2 Nothing selected > lighting full > ui tool show ""Side View"" > hbonds reveal true 3027 hydrogen bonds found > ~hbonds > undo [Repeated 3 time(s)] > hide #2 > show #2/E:5-9 > show #2/F:38-41 > hide #2/E:5 > hide #2/E:6 > select #2/D:159 6 atoms, 5 bonds, 1 residue, 1 model selected > show (sel-residues & sidechain) target ab > select #2/A:434 11 atoms, 10 bonds, 1 residue, 1 model selected > show (sel-residues & sidechain) target ab > select #2/A:405 9 atoms, 8 bonds, 1 residue, 1 model selected > show (sel-residues & sidechain) target ab > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #2 Nothing selected > cartoon hide > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #2 Nothing selected > volume #4 level 0.2175 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > color #3 #f7f9fbff models > color #3 #caccce8c models > volume #3 step 1 > volume #3 level 0.1426 > color #3 lighskyblue transparency 60 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select add #3 4 models selected > ui tool show ""Color Actions"" > color sel light sky blue > ui tool show ""Color Actions"" > volume #3 color #87cefa66 > volume #3 level 0.1376 > volume #4 level 0.1377 > volume zone #4 nearAtoms #2/A range 3 > volume #3 level 0.1526 > volume #4 level 0.1477 > volume #4 level 0.2 > volume #1 level 0.1762 > volume #1 level 0.2484 > lighting full > lighting flat > volume #4 level 0.21 > volume #4 level 0.2274 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM1.cxs"" ——— End of log from Sun Feb 1 21:27:29 2026 ——— > view name session-start opened ChimeraX session > select #2/A:1-404,406-433,435-600 4458 atoms, 4560 bonds, 1 pseudobond, 548 residues, 2 models selected > surface (#!2 & sel) > hide #!4 models > surface sel transparency 90 > hide #!1 models > select #2/D:1-158, 160-500 2432 atoms, 2489 bonds, 296 residues, 1 model selected > surface sel > surface sel transparency 90 > undo > surface #2/A transparecy 90 Expected a keyword > surface #2/A transparency 90 > surface #2/D transparency 90 > ui tool show ""Side View"" > hide #2/E:6 > hide #2/F:41 > select add #2 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 7 models selected > select subtract #2 2 models selected > show #2/A:532 & ~@N,CA,C,O > show #2/A:532 & ~@N,C,O > save /Users/xuchengtao/Desktop/image216.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM3.cxs"" > save /Users/xuchengtao/Desktop/image217.png supersample 3 > lighting soft > lighting full > lighting simple > lighting soft > lighting simple > lighting soft > ui tool show ""Color Actions"" > color #2/F dodgerblue > color byhetero > undo > color #2/F byhetero > save /Users/xuchengtao/Desktop/image218.png supersample 3 > save /Users/xuchengtao/Desktop/image219.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM2.cxs"" > close session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"" Chain information for merged_real_space_refined_011.pdb #1 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb --- warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 Chain information for merged_ivc_apo_refine_007.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E F G H | No description available I | No description available J | No description available K L M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available > combine #1 > combine #2 > hide > show #3/A > show #4/A > style stick Changed 124372 atom styles > color byhetero > show #3/E:1-10 > show #3/F:37-47 > mmaker #4/A to #3/A 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 copy of merged_real_space_refined_011.pdb, chain A (#3) with copy of merged_ivc_apo_refine_007.pdb, chain A (#4), sequence alignment score = 2305.8 RMSD between 212 pruned atom pairs is 1.103 angstroms; (across all 504 pairs: 3.208) > show cartoons > undo > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > hide #!1 models > select #3/A 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > show sel cartoons > ui tool show ""Color Actions"" > color sel light sky blue > color sel byhetero > cartoon style (#!3 & sel) xsection oval modeHelix default > cartoon style (#!3 & sel) modeHelix tube sides 20 > hide (#!3 & sel) target a > color #3/A transparency 10 > select #3/E,F 1172 atoms, 1312 bonds, 57 residues, 1 model selected > show sel cartoons > undo > select #3/E:1-10 200 atoms, 222 bonds, 10 residues, 1 model selected > show sel cartoons > select #3/F:37-47 232 atoms, 261 bonds, 11 residues, 1 model selected > show sel cartoons > ui tool show ""Color Actions"" > color sel dodger blue > color sel byhetero > select #3/E:1-10 200 atoms, 222 bonds, 10 residues, 1 model selected > ui tool show ""Color Actions"" > color sel hot pink > color sel byhetero > nucleotides sel fill > style nucleic & sel stick Changed 200 atom styles > select #3/F:37-47 232 atoms, 261 bonds, 11 residues, 1 model selected > nucleotides sel fill > style nucleic & sel stick Changed 232 atom styles > select #4/A 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected > show #!3 cartoons > undo > show sel cartoons > show #!4 models > hide sel atoms > color sel white transcparency 70 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel white transparency 70 > lighting soft > select add #4 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #4 Nothing selected > mmaker #4/A: 70, 93, 94, 115,146,147,159 > matchmaker #4/A: 70, 93, 94, 115,146,147,159 Missing required ""to"" argument > mmaker #4/A: 70, 93, 94, 115,146,147,159 to #3/A 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 copy of merged_real_space_refined_011.pdb, chain A (#3) with copy of merged_ivc_apo_refine_007.pdb, chain A (#4), sequence alignment score = 45.3 RMSD between 7 pruned atom pairs is 0.873 angstroms; (across all 7 pairs: 0.873) > select #4/A 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected > cartoon style (#!4 & sel) modeHelix tube sides 20 > select add #4 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #4 Nothing selected > select #3/A 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > color sel transparency 30 > select add #3 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #3 Nothing selected > save /Users/xuchengtao/Desktop/image220.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_1.cxs"" > measure motion #3/A toModel #4/A showVectors true color cyan Missing or invalid ""surface"" argument: Require 1 surface, got 0 > measure rotation #3/A toModel #4/A showVectors true color cyan Expected a keyword > measure rotation #3/A toModel #4/A showAxis true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3/A toModel #4/A coordinateSystem#4/A showAxis true color > cyan Expected a keyword > measure rotation #3/A toModel #4/A coordinateSystem #4/A showAxis true color > cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 in copy of merged_ivc_apo_refine_007.pdb #4 coordinate system: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3/A toModel #4/A coordinateSystem #4/A showSlabs true > color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 in copy of merged_ivc_apo_refine_007.pdb #4 coordinate system: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3/A toModel #4/A showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3 toModel #4/A showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3 toModel #4 showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3 toModel #4 showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3 toModel #4 showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3 toModel #4 showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > measure rotation #3 toModel #4 showSlabs true color cyan Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of merged_ivc_apo_refine_007.pdb #4 coordinates: Matrix rotation and translation -0.99736182 -0.00562907 0.07237203 460.06370117 0.01683128 0.95188599 0.30598983 -17.09119514 -0.07061236 0.30640068 -0.94928000 404.90437477 Axis 0.00283863 0.98788229 0.15517902 Axis point 237.34717297 0.00000000 195.36024542 Rotation angle (degrees) 175.84992537 Shift along axis 47.25452561 > close #5-22 > morph #4/A,#3/A frames 2 showVectors true Missing or invalid ""structures"" argument: only initial part ""#4/A"" of atom specifier valid > morph #4/A #3/A frames 2 showVectors true Expected a keyword > morph #4/A #3/A frames 60 models have different number of chains, 19 (Morph - copy of merged_ivc_apo_refine_007.pdb #/A,Morph - copy of merged_ivc_apo_refine_007.pdb #/B,Morph - copy of merged_ivc_apo_refine_007.pdb #/C,Morph - copy of merged_ivc_apo_refine_007.pdb #/D,Morph - copy of merged_ivc_apo_refine_007.pdb #/E,Morph - copy of merged_ivc_apo_refine_007.pdb #/F,Morph - copy of merged_ivc_apo_refine_007.pdb #/G,Morph - copy of merged_ivc_apo_refine_007.pdb #/H,Morph - copy of merged_ivc_apo_refine_007.pdb #/I,Morph - copy of merged_ivc_apo_refine_007.pdb #/J,Morph - copy of merged_ivc_apo_refine_007.pdb #/K,Morph - copy of merged_ivc_apo_refine_007.pdb #/L,Morph - copy of merged_ivc_apo_refine_007.pdb #/M,Morph - copy of merged_ivc_apo_refine_007.pdb #/N,Morph - copy of merged_ivc_apo_refine_007.pdb #/O,Morph - copy of merged_ivc_apo_refine_007.pdb #/P,Morph - copy of merged_ivc_apo_refine_007.pdb #/Q,Morph - copy of merged_ivc_apo_refine_007.pdb #/R,Morph - copy of merged_ivc_apo_refine_007.pdb #/S) and 18 (copy of merged_real_space_refined_011.pdb #3/A,copy of merged_real_space_refined_011.pdb #3/C,copy of merged_real_space_refined_011.pdb #3/D,copy of merged_real_space_refined_011.pdb #3/E,copy of merged_real_space_refined_011.pdb #3/F,copy of merged_real_space_refined_011.pdb #3/G,copy of merged_real_space_refined_011.pdb #3/H,copy of merged_real_space_refined_011.pdb #3/I,copy of merged_real_space_refined_011.pdb #3/J,copy of merged_real_space_refined_011.pdb #3/K,copy of merged_real_space_refined_011.pdb #3/L,copy of merged_real_space_refined_011.pdb #3/M,copy of merged_real_space_refined_011.pdb #3/N,copy of merged_real_space_refined_011.pdb #3/O,copy of merged_real_space_refined_011.pdb #3/P,copy of merged_real_space_refined_011.pdb #3/Q,copy of merged_real_space_refined_011.pdb #3/R,copy of merged_real_space_refined_011.pdb #3/S) > morph #4/A,#3/A frames 60 Missing or invalid ""structures"" argument: only initial part ""#4/A"" of atom specifier valid > select #3/A 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb"" models #3 > selectedOnly true relModel #3 > select #4/A 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb"" models #4 > selectedOnly true relModel #3 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb --- warnings | Start residue of secondary structure not found: HELIX 19 19 LEU B 30 ASN B 46 1 17 Start residue of secondary structure not