id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19516 Crash during window geometry change in QDockWidget::event() chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.0.1-arm64-arm-64bit ChimeraX Version: 1.11.dev202510240114 (2025-10-24 01:14:27 UTC) Description Last time you used ChimeraX it crashed. 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swapped_out=15.4M(1%) unallocated=1.0G(98%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 64K 4 ColorSync 704K 33 CoreAnimation 1440K 73 CoreGraphics 80K 5 CoreServices 688K 3 CoreUI image data 4528K 33 Foundation 48K 2 Kernel Alloc Once 32K 1 MALLOC 472.5M 113 MALLOC guard page 3264K 4 Mach message 64K 4 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 656K 41 Stack 232.4M 42 Stack Guard 56.0M 1 VM_ALLOCATE 232.3M 194 VM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated) __AUTH 5876K 658 __AUTH_CONST 90.1M 1051 __CTF 824 1 __DATA 38.0M 1147 __DATA_CONST 59.6M 1194 __DATA_DIRTY 8928K 910 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __INFO_FILTER 8 1 __LINKEDIT 625.4M 139 __OBJC_RO 78.1M 1 __OBJC_RW 2561K 1 __TEXT 1.5G 1200 __TEXT (graphics) 1568K 18 __TPRO_CONST 128K 2 dyld private memory 1200K 12 mapped file 311.8M 60 page table in kernel 1349K 1 shared memory 3696K 24 =========== ======= ======= TOTAL 3.8G 6983 TOTAL, minus reserved VM space 3.6G 6983 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""logWritingSignature"" : ""1a6d6853cf654d37fa8b6abcf5b5cd12d002ede3"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000506 }, { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000010 } ], ""experiments"" : [ ] } } Log: UCSF ChimeraX version: 1.11.dev202510240114 (2025-10-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 > structure/AF3-VDAC2-BAK1 8UKY-monomer and 7LK4.cxs"" Updated animation length to 0:05.00 [Repeated 1 time(s)]Log from Sun Dec 14 15:41:23 2025UCSF ChimeraX version: 1.11.dev202510240114 (2025-10-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 > structure/AF3-VDAC2-BAK1 complex with 8UKY-monomer.cxs"" Updated animation length to 0:05.00 [Repeated 1 time(s)]Log from Tue Dec 9 17:05:55 2025UCSF ChimeraX version: 1.11.dev202510240114 (2025-10-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/AF of > VDAC-BAK/Sessions for check/Monomer of VDAC2-BAK1.cxs"" Updated animation length to 0:05.00 Log from Sat Jul 12 21:05:13 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202501140846 (2025-01-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/haofeng/Desktop/Immunity > Paper/dimer_of_bak1_and_vdac2/fold_dimer_of_bak1_and_vdac2_model_0.cif"" Chain information for fold_dimer_of_bak1_and_vdac2_model_0.cif #1 --- Chain | Description A B | . C D | . Computing secondary structure > lighting soft > set bgColor white > select /A:1-211 1653 atoms, 1694 bonds, 211 residues, 1 model selected Drag select of 35 residues > select up 2100 atoms, 2154 bonds, 267 residues, 1 model selected > select up 3306 atoms, 3388 bonds, 422 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > select clear Drag select of 49 residues Drag select of 29 residues > select up 1670 atoms, 1698 bonds, 214 residues, 1 model selected > select up 4436 atoms, 4522 bonds, 588 residues, 1 model selected > ui tool show ""Color Actions"" > color sel hot pink > color sel dark salmon > color sel violet > color sel misty rose > color sel pink > color sel plum > color sel light pink > color sel hot pink > color sel light salmon > color sel dark salmon > color sel gold > color sel orange > color sel olive drab > color sel old lace > color sel light salmon > select clear > save ""/Users/haofeng/Desktop/Immunity Paper/VDAC2-BAK1 Projects/Dimer of > VDAC2-BAK1.cxs"" includeMaps true > save ""/Users/haofeng/Desktop/Immunity Paper/VDAC2-BAK1 Projects/Dimer of > VDAC2-BAK1.cxs"" Drag select of 321 residues > select up 2790 atoms, 2847 bonds, 363 residues, 1 model selected > select up 3871 atoms, 3955 