found: HELIX 20 20 ARG B 51 THR B 60 1 10 Start residue of secondary structure not found: HELIX 21 21 LYS B 135 LEU B 143 1 9 Start residue of secondary structure not found: HELIX 22 22 GLN B 187 LYS B 199 1 13 Start residue of secondary structure not found: HELIX 23 23 PRO B 249 THR B 257 1 9 209 messages similar to the above omitted Chain information for Cas10_apo.pdb #5 --- Chain | Description A | No description available > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb --- warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27 Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88 1 8 Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C 111 1 7 Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C 122 1 6 Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C 184 1 5 203 messages similar to the above omitted Chain information for Cas10_bound.pdb #6 --- Chain | Description A | No description available > hide #!3 models > hide #!4 models > select add #4 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #4 Nothing selected > select add #6 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > select add #5 8577 atoms, 8775 bonds, 4 pseudobonds, 1054 residues, 4 models selected > select subtract #6 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected > ui tool show ""Color Actions"" > color sel white > color #5 #ffffffb3 > color #5 #ffffff4d > select add #6 8577 atoms, 8775 bonds, 4 pseudobonds, 1054 residues, 4 models selected > cartoon style (#!5-6 & sel) modeHelix tube sides 20 > select subtract #5 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > select subtract #6 Nothing selected > morph #5,#6 frames 60 Missing or invalid ""structures"" argument: only initial part ""#5"" of atom specifier valid > morph #5 #6 frames 60 Computed 61 frame morph #7 > coordset #7 1,61 > morph #5 #6 frames 30 Computed 31 frame morph #8 > coordset #8 1,31 > close #7 > select add #8 4095 atoms, 4189 bonds, 3 pseudobonds, 504 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > select subtract #8 Nothing selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_2_movie1.cxs"" ——— End of log from Mon Feb 2 10:29:38 2026 ——— > view name session-start opened ChimeraX session > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > show #1 > hide #!1 models > show #!2 models > show #2 > mmaker #2 to #1 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 merged_real_space_refined_011.pdb, chain A (#1) with merged_ivc_apo_refine_007.pdb, chain A (#2), sequence alignment score = 2305.8 RMSD between 212 pruned atom pairs is 1.103 angstroms; (across all 504 pairs: 3.208) > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb --- warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27 Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88 1 8 Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C 111 1 7 Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C 122 1 6 Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C 184 1 5 203 messages similar to the above omitted Chain information for Cas10_bound.pdb #7 --- Chain | Description A | No description available > close session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb"" format pdb Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb --- warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27 Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88 1 8 Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C 111 1 7 Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C 122 1 6 Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C 184 1 5 203 messages similar to the above omitted Chain information for Cas10_bound.pdb #1 --- Chain | Description A | No description available > select #1/A:1-335 2374 atoms, 2430 bonds, 1 pseudobond, 290 residues, 2 models selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_1_335.pdb"" > selectedOnly true relModel #1 > select #1/A:335-437 801 atoms, 815 bonds, 103 residues, 1 model selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb"" > selectedOnly true relModel #1 > select #1/A:437-900 1314 atoms, 1347 bonds, 159 residues, 1 model selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_437_Cterm.pdb"" > relModel #1 > view matrix models #1,1,0,0,0.00059032,0,1,0,-0.020052,0,0,1,0.0076704 > select #1/A:50-180 1058 atoms, 1086 bonds, 131 residues, 1 model selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_50_180.pdb"" > selectedOnly true relModel #1 > open 7tr8 7tr8 title: Cascade complex from type I-A CRISPR-Cas system [more info...] Chain information for 7tr8 #2 --- Chain | Description | UniProt A | CRISPR-associated helicase Cas3 | A0A5C0XNV5_PYRFU 10-516 C | Cas8 | Q8U338_PYRFU 2-342 D E F G H | Cas11a | Q8U332_PYRFU 2-109 I J K L M N O | Cas7a | Q8U333_PYRFU 1-336 P | Cas5a | A0A5C0XNV9_PYRFU 1-256 Q | CRISPR-associated endonuclease Cas3-HD | CS3HD_PYRFU 2-216 R | crRNA (45-MER) | Non-standard residues in 7tr8 #2 --- NI — nickel (II) ion > select add #1 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > hide #!1 models > select subtract #1 Nothing selected > style #!2 stick Changed 33581 atom styles > show #!2 atoms > show #!2 cartoons > color #!2 byhetero > hide #!2 atoms > cartoon style #2 modeHelix tube sides 20 > show #!2 cartoons > show #!2 atoms > hide #!2 cartoons > show #!2 atoms > show #!2 cartoons > hide #!2 atoms > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 40 SER A 44 1 5 Start residue of secondary structure not found: HELIX 2 2 LEU A 67 PHE A 81 1 15 Start residue of secondary structure not found: HELIX 3 3 GLY A 84 ILE A 92 1 9 Start residue of secondary structure not found: HELIX 4 4 GLN A 120 PHE A 130 1 11 Start residue of secondary structure not found: HELIX 5 5 LYS A 138 LYS A 144 1 7 18 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (152 ) Chain information for Cas10_bound_335_437.pdb #3 --- Chain | Description A | No description available > mmaker #3 to #2 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 7tr8, chain A (#2) with Cas10_bound_335_437.pdb, chain A (#3), sequence alignment score = 65.9 RMSD between 7 pruned atom pairs is 1.051 angstroms; (across all 100 pairs: 14.603) > close #2 > open /Users/xuchengtao/Downloads/AF-A0A7V6NIE4-F1-model_v6.pdb Summary of feedback from opening /Users/xuchengtao/Downloads/AF-A0A7V6NIE4-F1-model_v6.pdb --- warning | Ignored bad PDB record found on line 38 DBREF XXXX A 1 478 UNP A0A7V6NIE4 A0A7V6NIE4_9CLOT 1 478 AF-A0A7V6NIE4-F1-model_v6.pdb title: Alphafold monomer V2.0 prediction for type I-B crispr-associated protein CAS8B1/CST1 (A0A7V6NIE4) [more info...] Chain information for AF-A0A7V6NIE4-F1-model_v6.pdb #2 --- Chain | Description A | type I-B crispr-associated protein CAS8B1/CST1 Computing secondary structure > mmaker #3 to #2 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 AF-A0A7V6NIE4-F1-model_v6.pdb, chain A (#2) with Cas10_bound_335_437.pdb, chain A (#3), sequence alignment score = 104.6 RMSD between 26 pruned atom pairs is 0.744 angstroms; (across all 98 pairs: 9.407) > ui tool show ""Selection Inspector"" > center #2 Unknown command: center #2 > center Unknown command: center > cofr Center of rotation: -9.0432 -2.4508 11.129 front center > cofr #2 > show #!1 models > hide #!1 models > show #!1 models > select #1/A:55-150 785 atoms, 809 bonds, 96 residues, 1 model selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_55_150.pdb"" > models #1 selectedOnly true relModel #1 > select #1/A:437-500 539 atoms, 550 bonds, 64 residues, 1 model selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_437_Cterm.pdb"" > models #1 selectedOnly true relModel #1 > open 6TH '6TH' has no suffix > open 6THH Summary of feedback from opening 6THH fetched from pdb --- note | Fetching compressed mmCIF 6thh from http://files.rcsb.org/download/6thh.cif 6thh title: Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in complex with the SIRV3 AcrID1 (gp02) anti-CRISPR protein [more info...] Chain information for 6thh #4 --- Chain | Description | UniProt A B | SIRV3 AcrID1 (gp02) anti-CRISPR protein | A0A1B3SN05_9VIRU 1-96 C | CRISPR-associated protein, CscA | M9U4Y8_SULIS 1-847 Non-standard residues in 6thh #4 --- PO4 — phosphate ion ZN — zinc ion 6thh mmCIF Assemblies --- 1| author_defined_assembly > select add #1 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > select add #4 12721 atoms, 12994 bonds, 8 pseudobonds, 1560 residues, 6 models selected > mmaker #1 to #4 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 6thh, chain C (#4) with Cas10_bound.pdb, chain A (#1), sequence alignment score = 154.1 RMSD between 22 pruned atom pairs is 1.050 angstroms; (across all 409 pairs: 40.667) > select subtract #4 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > select subtract #1 Nothing selected > cofr #4/C > open 6Yes Summary of feedback from opening 6Yes fetched from pdb --- note | Fetching compressed mmCIF 6yes from http://files.rcsb.org/download/6yes.cif 6yes title: Crystal structure of type I-D CRISPR-Cas nuclease Cas10d [more info...] Chain information for 6yes #5 --- Chain | Description | UniProt A B | CRISPR-associated protein, CscA | M9U4Y8_SULIS 1-847 Non-standard residues in 6yes #5 --- ZN — zinc ion 6yes mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select #5/A:14-847 6325 atoms, 6448 bonds, 3 pseudobonds, 791 residues, 2 models selected > hide #2 models > hide #3 models > mmaker #1 to #5 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 6yes, chain A (#5) with Cas10_bound.pdb, chain A (#1), sequence alignment score = 135.7 RMSD between 11 pruned atom pairs is 1.193 angstroms; (across all 431 pairs: 32.783) > hide #!1 models > select add #5 12534 atoms, 12775 bonds, 10 pseudobonds, 1569 residues, 4 models selected > show #!1 models > select subtract #5 Nothing selected > select #5/B:14-844 6207 atoms, 6327 bonds, 2 pseudobonds, 776 residues, 2 models selected > hide #5/B cartoons > hide #5/B > select add #1 10685 atoms, 10909 bonds, 3 pseudobonds, 1326 residues, 4 models selected > select add #5 17012 atoms, 17357 bonds, 11 pseudobonds, 2119 residues, 6 models selected > select subtract #5 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > view matrix models > #1,0.66911,0.7076,-0.22714,-278.82,-0.74159,0.61589,-0.26594,125.06,-0.048282,0.34639,0.93685,-320.82 > view matrix models > #1,0.10857,0.58169,-0.80613,28.689,-0.99406,0.069538,-0.083697,235.53,0.0073718,0.81043,0.58578,-325.5 > view matrix models > #1,-0.049471,0.44584,-0.89374,113.79,-0.99529,0.052664,0.081364,193.82,0.083344,0.89356,0.44114,-318.66 > view matrix models > #1,0.21172,0.80335,-0.5566,-104.87,-0.96736,0.091101,-0.23648,267.3,-0.13927,0.5885,0.79641,-308.2 > view matrix models > #1,0.30895,0.91561,-0.25732,-216.38,-0.8958,0.18925,-0.40214,261.48,-0.31951,0.35475,0.87867,-230.9 > select subtract #1 Nothing selected > select add #1 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > select subtract #1 Nothing selected > cofr #1 > select add #1 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > view matrix models > #1,0.30895,0.91561,-0.25732,-257.59,-0.8958,0.18925,-0.40214,262.52,-0.31951,0.35475,0.87867,-278.37 > ui tool show ""Show Sequence Viewer"" > sequence chain #4/C #5/A #5/B Alignment identifier is 1 > close #4 > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A #5/B Alignment identifier is 1 > select #5/A-B:93 20 atoms, 20 bonds, 2 residues, 1 model selected > select #5/A-B:93-94 36 atoms, 36 bonds, 4 residues, 1 model selected > show sel atoms > select add #5 12534 atoms, 12775 bonds, 10 pseudobonds, 1569 residues, 4 models selected > show sel atoms > close #5 > open 7SBA Summary of feedback from opening 7SBA fetched from pdb --- note | Fetching compressed mmCIF 7sba from http://files.rcsb.org/download/7sba.cif 7sba title: Structure of type I-D Cascade bound to a dsDNA target [more info...] Chain information for 7sba #4 --- Chain | Description | UniProt A B C D E F G | Cas7d | Q6ZEI6_SYNY3 1-329 H | Cas5d | Q6ZEI5_SYNY3 1-254 I | Cas10d | Q6ZEI7_SYNY3 1-975 J K | Cas11d | Q6ZEI7_SYNY3 1-146 X | DNA target strand | Y | DNA non-target strand | Z | crRNA | > sequence chain #4/I Alignment identifier is 4/I > mmaker #1 to #4/I 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 7sba, chain I (#4) with Cas10_bound.pdb, chain A (#1), sequence alignment score = 131.1 RMSD between 14 pruned atom pairs is 1.230 angstroms; (across all 409 pairs: 37.869) > cofr #4/I > show #!1,4 atoms > hide #!1,4 atoms > show #!1,4 cartoons > select #4/I:975 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/I:767-975 1719 atoms, 1747 bonds, 209 residues, 1 model selected > select add #4 30651 atoms, 31399 bonds, 35 pseudobonds, 3741 residues, 3 models selected > select subtract #4 Nothing selected > select clear > select #4/I:2-226 1300 atoms, 1329 bonds, 3 pseudobonds, 159 residues, 2 models selected > select #4/I:115-116 18 atoms, 18 bonds, 2 residues, 1 model selected > select #4/I:115-116 18 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > color sel byhetero > select #4/I:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/I:210-211 15 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 15 atom styles > color sel byhetero > select #4/I:81 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/I:81-83 26 atoms, 26 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 26 atom styles > color sel byhetero > select add #1 4504 atoms, 4608 bonds, 1 pseudobond, 553 residues, 3 models selected > select subtract #1 26 atoms, 26 bonds, 3 residues, 1 model selected > select add #4 30651 atoms, 31399 bonds, 35 pseudobonds, 3741 residues, 3 models selected > select subtract #4 Nothing selected > select add #1 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.92899,-0.15763,0.33486,365.26,0.26402,-0.9163,0.30113,305.54,0.25937,0.36815,0.89286,-130.81 > view matrix models > #1,-0.92168,0.011683,0.38778,316.88,0.0013436,-0.99944,0.033304,453.28,0.38795,0.031217,0.92115,-103.03 > view matrix models > #1,-0.97299,-0.20139,0.11281,444.21,0.17741,-0.96509,-0.19269,469.37,0.14768,-0.16747,0.97475,-26.294 > view matrix models > #1,-0.95377,-0.085947,0.28798,372.04,0.068101,-0.99512,-0.071442,471.83,0.29272,-0.048527,0.95497,-83.653 > view matrix models > #1,-0.95377,-0.085947,0.28798,372.22,0.068101,-0.99512,-0.071442,471.54,0.29272,-0.048527,0.95497,-83.902 > view matrix models > #1,-0.95377,-0.085947,0.28798,372.37,0.068101,-0.99512,-0.071442,467.5,0.29272,-0.048527,0.95497,-81.992 > view matrix models > #1,-0.92916,-0.3413,0.14206,455.49,0.36415,-0.77877,0.51079,200.84,-0.063704,0.52634,0.84789,-82.728 > view matrix models > #1,-0.92916,-0.3413,0.14206,455.32,0.36415,-0.77877,0.51079,188.2,-0.063704,0.52634,0.84789,-75.666 > view matrix models > #1,-0.92916,-0.3413,0.14206,451.36,0.36415,-0.77877,0.51079,174.97,-0.063704,0.52634,0.84789,-54.964 > view matrix models > #1,-0.92916,-0.3413,0.14206,455.29,0.36415,-0.77877,0.51079,178.31,-0.063704,0.52634,0.84789,-63.121 > view matrix models > #1,-0.86919,-0.39526,0.29711,409.74,0.49112,-0.75998,0.42572,169.72,0.057532,0.51595,0.85469,-90.031 > select #1/A:94,93,159,115 37 atoms, 36 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 37 atom styles > color sel byhetero > view matrix models > #1,-0.86919,-0.39526,0.29711,405.12,0.49112,-0.75998,0.42572,166.84,0.057532,0.51595,0.85469,-75.68 > view matrix models > #1,-0.86919,-0.39526,0.29711,405.72,0.49112,-0.75998,0.42572,169.37,0.057532,0.51595,0.85469,-78.05 > view matrix models > #1,-0.87411,-0.48334,0.048136,491.77,0.45718,-0.78522,0.41763,183.96,-0.16406,0.38706,0.90734,-18.514 > view matrix models > #1,-0.87491,-0.482,0.047025,492.94,0.45544,-0.78588,0.41829,184.36,-0.16466,0.38738,0.90709,-21.008 > view matrix models > #1,-0.87491,-0.482,0.047025,492.77,0.45544,-0.78588,0.41829,184.58,-0.16466,0.38738,0.90709,-20.838 > view matrix models > #1,-0.88733,-0.45747,-0.058039,519.63,0.3877,-0.80823,0.44324,197.11,-0.24968,0.37079,0.89452,4.7181 > view matrix models > #1,-0.88334,-0.46707,-0.039382,515.36,0.40537,-0.80343,0.4361,193.64,-0.23533,0.36926,0.89904,0.93621 > view matrix models > #1,-0.89367,-0.4487,0.0058692,501.77,0.40237,-0.79548,0.45312,188.13,-0.19864,0.4073,0.89143,-12.406 > view matrix models > #1,-0.86852,-0.49445,-0.034478,515.93,0.43488,-0.79355,0.42562,188.05,-0.23781,0.35467,0.90424,2.8431 > view matrix models > #1,-0.86852,-0.49445,-0.034478,517.42,0.43488,-0.79355,0.42562,188.02,-0.23781,0.35467,0.90424,1.6296 > view matrix models > #1,-0.78923,-0.58513,-0.18638,558.61,0.48029,-0.77727,0.40641,180.06,-0.38267,0.23123,0.89448,60.114 > view matrix models > #1,-0.78129,-0.59771,-0.17979,558.76,0.50063,-0.77212,0.39142,178.15,-0.37278,0.2158,0.90248,57.532 > view matrix models > #1,-0.78129,-0.59771,-0.17979,558.66,0.50063,-0.77212,0.39142,178.63,-0.37278,0.2158,0.90248,57.646 > select #1/A:94,93,159,115,70 47 atoms, 46 bonds, 5 residues, 1 model selected > show sel atoms > view matrix models > #1,-0.80502,-0.59205,0.037748,503.3,0.57171,-0.75722,0.31587,180.64,-0.15843,0.27586,0.94805,-14.063 > view matrix models > #1,-0.80502,-0.59205,0.037748,503.39,0.57171,-0.75722,0.31587,182.05,-0.15843,0.27586,0.94805,-14.885 > view matrix models > #1,-0.81791,-0.57123,-0.068667,531.44,0.51406,-0.77917,0.35866,187.37,-0.25838,0.25805,0.93094,15.477 > view matrix models > #1,-0.81791,-0.57123,-0.068667,531,0.51406,-0.77917,0.35866,185.96,-0.25838,0.25805,0.93094,14.32 > view matrix models > #1,-0.81791,-0.57123,-0.068667,530.06,0.51406,-0.77917,0.35866,188.55,-0.25838,0.25805,0.93094,13.985 > view matrix models > #1,-0.77362,-0.6252,-0.1032,539.92,0.57011,-0.75783,0.31728,183.31,-0.27657,0.18662,0.9427,28.429 > view matrix models > #1,-0.76784,-0.63464,-0.087455,536.13,0.57323,-0.74157,0.34853,170.97,-0.28605,0.21749,0.93321,27.261 > view matrix models > #1,-0.76784,-0.63464,-0.087455,535.05,0.57323,-0.74157,0.34853,169.78,-0.28605,0.21749,0.93321,28.598 > view matrix models > #1,-0.76784,-0.63464,-0.087455,535.06,0.57323,-0.74157,0.34853,170.38,-0.28605,0.21749,0.93321,28.285 > view matrix models > #1,-0.76784,-0.63464,-0.087455,534.8,0.57323,-0.74157,0.34853,170.74,-0.28605,0.21749,0.93321,28.066 > view matrix models > #1,-0.75284,-0.64687,-0.12158,543.13,0.56806,-0.73187,0.37639,162.41,-0.33246,0.2143,0.91845,43.062 > view matrix models > #1,-0.75284,-0.64687,-0.12158,542.71,0.56806,-0.73187,0.37639,162.76,-0.33246,0.2143,0.91845,42.834 > view matrix models > #1,-0.75284,-0.64687,-0.12158,542.66,0.56806,-0.73187,0.37639,162.54,-0.33246,0.2143,0.91845,43.02 > view matrix models > #1,-0.75838,-0.63698,-0.13826,546.58,0.5545,-0.74197,0.37685,167.36,-0.34263,0.20913,0.9159,46.971 > view matrix models > #1,-0.7596,-0.63718,-0.13043,544.75,0.54112,-0.7304,0.41678,157.21,-0.36083,0.24601,0.8996,48.465 > view matrix models > #1,-0.7596,-0.63718,-0.13043,544.49,0.54112,-0.7304,0.41678,155.79,-0.36083,0.24601,0.8996,48.75 > select add #1 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > select subtract #1 Nothing selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_ID.cxs"" > hide #!1 models > show #!1 models > hide #!4 models > combine #1 > hide #!1 models > open 8BMW Summary of feedback from opening 8BMW fetched from pdb --- note | Fetching compressed mmCIF 8bmw from http://files.rcsb.org/download/8bmw.cif 8bmw title: SsoCsm [more info...] Chain information for 8bmw #6 --- Chain | Description | UniProt A B C D E | CRISPR-associated small subunit protein (Type III-D) | A0A157T170_SACSO 1-139 F G | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T0X8_SACSO 1-248 H I | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T120_SACSO 1-278 J | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T1A2_SACSO 3-274 K | CRISPR-associated protein Cas10 (Type III-D) | A0A157T112_SACSO 1-829 L | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T2I3_SACSO 1-202 M | CRISPR-associated protein Cas5 (Type III-D) | A0A157T1I2_SACSO 1-300 N | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T1J6_SACSO 1-252 R | RNA (48-MER) | > select add #6 28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected > show sel cartoons > hide sel atoms > select #6/K:1-829 6678 atoms, 6805 bonds, 829 residues, 1 model selected > mmaker #5 to #6/K 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 8bmw, chain K (#6) with copy of Cas10_bound.pdb, chain A (#5), sequence alignment score = 185.2 RMSD between 25 pruned atom pairs is 1.021 angstroms; (across all 419 pairs: 31.068) > hide #!5 models > select add #6 28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected > select subtract #6 Nothing selected > cofr #6 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"" Chain information for merged_real_space_refined_011.pdb #7 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > select add #7 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > show sel atoms > style sel stick Changed 30524 atom styles > hide sel cartoons > show sel cartoons > hide sel atoms [Repeated 1 time(s)] > view matrix models #7,1,0,0,13.762,0,1,0,40.121,0,0,1,-62.573 > view matrix models > #7,-0.64946,0.021277,-0.7601,502.79,0.039004,0.99922,-0.0053566,33.191,0.7594,-0.033126,-0.64979,109.51 > view matrix models > #7,-0.64946,0.021277,-0.7601,532.01,0.039004,0.99922,-0.0053566,-59.316,0.7594,-0.033126,-0.64979,98.523 > view matrix models > #7,0.40297,0.91334,0.058558,-49.62,0.80765,-0.32479,-0.49215,160.87,-0.43048,0.24562,-0.86854,307.91 > view matrix models > #7,0.051556,0.95685,0.28596,-29.803,0.88581,0.088412,-0.45554,53.02,-0.46117,0.27679,-0.84304,302.94 > view matrix models > #7,-0.0029515,0.95165,0.30718,-42.665,0.90473,0.1334,-0.40456,25.462,-0.42598,0.27672,-0.86137,309.92 > view matrix models > #7,-0.53098,0.81849,0.2194,111.93,0.79275,0.57127,-0.21258,-78.241,-0.29934,0.061054,-0.95219,345.35 > view matrix models > #7,-0.53098,0.81849,0.2194,77.406,0.79275,0.57127,-0.21258,-90.854,-0.29934,0.061054,-0.95219,352.18 > view matrix models > #7,-0.8291,0.55788,0.037085,228.61,0.5408,0.81702,-0.20006,-90.982,-0.14191,-0.14581,-0.97908,367.19 > view matrix models > #7,-0.8291,0.55788,0.037085,228.55,0.5408,0.81702,-0.20006,-87.866,-0.14191,-0.14581,-0.97908,380.33 > view matrix models > #7,-0.85422,0.50761,-0.11238,273.39,0.51975,0.82842,-0.20876,-84.094,-0.01287,-0.23674,-0.97149,370.47 > view matrix models > #7,-0.96768,0.25114,-0.023036,331.89,0.25206,0.9601,-0.12111,-72.32,-0.0082982,-0.123,-0.99237,350.4 > view matrix models > #7,-0.70511,0.64449,0.29573,126.28,0.63304,0.76003,-0.14699,-101.62,-0.3195,0.083564,-0.9439,358.76 > view matrix models > #7,-0.65421,0.65946,0.37029,97.966,0.59449,0.75105,-0.28724,-64.214,-0.46753,0.032215,-0.88339,388.26 > view matrix models > #7,-0.65961,0.62754,0.41365,97.099,0.4846,0.77577,-0.40415,-23.387,-0.57452,-0.066127,-0.81582,417.4 > view matrix models > #7,-0.65961,0.62754,0.41365,89.815,0.4846,0.77577,-0.40415,-26.954,-0.57452,-0.066127,-0.81582,416.99 > view matrix models > #7,-0.65961,0.62754,0.41365,89.768,0.4846,0.77577,-0.40415,-27.843,-0.57452,-0.066127,-0.81582,415.91 > view matrix models > #7,-0.21793,0.93874,0.26696,-37.188,0.86475,0.31254,-0.3931,-14.808,-0.45246,0.14518,-0.87989,359.85 > view matrix models > #7,-0.21793,0.93874,0.26696,-36.18,0.86475,0.31254,-0.3931,-15.08,-0.45246,0.14518,-0.87989,359.07 > select subtract #7 Nothing selected > color #6 #e49e9eff > color #6 #e4e4e0ff > color #7 #6e7cf9ff > color #6 #8c8d8bff > color #6 #fefffdff > color #6 #f0ff73ff > select add #7 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > view matrix models > #7,-0.21793,0.93874,0.26696,-34.672,0.86475,0.31254,-0.3931,-15.515,-0.45246,0.14518,-0.87989,358.27 > view matrix models > #7,-0.29187,0.88991,0.35052,-25.674,0.67377,0.45141,-0.58503,33.657,-0.67886,0.065411,-0.73135,392.65 > view matrix models > #7,-0.29187,0.88991,0.35052,67.353,0.67377,0.45141,-0.58503,97.803,-0.67886,0.065411,-0.73135,380.41 > view matrix models > #7,0.12179,0.95469,0.27155,-16.692,0.79285,0.071016,-0.60526,154.58,-0.59712,0.28901,-0.74828,321.03 > view matrix models > #7,0.12179,0.95469,0.27155,-77.534,0.79285,0.071016,-0.60526,142.09,-0.59712,0.28901,-0.74828,314.91 > view matrix models > #7,-0.234,0.83803,0.4929,-22.917,0.69423,0.49895,-0.51874,58.323,-0.68066,0.2208,-0.69854,336.51 > view matrix models > #7,-0.234,0.83803,0.4929,-34.186,0.69423,0.49895,-0.51874,25.983,-0.68066,0.2208,-0.69854,350.78 > view matrix models > #7,-0.62708,0.76066,0.16784,127.43,0.6775,0.63893,-0.36437,-29.398,-0.3844,-0.11478,-0.916,400.14 > view matrix models > #7,-0.70238,0.68776,0.18344,149.83,0.60673,0.71324,-0.35096,-50.542,-0.37221,-0.13521,-0.91825,400.1 > view matrix models > #7,-0.69971,0.63699,0.32348,132.15,0.59564,0.77016,-0.22816,-83.951,-0.39447,0.033031,-0.91831,370.41 > view matrix models > #7,-0.69971,0.63699,0.32348,125.08,0.59564,0.77016,-0.22816,-76.844,-0.39447,0.033031,-0.91831,378.06 > view matrix models > #7,-0.69971,0.63699,0.32348,117.6,0.59564,0.77016,-0.22816,-76.942,-0.39447,0.033031,-0.91831,379.71 > view matrix models > #7,-0.83123,0.42438,0.35909,181.46,0.45119,0.89237,-0.010192,-114.53,-0.32477,0.15355,-0.93325,343.49 > view matrix models > #7,-0.88372,0.30166,0.35783,217.72,0.35464,0.93053,0.091374,-122.1,-0.3054,0.20765,-0.92931,327.63 > view matrix models > #7,-0.88372,0.30166,0.35783,211.66,0.35464,0.93053,0.091374,-122.07,-0.3054,0.20765,-0.92931,324.25 > view matrix models > #7,-0.56247,0.70283,0.43549,47.486,0.70514,0.6828,-0.19122,-89.18,-0.43175,0.19953,-0.87965,342.53 > mmaker #7 to #6 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 8bmw, chain K (#6) with merged_real_space_refined_011.pdb, chain A (#7), sequence alignment score = 185.2 RMSD between 25 pruned atom pairs is 1.021 angstroms; (across all 419 pairs: 31.068) > view matrix models > #7,0.30911,0.95069,0.025143,-88.754,0.88584,-0.27821,-0.37134,98.811,-0.34604,0.13706,-0.92816,340.69 > view matrix models > #7,0.30911,0.95069,0.025143,-90.701,0.88584,-0.27821,-0.37134,94.742,-0.34604,0.13706,-0.92816,346.99 > view matrix models > #7,-0.59825,0.78378,0.16671,104.93,0.78192,0.61649,-0.092444,-120.96,-0.17523,0.075052,-0.98166,334.5 > view matrix models > #7,-0.59825,0.78378,0.16671,98.447,0.78192,0.61649,-0.092444,-120.88,-0.17523,0.075052,-0.98166,337.15 > view matrix models > #7,-0.56838,0.80004,0.19201,83.93,0.77689,0.59871,-0.19489,-96.101,-0.27088,0.038403,-0.96185,360.7 > select subtract #7 Nothing selected > select add #7 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > view matrix models > #7,-0.56838,0.80004,0.19201,123.42,0.77689,0.59871,-0.19489,-29.729,-0.27088,0.038403,-0.96185,321.74 > view matrix models > #7,-0.81366,0.51412,0.27137,216.79,0.4764,0.8572,-0.19558,-20.449,-0.33317,-0.029854,-0.94239,344.64 > view matrix models > #7,-0.81292,0.51564,0.27069,170.28,0.47811,0.8563,-0.19535,-67.438,-0.33253,-0.029381,-0.94264,371.27 > view matrix models > #7,-0.81292,0.51564,0.27069,164.44,0.47811,0.8563,-0.19535,-70.198,-0.33253,-0.029381,-0.94264,377.77 > view matrix models > #7,-0.6748,0.63257,0.38012,92.37,0.6264,0.76328,-0.15819,-91.803,-0.39021,0.13137,-0.91131,350.78 > view matrix models > #7,-0.6748,0.63257,0.38012,105.27,0.6264,0.76328,-0.15819,-106.57,-0.39021,0.13137,-0.91131,348.68 > view matrix models > #7,-0.6748,0.63257,0.38012,102.03,0.6264,0.76328,-0.15819,-106.9,-0.39021,0.13137,-0.91131,344.75 > view matrix models > #7,-0.73464,0.5535,0.39235,128.26,0.6362,0.76291,0.11497,-162.48,-0.2357,0.33407,-0.9126,271.38 > view matrix models > #7,-0.73464,0.5535,0.39235,123.54,0.6362,0.76291,0.11497,-161.88,-0.2357,0.33407,-0.9126,275.9 > view matrix models > #7,-0.92912,0.23184,0.28807,250.25,0.23464,0.97175,-0.025291,-93.191,-0.2858,0.044095,-0.95727,354.33 > view matrix models > #7,-0.92912,0.23184,0.28807,250.78,0.23464,0.97175,-0.025291,-92.605,-0.2858,0.044095,-0.95727,360 > view matrix models > #7,-0.92912,0.23184,0.28807,250.51,0.23464,0.97175,-0.025291,-94.297,-0.2858,0.044095,-0.95727,360.58 > view matrix models > #7,-0.86677,0.46943,0.16836,212.49,0.47815,0.87818,0.013035,-133.53,-0.14173,0.091799,-0.98564,326.35 > view matrix models > #7,-0.75369,0.55111,0.3581,134.98,0.59561,0.80308,0.017645,-143.61,-0.27786,0.22659,-0.93352,317.01 > view matrix models > #7,-0.75369,0.55111,0.3581,134.9,0.59561,0.80308,0.017645,-139.03,-0.27786,0.22659,-0.93352,317.56 > view matrix models > #7,-0.75562,0.53048,0.38422,134.39,0.61149,0.78155,0.12352,-158.73,-0.23476,0.32828,-0.91494,284.16 > view matrix models > #7,-0.87839,0.1055,0.46616,230.69,0.23165,0.94709,0.22217,-132.62,-0.41806,0.30314,-0.85635,316.04 > view matrix models > #7,-0.87839,0.1055,0.46616,233.2,0.23165,0.94709,0.22217,-133.27,-0.41806,0.30314,-0.85635,318.67 > view matrix models > #7,-0.87839,0.1055,0.46616,227.55,0.23165,0.94709,0.22217,-131.84,-0.41806,0.30314,-0.85635,320.35 > view matrix models > #7,-0.93225,-0.14612,0.33099,316.69,-0.11028,0.98605,0.12469,-49.31,-0.34459,0.079745,-0.93536,366.13 > view matrix models > #7,-0.92482,0.31305,0.21613,243.94,0.26945,0.94012,-0.20873,-53.736,-0.26853,-0.1348,-0.95379,397.68 > view matrix models > #7,-0.92482,0.31305,0.21613,245.77,0.26945,0.94012,-0.20873,-54.196,-0.26853,-0.1348,-0.95379,393.98 > view matrix models > #7,-0.91926,0.28285,0.27379,239.46,0.2527,0.95729,-0.14052,-67.592,-0.30184,-0.059985,-0.95147,385.2 > view matrix models > #7,-0.87025,0.40939,0.27398,203.36,0.38118,0.91193,-0.15192,-82.905,-0.31205,-0.027772,-0.94966,380.4 > select subtract #7 Nothing selected > color #!6-7 bychain > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!6 models > hide #!7 models > show #!6 models > hide #!6 models > show #!7 models > show #!6 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > hide #!7 models > hide #!6 models > show #!7 models > show #!6 models > select add #7 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > view matrix models > #7,-0.82295,0.51309,0.24391,178.13,0.50778,0.85685,-0.089235,-110.38,-0.25478,0.050415,-0.96568,355.72 > view matrix models > #7,-0.78408,0.52693,0.32797,150.7,0.521,0.84596,-0.11358,-106.14,-0.3373,0.081817,-0.93783,361.06 > view matrix models > #7,-0.89777,0.38001,0.22271,225.07,0.38215,0.92343,-0.035182,-108.37,-0.21903,0.053522,-0.97425,349.31 > view matrix models > #7,-0.89849,0.35157,0.2629,223.14,0.33404,0.9361,-0.11019,-86.193,-0.28484,-0.011191,-0.95851,373.16 > view matrix models > #7,-0.89999,0.33607,0.27763,223.72,0.34879,0.93719,-0.0037997,-110.38,-0.26147,0.093416,-0.96068,347.35 > view matrix models > #7,-0.86687,0.36718,0.33723,198.77,0.38136,0.92407,-0.025835,-110.17,-0.32111,0.10621,-0.94107,353.34 > view matrix models > #7,-0.85053,0.42931,0.3038,189.23,0.44771,0.89412,-0.010102,-120.99,-0.27597,0.12742,-0.95268,341.87 > view matrix models > #7,-0.85053,0.42931,0.3038,188.25,0.44771,0.89412,-0.010102,-122.75,-0.27597,0.12742,-0.95268,342.46 > select subtract #7 Nothing selected > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_IIIA.cxs"" > open 7uzz Summary of feedback from opening 7uzz fetched from pdb --- note | Fetching compressed mmCIF 7uzz from http://files.rcsb.org/download/7uzz.cif 7uzz title: Staphylococcus epidermidis RP62a CRISPR tall effector complex [more info...] Chain information for 7uzz #8 --- Chain | Description | UniProt A B C D | CRISPR system Cms endoribonuclease Csm3 | Q5HK91_STAEQ 1-214 E | CRISPR system Cms protein Csm5 | Q5HK93_STAEQ 1-340 F | CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) | Q5HK89_STAEQ 1-757 G | RNA (37-MER) | H | CRISPR system Cms protein Csm4 | Q5HK92_STAEQ 1-304 I J K | CRISPR system Cms protein Csm2 | Q5HK90_STAEQ 14-141 > select add #8 19967 atoms, 20391 bonds, 20 pseudobonds, 2410 residues, 2 models selected > show sel cartoons > hide sel atoms > mmaker #8 to #6 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 8bmw, chain K (#6) with 7uzz, chain F (#8), sequence alignment score = 511.8 RMSD between 93 pruned atom pairs is 1.318 angstroms; (across all 573 pairs: 19.490) > hide #!6 models > hide #!7 models > select subtract #8 Nothing selected > show #!7 models > select