bonds, 505 residues, 1 model selected > hide sel cartoons > lighting simple [Repeated 1 time(s)] > lighting soft > save ""/Users/haofeng/Desktop/Immunity Paper/VDAC2-BAK1 Projects/Monomer of > VDAC2-BAK1.cxs"" ——— End of log from Sat Jul 12 21:05:13 2025 ——— > view name session-start opened ChimeraX session > open ""/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 AF3 files/BAK > structure/8UKY-monomer.pdb"" format pdb No such file/path: /Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 AF3 files/BAK structure/8UKY-monomer.pdb > open ""/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/BAK > structure/8UKY-monomer.pdb"" 8UKY-monomer.pdb title: Crystal structure of bak In complex with inhibiting antibody 14G6 [more info...] Chain information for 8UKY-monomer.pdb #2 --- Chain | Description | UniProt A | 14G6 fab light chain | B | 14G6 fab heavy chain | D | BCL-2 homologous antagonist/killer | BAK_HUMAN 23-186 Non-standard residues in 8UKY-monomer.pdb #2 --- 144 — tris-hydroxymethyl-methyl-ammonium 1PE — pentaethylene glycol (PEG400) EDO — 1,2-ethanediol (ethylene glycol) PEG — di(hydroxyethyl)ether PGE — triethylene glycol SO4 — sulfate ion 4486 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > lighting soft > graphics silhouettes true > ui tool show Matchmaker > matchmaker #1 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 8UKY-monomer.pdb, chain D (#2) with fold_dimer_of_bak1_and_vdac2_model_0.cif, chain A (#1), sequence alignment score = 795.2 RMSD between 134 pruned atom pairs is 0.770 angstroms; (across all 153 pairs: 3.312) Drag select of 359 residues, 297 atoms, 256 bonds > select clear Drag select of 79 atoms, 140 residues, 1 pseudobonds, 61 bonds > select up 1077 atoms, 1066 bonds, 1 pseudobond, 149 residues, 2 models selected > select up 1101 atoms, 1093 bonds, 1 pseudobond, 149 residues, 2 models selected > select up 1866 atoms, 1886 bonds, 1 pseudobond, 250 residues, 2 models selected > select up 4213 atoms, 4306 bonds, 1 pseudobond, 553 residues, 2 models selected > select up 4254 atoms, 4347 bonds, 1 pseudobond, 560 residues, 2 models selected > select up 4512 atoms, 4610 bonds, 1 pseudobond, 590 residues, 2 models selected > select up 4711 atoms, 4666 bonds, 1 pseudobond, 733 residues, 2 models selected > hide sel atoms > select clear Drag select of 27 residues > select up 574 atoms, 588 bonds, 69 residues, 1 model selected > select up 1653 atoms, 1694 bonds, 211 residues, 1 model selected > select down 574 atoms, 588 bonds, 69 residues, 1 model selected > select up 1653 atoms, 1694 bonds, 211 residues, 1 model selected Drag select of 35 residues > select up 2585 atoms, 2647 bonds, 320 residues, 2 models selected > select up 2880 atoms, 2949 bonds, 364 residues, 2 models selected > select up 2906 atoms, 2955 bonds, 384 residues, 2 models selected > select up 12453 atoms, 12576 bonds, 1743 residues, 2 models selected > select down 2906 atoms, 2955 bonds, 384 residues, 2 models selected > ui tool show Matchmaker > matchmaker #1 to #2 & sel 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 8UKY-monomer.pdb, chain D (#2) with fold_dimer_of_bak1_and_vdac2_model_0.cif, chain A (#1), sequence alignment score = 795.2 RMSD between 134 pruned atom pairs is 0.770 angstroms; (across all 153 pairs: 3.312) > matchmaker #1 to #2 & sel 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 8UKY-monomer.pdb, chain D (#2) with fold_dimer_of_bak1_and_vdac2_model_0.cif, chain A (#1), sequence alignment score = 795.2 RMSD between 134 pruned atom pairs is 0.770 angstroms; (across all 153 pairs: 3.312) No reference and/or match structure/chain chosen > ui tool show Matchmaker > matchmaker #2/D to #1/B & sel pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with 8UKY- monomer.pdb, chain D (#2), sequence alignment score = 795.2 RMSD between 134 pruned atom pairs is 0.778 angstroms; (across all 153 pairs: 3.308) > select clear > save ""/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/BAK > structure/AF3-VDAC2-BAK1 complex with 8UKY-monomer.cxs"" includeMaps true Drag select of 134 residues > select up 1212 atoms, 1234 bonds, 164 residues, 1 model selected > select up 3259 atoms, 3336 bonds, 430 residues, 1 model selected > select up 3458 atoms, 3405 bonds, 560 residues, 1 model selected > select up 4711 atoms, 4666 bonds, 733 residues, 1 model selected > color sel orange > color sel magenta > select clear > lighting soft > save ""/Users/jason/Desktop/ Papers to MBP/VDAC2/VDAC2-BAK1 Structures/BAK > structure/AF3-VDAC2-BAK1 complex with 8UKY-monomer.cxs"" includeMaps true ——— End of log from Tue Dec 9 17:05:55 2025 ——— > view name session-start opened ChimeraX session > open ""/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 > structure/9CPH-Structural basis of BAK sequestration by MCL-1 and > consequences for apoptosis initiation.cif"" ""/Users/jason/Desktop/Postdoc > Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 structure/5W5Z-Crystal structure > of BAXP168G in complex with an activating antibody at high resolution > 3C10.pdb"" ""/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 > Structures/BAK1 structure/7LK4-dimer.pdb"" 9CPH-Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation.cif title: Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation [more info...] Chain information for 9CPH-Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation.cif #3 --- Chain | Description | UniProt A | Induced myeloid leukemia cell differentiation protein Mcl-1 | B | Bcl-2 homologous antagonist/killer | BAK_HUMAN 69-89 H | Synthetic antibody, Fab fragment, Heavy Chain | L | Synthetic antibody, Fab fragment, Light Chain | Non-standard residues in 9CPH-Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation.cif #3 --- GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose) 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at high resolution 3C10.pdb title: Crystal structure of BAXP168G In complex with an activating antibody At high resolution [more info...] Chain information for 5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at high resolution 3C10.pdb #4 --- Chain | Description | UniProt A | apoptosis regulator bax | BAX_HUMAN 32-192 H | 3C10 fab heavy chain | L | 3C10 fab light chain | Non-standard residues in 5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at high resolution 3C10.pdb #4 --- EDO — 1,2-ethanediol (ethylene glycol) MES — 2-(N-morpholino)-ethanesulfonic acid PCA — pyroglutamic acid PG4 — tetraethylene glycol PGE — triethylene glycol 20 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 4022 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. 7LK4-dimer.pdb title: Crystal structure of bak L100A In complex with activating antibody fragments [more info...] Chain information for 7LK4-dimer.pdb #5 --- Chain | Description | UniProt C G | 7D10 antibody VL fragment | D H | 7D10 antibody VH fragment | Q S | BCL-2 homologous antagonist/killer | BAK_HUMAN 23-186 Non-standard residues in 7LK4-dimer.pdb #5 --- MPD — (4S)-2-methyl-2,4-pentanediol 17 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5807 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #1 models > hide #!2 models > close #3 > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > close #5 > open ""/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 > structure/7LK4-monomerpdb.pdb"" 7LK4-monomerpdb.pdb title: Crystal structure of bak L100A In complex with activating antibody fragments [more info...] Chain information for 7LK4-monomerpdb.pdb #3 --- Chain | Description | UniProt G | 7D10 antibody VL fragment | H | 7D10 antibody VH fragment | Q | BCL-2 homologous antagonist/killer | BAK_HUMAN 23-186 Non-standard residues in 7LK4-monomerpdb.pdb #3 --- MPD — (4S)-2-methyl-2,4-pentanediol 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2820 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Drag select