add #8 19967 atoms, 20391 bonds, 20 pseudobonds, 2410 residues, 2 models selected > view matrix models > #8,0.0845,-0.98012,-0.1795,412.25,0.90669,0.00092228,0.4218,-142.16,-0.41325,-0.19839,0.88875,35.585 > undo > select subtract #8 Nothing selected > select add #7 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > view matrix models > #7,-0.81633,0.44067,0.37339,165.14,0.45487,0.88888,-0.054584,-114.45,-0.35596,0.12529,-0.92607,354.36 > view matrix models > #7,-0.81662,0.49226,0.30135,168.81,0.46376,0.87044,-0.16511,-90.847,-0.34358,0.0049201,-0.93911,378.91 > view matrix models > #7,-0.81662,0.49226,0.30135,172.72,0.46376,0.87044,-0.16511,-86.119,-0.34358,0.0049201,-0.93911,377.93 > view matrix models > #7,-0.81662,0.49226,0.30135,172.89,0.46376,0.87044,-0.16511,-82.532,-0.34358,0.0049201,-0.93911,372.99 > view matrix models > #7,-0.82887,0.49346,0.26357,182.62,0.47056,0.86977,-0.14859,-87.056,-0.30257,0.00086647,-0.95313,368.01 > view matrix models > #7,-0.82416,0.50826,0.24988,181.3,0.47514,0.86059,-0.18336,-79.315,-0.30824,-0.032389,-0.95076,375.52 > view matrix models > #7,-0.83782,0.38323,0.38884,182.4,0.3359,0.92331,-0.18621,-62.502,-0.43038,-0.0254,-0.90229,390.07 > view matrix models > #7,-0.86925,0.25505,0.4235,207.88,0.18583,0.96239,-0.19816,-33.763,-0.45811,-0.093551,-0.88396,406.02 > view matrix models > #7,-0.88198,0.25193,0.3983,216.12,0.1757,0.95997,-0.21814,-27.234,-0.43731,-0.12241,-0.89094,408.95 > view matrix models > #7,-0.90652,0.17807,0.38277,239.36,0.088975,0.96691,-0.23911,-6.4377,-0.41268,-0.1827,-0.89237,416.39 > view matrix models > #7,-0.90652,0.17807,0.38277,245.13,0.088975,0.96691,-0.23911,-7.8887,-0.41268,-0.1827,-0.89237,419.89 > view matrix models > #7,-0.90652,0.17807,0.38277,245.84,0.088975,0.96691,-0.23911,-4.2885,-0.41268,-0.1827,-0.89237,420.93 > view matrix models > #7,-0.90652,0.17807,0.38277,246.4,0.088975,0.96691,-0.23911,-5.0303,-0.41268,-0.1827,-0.89237,419.99 > view matrix models > #7,-0.89684,0.24239,0.37004,233.75,0.15668,0.95634,-0.24671,-15.509,-0.41368,-0.16328,-0.89566,416.88 > select subtract #7 Nothing selected > select add #6 28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected > show #!6 models > hide #!8 models > select subtract #6 Nothing selected > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_IIIA_2.cxs"" [Repeated 1 time(s)] > close session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > close > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb --- warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 Chain information for merged_ivc_apo_refine_007.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E F G H | No description available I | No description available J | No description available K L M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available > open ""/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC > apo/cryosparc_P38_J47_006_volume_map.mrc"" Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512, pixel 1.07, shown at level 0.0338, step 2, values float32 > volume #2 step 1 > surface dust #2 size 10.7 > volume #2 level 0.1238 > hide cartoons > hide atoms > volume #2 level 0.1508 > volume #2 color #8d8d8d81 > volume #2 color #7d8d8d81 > volume #2 color #7d8d8d82 > select add #2 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > volume #2 color #87cefa60 > select subtract #2 Nothing selected > volume #2 color #87cefa61 > combine #1 > select add #2 2 models selected > select add #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 4 models selected > select add #3 63324 atoms, 64720 bonds, 34 pseudobonds, 7776 residues, 6 models selected > ui tool show ""Color Actions"" > color sel white > color #2 #ffffff6c models > color #2 #ffffff6b models > lighting soft > color #2 #e6e8e86b models > color #2 #e6e8e8d0 models > color #2 #969797d0 models > color #2 #aeb0b0d0 models > lighting full > select subtract #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 4 models selected > select subtract #3 2 models selected > select subtract #2 Nothing selected > select #1/A:54,70,93,97,115,146,159 69 atoms, 66 bonds, 7 residues, 1 model selected > show (sel-residues & sidechain) target ab > style sel stick Changed 69 atom styles > color sel byhetero > cofr #1/A > volume #2 level 0.2093 > volume #2 level 0.18 > volume #2 level 0.15 > volume #2 color #aeb0b03b > select add #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #1 Nothing selected > volume #2 level 0.14 > select /S:2-31 1232 atoms, 1380 bonds, 60 residues, 2 models selected > select /R:1-46 1960 atoms, 2194 bonds, 92 residues, 2 models selected > select /Q:43-121 452 atoms, 460 bonds, 2 pseudobonds, 56 residues, 4 models selected > select /P:17-124 1552 atoms, 1570 bonds, 4 pseudobonds, 196 residues, 4 models selected > select /O:15-124 1674 atoms, 1698 bonds, 4 pseudobonds, 210 residues, 4 models selected > select /N:15-124 1728 atoms, 1754 bonds, 2 pseudobonds, 218 residues, 4 models selected > select /B:1-297 4712 atoms, 4822 bonds, 2 pseudobonds, 570 residues, 4 models selected > select /C:1-303 4576 atoms, 4646 bonds, 2 pseudobonds, 588 residues, 4 models selected > select /D:1-303 4608 atoms, 4678 bonds, 2 pseudobonds, 592 residues, 4 models selected > select /I:1-303 4578 atoms, 4648 bonds, 2 pseudobonds, 586 residues, 4 models selected > select /J:1-303 4056 atoms, 4124 bonds, 2 pseudobonds, 524 residues, 4 models selected > select /K:16-124 1710 atoms, 1736 bonds, 2 pseudobonds, 216 residues, 4 models selected > select /L:16-124 1710 atoms, 1736 bonds, 2 pseudobonds, 216 residues, 4 models selected > select /H:1-303 4716 atoms, 4788 bonds, 606 residues, 2 models selected > select /G:1-303 4716 atoms, 4788 bonds, 606 residues, 2 models selected > select /F:1-303 4716 atoms, 4788 bonds, 606 residues, 2 models selected > select /E:1-303 4716 atoms, 4788 bonds, 606 residues, 2 models selected > select /C:1-303 4576 atoms, 4646 bonds, 2 pseudobonds, 588 residues, 4 models selected > select /B:1-297 4712 atoms, 4822 bonds, 2 pseudobonds, 570 residues, 4 models selected > select /A:40-593 8198 atoms, 8386 bonds, 6 pseudobonds, 1008 residues, 4 models selected > select /S:2-31 1232 atoms, 1380 bonds, 60 residues, 2 models selected > select /R:1-46 1960 atoms, 2194 bonds, 92 residues, 2 models selected > select /Q:43-121 452 atoms, 460 bonds, 2 pseudobonds, 56 residues, 4 models selected > select /P:17-124 1552 atoms, 1570 bonds, 4 pseudobonds, 196 residues, 4 models selected > show #1/T > select #1/T 2 atoms, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel slate gray > select add #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #1 Nothing selected > ui tool show ""Side View"" > select #3/A:94,147 18 atoms, 17 bonds, 2 residues, 1 model selected > show (sel-residues & sidechain) target ab > style sel stick Changed 18 atom styles > color sel byhetero > select add #3 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #3 Nothing selected > volume #2 level 0.135 > volume #2 level 0.138 > volume #2 level 0.139 > volume #2 color #8585872e > volume #2 color #7272732e > volume #2 color #7368732e > volume #2 color #d5c1d62e > volume #2 color #e5cfe62e > volume #2 color #d6c2d72e > lighting soft > lighting simple > lighting full > volume #2 color #e1769a2e > volume #2 color #e87a9f1b > volume #2 level 0.142 > select add #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select add #3 63324 atoms, 64720 bonds, 34 pseudobonds, 7776 residues, 4 models selected > ui tool show ""Color Actions"" > color sel pale violet red > color sel plum > color sel pink > color sel light pink > color sel byhetero > select #1/T 2 atoms, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel slate gray > select add #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #1 Nothing selected > save /Users/xuchengtao/Desktop/image221.png supersample 3 > save /Users/xuchengtao/Desktop/image222.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_Apo/IVC_apo_HD_1.cxs"" > lighting full > lighting soft > volume zone #2 nearAtoms #1range 3 Invalid ""nearAtoms"" argument: only initial part ""#1"" of atom specifier valid > volume zone #2 nearAtoms #1/A range 3 > volume zone #2 nearAtoms #1/A range 4 > save /Users/xuchengtao/Desktop/image223.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_Apo/IVC_apo_HD_1.cxs"" > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!2 models > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"" Chain information for merged_real_space_refined_011.pdb #4 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > mmaker #4/A: 54, 70,93,94,115,146,147,97 > matchmaker #4/A: 54, 70,93,94,115,146,147,97 Missing required ""to"" argument > mmaker #4/A: 54, 70,93,94,115,146,147,97 to #1 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 merged_ivc_apo_refine_007.pdb, chain A (#1) with merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score = 49.4 RMSD between 8 pruned atom pairs is 0.822 angstroms; (across all 8 pairs: 0.822) > style stick Changed 93848 atom styles > hide atoms [Repeated 1 time(s)] > show atoms > undo [Repeated 3 time(s)] > style stick Changed 93848 atom styles > color byhetero > hide #4 > show #4/A:54,70,93,94,115,146,147,159 > select #4/A:54,70,93,97,115,146,159 69 atoms, 66 bonds, 7 residues, 1 model selected > show (sel-residues & sidechain) target ab > select #4/A 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light sky blue > color sel byhetero > combine #4/A > select add #4 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > hide #!5 models > show #!5 models > hide #5 > show #5/A:94,147 > select #5/A:94,147 18 atoms, 17 bonds, 2 residues, 1 model selected > show (sel-residues & sidechain) target ab > color #1 #ffb6c17c [Repeated 1 time(s)] > color sel byhetero > color #1 #ffb6c17d > select add #1 31680 atoms, 32377 bonds, 17 pseudobonds, 3890 residues, 3 models selected > color sel byhetero > select subtract #1 18 atoms, 17 bonds, 2 residues, 1 model selected > color #3 #f1c3caff > color #3 #f1c3ca81 > color #3 #f1c3ca82 > select add #3 31680 atoms, 32377 bonds, 17 pseudobonds, 3890 residues, 3 models selected > color sel byhetero > select subtract #3 18 atoms, 17 bonds, 2 residues, 1 model selected > hide #1/T > select #1/T 2 atoms, 2 residues, 1 model selected > show (sel-residues & sidechain) target ab > show #1/T > ui tool show ""Color Actions"" > color sel slate gray > select add #1 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected > select subtract #1 Nothing selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"" > show #4/A:67-81, 86-96,112-118,136-160 cartoons > select #4/A:67-81, 86-96,112-118,136-160 cartoon Expected a keyword > select #4/A:67-81, 86-96,112-118,136-160 470 atoms, 480 bonds, 58 residues, 1 model selected > cartoon style sel modeHelix tube sides 20 > select #4/A:67-81, 86-98,112-118,136-160 486 atoms, 497 bonds, 60 residues, 1 model selected > show sel cartoons > select add #4 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #4 Nothing selected > hide #1/T > show #4/B > select #4/B 2 atoms, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel slate gray > select add #4 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #4 Nothing selected > select #4/B 2 atoms, 2 residues, 1 model selected > color sel byhetero > undo > color sel bychain > undo > style sel sphere Changed 2 atom styles > select add #4 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #4 Nothing selected > save /Users/xuchengtao/Desktop/image224.png supersample 3 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > save /Users/xuchengtao/Desktop/image225.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"" ——— End of log from Tue Feb 3 13:26:30 2026 ——— > view name session-start opened ChimeraX session > hide #!3 models > show #!3 models > show #1/A:136-160 cartoons > show #1/A:136-180 cartoons [Repeated 1 time(s)] > show #4/A:136-180 cartoons > select #4/A:136-180 352 atoms, 357 bonds, 45 residues, 1 model selected > cartoon style sel xsection oval modeHelix default > select add #4 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected > select subtract #4 Nothing selected > Unknown command: measure #1/A:159@CA #4/A:159@CA > ui tool show Distances > select #1/A:159@CA #4/A:159@CA 2 atoms, 2 residues, 2 models selected > distance #1/A:159@CA #4/A:159@CA Distance between merged_ivc_apo_refine_007.pdb #1/A GLU 159 CA and merged_real_space_refined_011.pdb #4/A GLU 159 CA: 1.998Å > hide #1/A:59 > hide #1/A:59 atoms > hide #1/A:54 atoms > hide #4/A:54 atoms > mmaker #4/A:115,94,146,147 to #1/A 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 merged_ivc_apo_refine_007.pdb, chain A (#1) with merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score = 25.8 RMSD between 4 pruned atom pairs is 0.509 angstroms; (across all 4 pairs: 0.509) > mmaker #4/A:115,94,146,147,70 to #1/A 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 merged_ivc_apo_refine_007.pdb, chain A (#1) with merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score = 33.2 RMSD between 5 pruned atom pairs is 0.579 angstroms; (across all 5 pairs: 0.579) > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"" ——— End of log from Tue Feb 3 15:37:02 2026 ——— > view name session-start opened ChimeraX session > show #!2 models > hide #!2 models > hide #!1 models > hide #!3 models > hide #!4 models > hide #!5 models > close #7#1-6 > open ""/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC > apo/merged_ivc_apo_refine_007.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Building models undergoing/20260114 IVC apo/merged_ivc_apo_refine_007.pdb --- warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 Chain information for merged_ivc_apo_refine_007.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E F G H | No description available I | No description available J | No description available K L M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available > style stick Changed 31663 atom styles > hide atoms > show atoms > style stick Changed 31663 atom styles > show cartoons > hide cartoons > hide #1 > open ""/Users/xuchengtao/Documents/Building models > undergoing/20251003IVC/20251222 Xiaomeng AI > IVC/merged_real_space_refined_014.pdb"" Chain information for merged_real_space_refined_014.pdb #2 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > hide atoms > mmaker #1/A:70,93,94,146,147 to #2/A 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 merged_real_space_refined_014.pdb, chain A (#2) with merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 33.2 RMSD between 5 pruned atom pairs is 0.530 angstroms; (across all 5 pairs: 0.530) > show #1/A:70,93,94,146,147 > select #1/A:70,93,94,146,147 48 atoms, 49 bonds, 5 residues, 1 model selected > style sel stick Changed 48 atom styles > color sel byhetero > select #2/A:70,93,94,146,147 48 atoms, 49 bonds, 5 residues, 1 model selected > color sel byhetero > show sel atoms > style sel stick Changed 48 atom styles > cofr sel > select #2/A:70,93,94,146,147,115 58 atoms, 59 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 58 atom styles > color sel byhetero > select #1/A:70,93,94,146,147,115 58 atoms, 59 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > mmaker #1/A:70,93,94,146,147,115 to #2/A 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 merged_real_space_refined_014.pdb, chain A (#2) with merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 40 RMSD between 6 pruned atom pairs is 0.637 angstroms; (across all 6 pairs: 0.637) > select #1/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select #1/A:159, #2/A:159 Expected an objects specifier or a keyword > show sel atoms > select #2/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > color #1 #eceeedff > open ""/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC > apo/merged_ivc_apo_refine_008.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Building models undergoing/20260114 IVC apo/merged_ivc_apo_refine_008.pdb --- warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 Chain information for merged_ivc_apo_refine_008.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E F G H | No description available I | No description available J | No description available K L M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available > mmaker #3 to #1 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 merged_ivc_apo_refine_007.pdb, chain A (#1) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 2572.9 RMSD between 504 pruned atom pairs is 0.004 angstroms; (across all 504 pairs: 0.004) > style sel stick Changed 9 atom styles > hide sel atoms > undo > hide #!3 models > select add #2 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > select subtract #2 Nothing selected > select add #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > hide #3 > show #!3 models > select subtract #3 Nothing selected > show #3/A:70, 115,146,147,93,94,159 > style stick Changed 93851 atom styles > hide #!1 models > color #3 #e1e4eeff > color #3 #b2b5bdff > mmaker #3/A:70, 115,146,147,93,94,159 to #2/A 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 merged_real_space_refined_014.pdb, chain A (#2) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 45.3 RMSD between 7 pruned atom pairs is 0.851 angstroms; (across all 7 pairs: 0.851) > show #1/A:97 > show #!1 models > hide #!1 models > show #2/A:97 > show #3/A:97 > hide #!3 models > show #!3 models > open ""/Users/xuchengtao/Documents/Building models > undergoing/20251003IVC/20251222 Xiaomeng AI > IVC/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > volume #4 step 1 > volume #4 level 0.1661 > ui tool show ""Hide Dust"" > surface dust #4 size 11.38 > surface dust #4 size 12.58 > surface dust #4 size 10.12 > volume #4 color #b2b2b2ab > ui tool show ""Color Actions"" > color light sky blue > hide #!4 models > hide #!3 models > show #!3 models > select #2 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > color sel byhetero > select #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > color sel byhetero > select subtract #3 Nothing selected > open ""/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC > apo/cryosparc_P38_J47_006_volume_map.mrc"" Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512, pixel 1.07, shown at level 0.0338, step 2, values float32 > volume #5 step 1 > surface dust #5 size 9.46 > mmaker #5 to #4 No 'to' model specified > mmaker #5 to #3 No molecules/chains to match specified > surface dust #5 size 9.3 > surface dust #5 size 11.38 > surface dust #5 size 9.62 > surface dust #5 size 10.29 > surface dust #5 size 13.23 > volume #5 level 0.09228 > ui tool show ""Fit in Map"" > ui mousemode right ""translate selected models"" > select add #5 2 models selected > view matrix models > #5,-0.97381,-0.031588,0.22517,490.36,-0.071884,0.98228,-0.17308,73.711,-0.21571,-0.18473,-0.95882,664.68 > view matrix models > #5,-0.97381,-0.031588,0.22517,436.09,-0.071884,0.98228,-0.17308,0.20124,-0.21571,-0.18473,-0.95882,557.69 > volume #5 level 0.1173 > view matrix models > #5,-0.93478,0.30346,0.18464,345.57,0.2887,0.95188,-0.10282,-106.34,-0.20696,-0.042808,-0.97741,523.25 > fitmap #5 inMap #4 Fit map cryosparc_P38_J47_006_volume_map.mrc in map cryosparc_P6_J91_004_volume_map.mrc using 310271 points correlation = 0.9347, correlation about mean = 0.7922, overlap = 1.556e+04 steps = 220, shift = 18.3, angle = 17.3 degrees Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.97760466 0.20023007 -0.06478454 435.09526992 0.19862444 0.97960384 0.03040797 -118.87262867 0.06955178 0.01685918 -0.99743587 434.81572276 Axis -0.10034105 -0.99488204 -0.01189115 Axis point 216.14301063 0.00000000 225.62653040 Rotation angle (degrees) 176.12880575 Shift along axis 69.43586944 > view matrix models > #5,-0.99043,0.12889,-0.049357,453.43,0.1291,0.99163,-0.0012337,-93.971,0.048785,-0.0075941,-0.99878,447.49 > volume #5 level 0.1674 > view matrix models > #5,-0.98693,0.15429,-0.046578,444.85,0.15422,0.98802,0.0051166,-101.57,0.04681,-0.0021338,-0.9989,446.59 > view matrix models > #5,-0.99436,0.088993,0.057707,435.97,0.099112,0.97336,0.20674,-137.79,-0.037772,0.21129,-0.97669,405.88 > view matrix models > #5,-0.99438,0.087718,0.059321,435.88,0.098341,0.97272,0.21009,-138.33,-0.039274,0.21474,-0.97588,405.13 > undo > view matrix models > #5,-0.98265,0.16324,-0.088032,452.62,0.16414,0.98643,-0.0029871,-101.62,0.08635,-0.017385,-0.99611,439.18 > volume #5 level 0.2085 > color sel pink > volume #5 color #ffc0cbad > volume #4 level 0.12 > show #2/B > select #2/B 2 atoms, 2 residues, 1 model selected > style sel sphere Changed 2 atom styles > ui tool show ""Color Actions"" > color sel slate gray > hide #!3 models > volume #4 level 0.13 > volume #4 level 0.14 > matchmaker #4 to #2 No molecules/chains to match specified > select add #2 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > select subtract #2 Nothing selected > hide #!2 models > close #2 > open ""/Users/xuchengtao/Documents/Building models > undergoing/20251003IVC/20251222 Xiaomeng AI > IVC/merged_real_space_refined_015.pdb"" Chain information for merged_real_space_refined_015.pdb #2 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > hide #2 > combine #2 > color #2 lightskyblue > color #6 lightskyblue > select #2/A:70,93,94,97,115,146,159 66 atoms, 64 bonds, 7 residues, 1 model selected > show (sel-residues & sidechain) target ab > style sel stick Changed 66 atom styles > color sel byhetero > select #2/B 2 atoms, 2 residues, 1 model selected > style sel sphere Changed 2 atom styles > show sel atoms > color sel gray > ui tool show ""Color Actions"" > color sel slate gray > volume #4 color #87cefa27 > volume #4 color #87cefa26 > lighting full > lighting soft > lighting full > hide #2/A:94 > select #5/A:94,147 Nothing selected > show #5/A:94,147 & ~@N,C,O > show #!5 models > hide #!5 models > show #6/A:94,147 & ~@N,C,O > select #6/A 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected > style sel stick Changed 4478 atom styles > color sel byhetero > select add #6 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > select subtract #6 Nothing selected > combine #3 > hide #3 > hide #7 > show #!5 models > volume #5 level 0.1566 > volume #5 color #ffc0cb2b > select #3/A:70,93,97,115,146,159 58 atoms, 56 bonds, 6 residues, 1 model selected > show (#2,4,6-7 & sidechain) target ab > select #3/A:70,93,97,115,146,159 58 atoms, 56 bonds, 6 residues, 1 model selected > show #3/A:70,93,97,115,146,159& ~@N,,C,O Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #3/A:70,93,97,115,146,159& ~@N,C,O > show #!3 models > hide #2/A:97 > hide #3/A:97 > mmaker #3/A:70,93,94,115 to #2/A 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 merged_real_space_refined_015.pdb, chain A (#2) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 26.4 RMSD between 4 pruned atom pairs is 0.646 angstroms; (across all 4 pairs: 0.646) > mmaker #3/A:70,93,94,115,146 to #2/A 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 merged_real_space_refined_015.pdb, chain A (#2) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 33.2 RMSD between 5 pruned atom pairs is 0.680 angstroms; (across all 5 pairs: 0.680) > close #7 > combine #3 > hide #7 > show #7/A:94,147 & ~@N,CA,C,O > show #7/A:94,147 & ~@N,,C,O Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #7/A:94,147 & ~@N,C,O > select add #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > select subtract #3 Nothing selected > hide #!2 models > show #!2 models > hide #!4 models > show #!5 models > show #!4 models > select add #5 2 models selected > view matrix models > #5,-0.97841,0.20197,-0.043758,428.89,0.20245,0.97927,-0.0068224,-109.08,0.041473,-0.015534,-0.99902,451.71 > undo > select subtract #5 Nothing selected > select add #4 2 models selected > select subtract #4 Nothing selected > hide #!4 models > hide #!2 models > hide #!6 models > select add #5 2 models selected > view matrix models > #5,-0.95877,0.093992,-0.2682,514.11,0.090359,0.99557,0.025885,-91.881,0.26944,0.00058378,-0.96302,375.36 > volume #5 level 0.1727 > view matrix models > #5,-0.97116,0.2003,-0.12934,450.76,0.20327,0.97907,-0.010053,-108.32,0.12462,-0.036052,-0.99155,432.49 > cofr @3/A > cofr #3/A > view matrix models > #5,-0.96897,0.21997,-0.11274,440.16,0.22373,0.97441,-0.021689,-109.42,0.10508,-0.046238,-0.99339,440.91 > view matrix models > #5,-0.98673,0.16214,0.0085692,427.41,0.16178,0.98627,-0.033106,-92.633,-0.013819,-0.03128,-0.99942,470.88 > view matrix models > #5,-0.99996,-0.0010926,-0.0093869,480.02,-0.0013883,0.9995,0.031557,-69.497,0.0093478,0.031569,-0.99946,447.61 > view matrix models > #5,-0.99994,-0.010838,0.0021348,479.5,-0.010849,0.99993,-0.0051597,-56.987,-0.0020787,-0.0051825,-0.99998,460.79 > view matrix models > #5,-0.99926,-0.0041216,0.038311,467.59,-0.0039274,0.99998,0.0051435,-61.705,-0.038331,0.0049892,-0.99925,467.71 > view matrix models > #5,-0.99926,-0.0041216,0.038311,467.58,-0.0039274,0.99998,0.0051435,-61.937,-0.038331,0.0049892,-0.99925,467.37 > volume #5 level 0.16 > volume #5 color #ffc0cbd6 > volume #5 level 0.17 > view matrix models > #5,-0.9987,-0.049666,0.011361,487.1,-0.049572,0.99873,0.0084327,-50.07,-0.011765,0.0078586,-0.9999,459.55 > view matrix models > #5,-0.9987,-0.049666,0.011361,486.96,-0.049572,0.99873,0.0084327,-49.824,-0.011765,0.0078586,-0.9999,459.82 > volume #5 level 0.15 > volume #5 level 0.175 > view matrix models > #5,-0.9987,-0.049666,0.011361,487.47,-0.049572,0.99873,0.0084327,-50.955,-0.011765,0.0078586,-0.9999,458.34 > view matrix models > #5,-0.99639,-0.068145,-0.0506,508.8,-0.077294,0.97481,0.20922,-91.913,0.035067,0.21238,-0.97656,383.96 > undo > view matrix models > #5,-0.90445,-0.37278,0.20738,495.44,-0.36083,0.92786,0.094206,29.42,-0.22754,0.010378,-0.97371,509.22 > view matrix models > #5,-0.90445,-0.37278,0.20738,496,-0.36083,0.92786,0.094206,27.507,-0.22754,0.010378,-0.97371,509.24 > view matrix models > #5,-0.90445,-0.37278,0.20738,506.69,-0.36083,0.92786,0.094206,29.176,-0.22754,0.010378,-0.97371,509.83 > view matrix models > #5,-0.90435,-0.36259,0.22513,499.05,-0.35913,0.93151,0.05762,37.745,-0.2306,-0.028742,-0.97262,520.93 > view matrix models > #5,-0.90435,-0.36259,0.22513,500.51,-0.35913,0.93151,0.05762,36.126,-0.2306,-0.028742,-0.97262,518.8 > view matrix models > #5,-0.90384,-0.33625,0.2646,482.45,-0.35563,0.93422,-0.027601,57.769,-0.23792,-0.11905,-0.96396,542.81 > view matrix models > #5,-0.90384,-0.33625,0.2646,487.46,-0.35563,0.93422,-0.027601,49.35,-0.23792,-0.11905,-0.96396,540.04 > view matrix models > #5,-0.9033,-0.31727,0.28876,475.58,-0.3537,0.93169,-0.082759,64.605,-0.24278,-0.17689,-0.95382,554.21 > view matrix models > #5,-0.9033,-0.31727,0.28876,479.2,-0.3537,0.93169,-0.082759,57.847,-0.24278,-0.17689,-0.95382,553.3 > volume #5 level 0.1947 > volume #5 level 0.175 > show #!2 models > hide #!2 models > show #!4 models > view matrix models > #5,-0.90789,-0.32005,0.27076,486.12,-0.35802,0.92795,-0.1036,65.738,-0.21809,-0.19099,-0.95706,551.27 > fitmap #5 inMap #4 Fit map cryosparc_P38_J47_006_volume_map.mrc in map cryosparc_P6_J91_004_volume_map.mrc using 186216 points correlation = 0.9452, correlation about mean = 0.7716, overlap = 1.379e+04 steps = 380, shift = 27.5, angle = 38 degrees Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.97747656 0.20090883 -0.06461583 434.82603912 0.19929299 0.97946158 0.03061556 -119.07093066 0.06943966 0.01704851 -0.99744046 434.80014734 Axis -0.10068315 -0.99484628 -0.01199138 Axis point 216.05419591 0.00000000 225.60664569 Rotation angle (degrees) 176.13677177 Shift along axis 69.46376469 > hide #!4 models > volume #5 level 0.1589 > volume #5 level 0.15 > view matrix models > #5,-0.97451,0.21473,-0.064928,430.36,0.21213,0.97622,0.044705,-125.65,0.072984,0.029792,-0.99689,430.23 > undo > view matrix models > #5,-0.97748,0.20091,-0.064616,436.21,0.19929,0.97946,0.030616,-119.26,0.06944,0.017049,-0.99744,436.08 > view matrix models > #5,-0.97239,0.22414,-0.065027,428.65,0.22083,0.9738,0.054308,-130.26,0.075496,0.038448,-0.9964,428.35 > view matrix models > #5,-0.97239,0.22414,-0.065027,428.82,0.22083,0.9738,0.054308,-127.24,0.075496,0.038448,-0.9964,428.69 > undo > hide #!4 models > volume #5 level 0.1661 > view matrix models > #5,-0.96662,0.25053,-0.05365,415.47,0.24919,0.96798,0.030408,-129.49,0.05955,0.016024,-0.9981,437.95 > view matrix models > #5,-0.96653,0.25013,-0.056982,416.46,0.2497,0.96821,0.01465,-125.38,0.058835,-6.834e-05,-0.99827,442.54 > view matrix models > #5,-0.96653,0.25013,-0.056982,416.26,0.2497,0.96821,0.01465,-126.49,0.058835,-6.834e-05,-0.99827,443.79 > undo > view matrix models > #5,-0.97268,0.22126,-0.070311,429.58,0.21796,0.97459,0.051693,-128.6,0.079962,0.034956,-0.99618,426.75 > view matrix models > #5,-0.97268,0.22126,-0.070311,430.14,0.21796,0.97459,0.051693,-126.95,0.079962,0.034956,-0.99618,427.81 > view matrix models > #5,-0.97268,0.22126,-0.070311,430.12,0.21796,0.97459,0.051693,-127.05,0.079962,0.034956,-0.99618,427.18 > volume #5 level 0.1589 > view matrix models > #5,-0.97111,0.22523,-0.078833,430.95,0.22249,0.97403,0.042032,-125.48,0.086252,0.023278,-0.996,428.57 > undo > view matrix models > #5,-0.96202,0.25857,-0.087537,421.85,0.25149,0.96419,0.084256,-142.27,0.10619,0.059042,-0.99259,412.55 > view matrix models > #5,-0.96202,0.25857,-0.087537,422.58,0.25149,0.96419,0.084256,-138.97,0.10619,0.059042,-0.99259,414.88 > volume #5 level 0.1446 > undo > volume #5 level 0.1607 > volume #5 level 0.1446 > view matrix models > #5,-0.9737,0.21948,-0.061119,428.33,0.21816,0.97552,0.027604,-120.53,0.065681,0.013544,-0.99775,437.95 > view matrix models > #5,-0.9737,0.21948,-0.061119,429.45,0.21816,0.97552,0.027604,-123.69,0.065681,0.013544,-0.99775,436.46 > view matrix models > #5,-0.9737,0.21948,-0.061119,430.1,0.21816,0.97552,0.027604,-123.83,0.065681,0.013544,-0.99775,436.76 > view matrix models > #5,-0.96936,0.23489,-0.071894,427.76,0.23263,0.9718,0.038497,-129.84,0.07891,0.020593,-0.99667,430.93 > view matrix models > #5,-0.96936,0.23489,-0.071894,427.42,0.23263,0.9718,0.038497,-128.58,0.07891,0.020593,-0.99667,431.63 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.29,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.72 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.23,0.23421,0.97154,0.035438,-127.81,0.091031,0.014376,-0.99574,429.7 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.59,0.23421,0.97154,0.035438,-127.05,0.091031,0.014376,-0.99574,429.19 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.19,0.23421,0.97154,0.035438,-128.03,0.091031,0.014376,-0.99574,428.89 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.53,0.23421,0.97154,0.035438,-128.27,0.091031,0.014376,-0.99574,428.38 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.63,0.23421,0.97154,0.035438,-128.15,0.091031,0.014376,-0.99574,429.1 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.12,0.091031,0.014376,-0.99574,428.9 > view matrix models > #5,-0.96958,0.23531,-0.067362,425.42,0.23325,0.97171,0.037075,-128.3,0.074181,0.020235,-0.99704,432.33 > view matrix models > #5,-0.9663,0.24851,-0.0672,420.91,0.24554,0.96813,0.049372,-134.15,0.077327,0.031207,-0.99652,428.36 > view matrix models > #5,-0.9663,0.24851,-0.0672,422.24,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.54 > view matrix models > #5,-0.9663,0.24851,-0.0672,422.17,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.18 > view matrix models > #5,-0.9663,0.24851,-0.0672,422.48,0.24554,0.96813,0.049372,-132.23,0.077327,0.031207,-0.99652,429.48 > view matrix models > #5,-0.96297,0.26101,-0.067585,418.3,0.25702,0.96439,0.062399,-138.01,0.081465,0.042718,-0.99576,425.02 > view matrix models > #5,-0.96297,0.26101,-0.067585,418.54,0.25702,0.96439,0.062399,-136.93,0.081465,0.042718,-0.99576,425.35 > undo > volume #5 level 0.1339 > volume #5 color #ffc0cb29 > volume #5 color #ffc0cb61 > show #!4 models > view matrix models > #5,-0.96792,0.23643,-0.085073,429.64,0.23421,0.97154,0.035438,-128.16,0.091031,0.014376,-0.99574,429.11 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.26,0.091031,0.014376,-0.99574,429.29 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.69,0.23421,0.97154,0.035438,-128.37,0.091031,0.014376,-0.99574,429.46 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.4,0.23421,0.97154,0.035438,-128.44,0.091031,0.014376,-0.99574,429.31 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.37,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.16 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.43,0.23421,0.97154,0.035438,-128.61,0.091031,0.014376,-0.99574,429.7 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.22,0.23421,0.97154,0.035438,-128.65,0.091031,0.014376,-0.99574,429.53 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.16,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.54 > hide #!3 models > show #!3 models > hide #!4 models > view matrix models > #5,-0.96792,0.23643,-0.085073,429.36,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.64 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.21,0.23421,0.97154,0.035438,-127.78,0.091031,0.014376,-0.99574,429.58 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.37,0.23421,0.97154,0.035438,-127.04,0.091031,0.014376,-0.99574,429.41 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.35,0.23421,0.97154,0.035438,-126.11,0.091031,0.014376,-0.99574,429.73 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.3,0.23421,0.97154,0.035438,-126,0.091031,0.014376,-0.99574,429.7 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.24,0.23421,0.97154,0.035438,-126.37,0.091031,0.014376,-0.99574,429.57 > volume #5 level 0.1464 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.2,0.23421,0.97154,0.035438,-126.21,0.091031,0.014376,-0.99574,429.4 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.13,0.23421,0.97154,0.035438,-125.77,0.091031,0.014376,-0.99574,429.31 > show #3/T > select #3/T 2 atoms, 2 residues, 1 model selected > style sel sphere Changed 2 atom styles > ui tool show ""Color Actions"" > color sel slate gray > select add #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > select subtract #3 Nothing selected > ui tool show ""Side View"" > hide #!3 models > hide #!5 models > hide #!7 models > show #!4 models > show #!6 models > show #!2 models > volume #4 level 0.12 > volume #4 level 0.125 > lighting full > lighting soft > lighting simple > lighting full > lighting flat > lighting full > lighting simple > lighting full > volume #4 level 0.13 > save /Users/xuchengtao/Desktop/image275.png supersample 3 > hide #!4 models > hide #!2 models > show #!3 models > show #!5 models > hide #!6 models > show #!7 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"" > save /Users/xuchengtao/Desktop/image276.png supersample 3 > hide #!3 models > hide #!5 models > hide #!7 models > show #!3 models > show #!7 models > hide #!7 models > show #!7 models > hide #3/T > show #!4 models > hide #!4 models > show #!2 models > show #!6 models > show #2/A:86-96 cartoons > cartoon style #2-3,6-7 modeHelix tube sides 20 > cartoon style (#2-3,6-7 & coil) xsection oval > cartoon style #2-3,6-7 xsection barbell modeHelix default > cartoon style #2-3,6-7 modeHelix tube sides 20 > show #2/A:136-160 cartoons > combine #7 > color #8 white > color #8 #ffffffb4 > color #8 #ffffff82 > color #8 #ffffff80 > color #8 #f5f4f680 > show #8/A:136-160 cartoons > show #8/A:86-96 cartoons > show #8/A:136-180 cartoons > show #2/A:136-180 cartoons > show #2/A:136-160 cartoons > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"" > hide #2/A:161-180 cartoons > hide #8/A:161-180 cartoons > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > hide #8/A:147 > hide #8/A:94] > hide #8/A:94 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > lighting full > lighting soft > hide #!2 models > hide #!6 models > show #!2 models > show #!6 models > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > save /Users/xuchengtao/Desktop/image277.png supersample 3 > ui tool show Distances > select #2/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:159, #2/A:159 Expected an objects specifier or a keyword Exactly two atoms must be selected! > select #2,3/A:159@CA 2 atoms, 2 residues, 2 models selected > distance #3/A:159@CA #2/A:159@CA Distance between merged_ivc_apo_refine_008.pdb #3/A GLU 159 CA and merged_real_space_refined_015.pdb #2/A GLU 159 CA: 2.124Å > undo > ~distance #3/A:159@CA #2/A:159@CA > lighting shadows true > lighting full > lighting soft > depthCue true Unknown command: depthCue true > depthCue true Unknown command: depthCue true > depthCue true Unknown command: depthCue true > depthCue Unknown command: depthCue > lighting depthCue true > lighting depthCueStart 0.4 depthCueEnd 0.9 > lighting depthCueStart 0.4 depthCueEnd 0.8 > lighting depthCueStart 0.2 depthCueEnd 0.8 > lighting depthCueStart 0.1 depthCueEnd 0.8 > lighting depthCueStart 0.1 depthCueEnd 0.4 > lighting depthCueStart 0.2 depthCueEnd 0.4 > lighting depthCueStart 0.3 depthCueEnd 0.4 > lighting simple > lighting flat > lighting full > lighting soft > lighting depthCueStart 0.3 depthCueEnd 0.4 > lighting depthCueStart 0.4 depthCueEnd 0.9 > lighting depthCueStart 0.4 depthCueEnd 0.5 > lighting depthCueStart 0.3 depthCueEnd 0.5 > lighting depthCueStart 0.3 depthCueEnd 0.4 > lighting depthCueStart 0.4 > lighting depthCueStart 0.9 > lighting depthCueStart 0. > lighting depthCueStart 0.5 > lighting depthCueStart 0.4 > show #!2 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM6.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.227, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384, pixel 1.07, shown at level 0.266, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel 1.07, shown at level 0.153, step 1, values float32 > view name session-start opened ChimeraX session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.13, step 1, values float32 Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512, pixel 1.07, shown at level 0.146, step 1, values float32 > view name session-start opened ChimeraX session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.13, step 1, values float32 Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512, pixel 1.07, shown at level 0.146, step 1, values float32 > view name session-start opened ChimeraX session > lighting depthCueStart 0.4 depthCueStart 0.9 Repeated keyword argument ""depthCueStart"" > lighting depthCueStart 0.4 depthCueEnd 0.9 > lighting depthCueStart 0.4 depthCueEnd 0.6 > lighting depthCueStart 0.1 depthCueEnd 0.6 > lighting depthCueStart 0.2 depthCueEnd 0.6 > lighting depthCueStart 0.2 depthCueEnd 0.3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > lighting depthCueStart 0.2 depthCueEnd 0.25 > lighting depthCueStart 0.2 depthCueEnd 0.5 > lighting depthCueStart 0.2 depthCueEnd 0.25 > lighting depthCueStart 0.2 depthCueEnd 0.28 > lighting depthCueStart 0.2 depthCueEnd 0.3 > lighting depthCueStart 0.2 depthCueEnd 0.34 > save /Users/xuchengtao/Desktop/image278.png supersample 3 > save /Users/xuchengtao/Desktop/image279.png supersample 3 > lighting depthCueStart 0.2 depthCueEnd 0.33 > lighting depthCueStart 0.2 depthCueEnd 0.3 > save /Users/xuchengtao/Desktop/image280.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > lighting depthCue false > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > close session > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_00_00162_volume.mrc Opened J31_class_00_00162_volume.mrc as #1, grid size 128,128,128, pixel 3.01, shown at level 0.108, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_01_00162_volume.mrc Opened J31_class_01_00162_volume.mrc as #2, grid size 128,128,128, pixel 3.01, shown at level 0.126, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_02_00162_volume.mrc Opened J31_class_02_00162_volume.mrc as #3, grid size 128,128,128, pixel 3.01, shown at level 0.0868, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_03_00162_volume.mrc Opened J31_class_03_00162_volume.mrc as #4, grid size 128,128,128, pixel 3.01, shown at level 0.241, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_04_00162_volume.mrc Opened J31_class_04_00162_volume.mrc as #5, grid size 128,128,128, pixel 3.01, shown at level 0.105, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_05_00162_volume.mrc Opened J31_class_05_00162_volume.mrc as #6, grid size 128,128,128, pixel 3.01, shown at level 0.27, step 1, values float32 > color #1-6 lightgrey > ui tool show ""Hide Dust"" > surface dust #1 size 18.06 > surface dust #1 size 30.1 > surface dust #2 size 30.1 > surface dust #3 size 30.1 > surface dust #4 size 30.1 > surface dust #5 size 30.1 > surface dust #6 size 30.1 > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!6 models > hide #!4 models > hide #!3 models > hide #!2 models > save /Users/xuchengtao/Desktop/image281.png supersample 3 > lighting full > lighting soft > save /Users/xuchengtao/Desktop/image282.png supersample 3 > hide #!1 models > show #!2 models > save /Users/xuchengtao/Desktop/image283.png supersample 3 > hide #!2 models > show #!3 models > save /Users/xuchengtao/Desktop/image284.png supersample 3 > hide #!3 models > show #!4 models > save /Users/xuchengtao/Desktop/image285.png supersample 3 > hide #!4 models > show #!5 models > save /Users/xuchengtao/Desktop/image286.png supersample 3 > hide #!5 models > show #!6 models > save /Users/xuchengtao/Desktop/image287.png supersample 3 > hide #!6 models > open /Users/xuchengtao/Downloads/cryosparc_P9_J32_007_volume_map.mrc Opened cryosparc_P9_J32_007_volume_map.mrc as #7, grid size 360,360,360, pixel 1.07, shown at level 0.0564, step 2, values float32 > color #7 #f4f6fcff models > volume #7 step 1 > volume #7 level 0.07916 > surface dust #7 size 10.7 > volume #7 level 0.11 > lighting full > volume #7 color #cecfd4 > lighting simple > volume #7 color #a3a4a7 > color #7 lightgrey > color #7 grey > volume #7 color #b6b6b6 > save /Users/xuchengtao/Desktop/image288.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: Z1FF000ENLL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 48 GB System Firmware Version: 13822.1.2 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.1 (24G231) Kernel Version: Darwin 24.6.0 Time since boot: 26 days, 11 hours, 19 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 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 HP 23f: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.1 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: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.19.1 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: 2.5.2 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: 1.45.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect new normal Unassigned