of 33 atoms, 28 bonds > select up 40 atoms, 28 bonds, 12 residues, 1 model selected > select up 2866 atoms, 2914 bonds, 385 residues, 1 model selected > select down 40 atoms, 28 bonds, 12 residues, 1 model selected > delete atoms sel > delete bonds sel > show #1 models Drag select of 19 residues > select up 533 atoms, 543 bonds, 64 residues, 1 model selected > select up 1653 atoms, 1694 bonds, 211 residues, 1 model selected Drag select of 38 residues > select up 2194 atoms, 2247 bonds, 281 residues, 2 models selected > select up 2368 atoms, 2425 bonds, 303 residues, 2 models selected > select up 2476 atoms, 2533 bonds, 320 residues, 2 models selected > select down 2368 atoms, 2425 bonds, 303 residues, 2 models selected Drag select of 63 residues > select up 3274 atoms, 3348 bonds, 418 residues, 3 models selected > select up 3545 atoms, 3627 bonds, 457 residues, 3 models selected > ui tool show Matchmaker > matchmaker #!4 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with 5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at high resolution 3C10.pdb, chain A (#4), sequence alignment score = 166.7 RMSD between 38 pruned atom pairs is 1.041 angstroms; (across all 107 pairs: 11.507) > matchmaker #!3 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with 7LK4-monomerpdb.pdb, chain Q (#3), sequence alignment score = 751.3 RMSD between 97 pruned atom pairs is 0.673 angstroms; (across all 137 pairs: 16.033) > show #!2 models > hide #!2 models > hide #!4 models > show #!2 models > show #!4 models > hide #!2 models > hide #!3 models > select clear > hide #!4 models > show #!4 models > select add #4 4198 atoms, 4181 bonds, 4 pseudobonds, 645 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.068996,0.17991,-0.98126,-45.986,-0.81343,0.5593,0.15974,38.114,0.57756,0.80921,0.10775,61.696 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.46832,-0.81861,0.33251,-57.887,0.76528,-0.5639,-0.31043,61.236,0.44163,0.10908,0.89054,55.945 > undo > ui mousemode right zoom > ui mousemode right translate > select clear > select add #1/B:29 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:162 17 atoms, 15 bonds, 2 residues, 2 models selected > select up 330 atoms, 337 bonds, 39 residues, 2 models selected > select up 1983 atoms, 2033 bonds, 253 residues, 2 models selected > select up 2014 atoms, 2064 bonds, 257 residues, 2 models selected > select up 2231 atoms, 2289 bonds, 283 residues, 2 models selected > select up 2264 atoms, 2321 bonds, 287 residues, 2 models selected > select up 2368 atoms, 2425 bonds, 303 residues, 2 models selected > select up 2476 atoms, 2533 bonds, 320 residues, 2 models selected > select up 2481 atoms, 2533 bonds, 325 residues, 2 models selected > select up 11940 atoms, 12091 bonds, 1655 residues, 2 models selected > select down 2481 atoms, 2533 bonds, 325 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!3 to #1/B & sel pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with 7LK4-monomerpdb.pdb, chain Q (#3), sequence alignment score = 751.3 RMSD between 97 pruned atom pairs is 0.673 angstroms; (across all 137 pairs: 16.033) > matchmaker #!3 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_dimer_of_bak1_and_vdac2_model_0.cif, chain B (#1) with 7LK4-monomerpdb.pdb, chain Q (#3), sequence alignment score = 751.3 RMSD between 97 pruned atom pairs is 0.673 angstroms; (across all 137 pairs: 16.033) > ui tool show Matchmaker > matchmaker #!4 to #2 & sel No 'to' model specified > hide #!4 models > show #!3 models > select clear > hide #1 models > show #!4 models Drag select of 150 residues, 2 pseudobonds > select up 1609 atoms, 1642 bonds, 2 pseudobonds, 205 residues, 4 models selected > select up 1892 atoms, 1933 bonds, 2 pseudobonds, 246 residues, 4 models selected > select up 1897 atoms, 1933 bonds, 2 pseudobonds, 251 residues, 4 models selected > select down 1892 atoms, 1933 bonds, 2 pseudobonds, 246 residues, 4 models selected > select up 1897 atoms, 1933 bonds, 2 pseudobonds, 251 residues, 4 models selected > select up 7024 atoms, 7067 bonds, 6 pseudobonds, 1018 residues, 4 models selected > select down 1897 atoms, 1933 bonds, 2 pseudobonds, 251 residues, 4 models selected > select clear Drag select of 82 residues > select up 1222 atoms, 1251 bonds, 148 residues, 2 models selected > select up 1784 atoms, 1825 bonds, 229 residues, 2 models selected > select down 1222 atoms, 1251 bonds, 148 residues, 2 models selected > select up 1784 atoms, 1825 bonds, 229 residues, 2 models selected > select up 1892 atoms, 1933 bonds, 246 residues, 2 models selected > select clear > hide #!3 models > show #!2 models Drag select of 131 residues, 2 pseudobonds > select up 1809 atoms, 1844 bonds, 2 pseudobonds, 227 residues, 3 models selected > select up 2050 atoms, 2094 bonds, 2 pseudobonds, 262 residues, 3 models selected > select up 2081 atoms, 2100 bonds, 2 pseudobonds, 287 residues, 3 models selected > select up 8909 atoms, 8847 bonds, 4 pseudobonds, 1378 residues, 3 models selected > select down 2081 atoms, 2100 bonds, 2 pseudobonds, 287 residues, 3 models selected > ui tool show Matchmaker > matchmaker #!4 to #2 & sel 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 8UKY-monomer.pdb, chain D (#2) with 5W5Z-Crystal structure of BAXP168G in complex with an activating antibody at high resolution 3C10.pdb, chain A (#4), sequence alignment score = 151.8 RMSD between 39 pruned atom pairs is 1.104 angstroms; (across all 81 pairs: 5.244) > show #1 models > show #!3 models > close #4 > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > hide #1 models > show #!3 models > hide #!3 models > show #1 models > select clear > show #!3 models > save ""/Users/jason/Desktop/Postdoc Work/VDAC2-BAK/VDAC2-BAK1 Structures/BAK1 > structure/AF3-VDAC2-BAK1 8UKY-monomer and 7LK4.cxs"" includeMaps true ——— End of log from Sun Dec 14 15:41:23 2025 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGP3KH/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 13822.1.2 OS Loader Version: 13822.1.2 Software: System Software Overview: System Version: macOS 26.0.1 (25A362) Kernel Version: Darwin 25.0.0 Time since boot: 10 days, 19 hours, 18 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.11.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.10.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.19 ChimeraX-AtomicLibrary: 14.2.1 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: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.dev202510240114 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.2 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.2.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.2 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: 1.48.4 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.1 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 click: 8.3.0 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.11.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.17 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.60.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.7 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.5 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 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: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.3 pydantic-settings: 2.11.0 pydantic_core: 2.41.4 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 8.4.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.1.1 python-multipart: 0.0.20 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals-py: 3.1.0 rpds-py: 0.28.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 sniffio: 1.3.1 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.0.2 stack-data: 0.6.3 starlette: 0.48.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.2 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.2 urllib3: 2.5.0 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX