id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10037 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""rollouts"" : [ { ""rolloutId"" : ""62c74108bcb0435c2153f963"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""651df1e7be905e686a05edc8"" }, ""deploymentId"" : 240000367 }, { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/hld575/Documents/PHD_LAB/230829_AlphaPulldownPEPTIDES/230911.cxs > format session opened ChimeraX session > save > /Users/hld575/Documents/PHD_LAB/230829_AlphaPulldownPEPTIDES/231020_CMGPeptidesRrm3Pif1.cxs > close session > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_1.pdb Chain information for ranked_1.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_2.pdb Chain information for ranked_2.pdb #3 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_3.pdb Chain information for ranked_3.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/ranked_4.pdb Chain information for ranked_4.pdb #5 --- Chain | Description B | No description available C | No description available D | No description available > select add #1 2137 atoms, 2164 bonds, 276 residues, 1 model selected > select add #2 4274 atoms, 4328 bonds, 552 residues, 2 models selected > select add #3 6411 atoms, 6492 bonds, 828 residues, 3 models selected > select add #4 8548 atoms, 8656 bonds, 1104 residues, 4 models selected > select add #5 10685 atoms, 10820 bonds, 1380 residues, 5 models selected > ui tool show Matchmaker > matchmaker #2-5 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 ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2), sequence alignment score = 637.4 RMSD between 108 pruned atom pairs is 0.460 angstroms; (across all 130 pairs: 4.456) Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3), sequence alignment score = 648.2 RMSD between 98 pruned atom pairs is 0.521 angstroms; (across all 130 pairs: 2.418) Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4), sequence alignment score = 648.2 RMSD between 95 pruned atom pairs is 0.382 angstroms; (across all 130 pairs: 22.713) Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5), sequence alignment score = 637.4 RMSD between 101 pruned atom pairs is 0.312 angstroms; (across all 130 pairs: 20.966) > select clear > set bgColor white > select #1/C 995 atoms, 1007 bonds, 130 residues, 1 model selected > select #*/C 4975 atoms, 5035 bonds, 650 residues, 5 models selected > color sel forest green > select #*/D 4880 atoms, 4955 bonds, 630 residues, 5 models selected > color sel cornflower blue > select #*/B 830 atoms, 830 bonds, 100 residues, 5 models selected > color sel red > select clear > select #*/C,D 9855 atoms, 9990 bonds, 1280 residues, 5 models selected > show sel surfaces > transperancy 20 Unknown command: transperancy 20 > transparency 20 > transparency 30 > hide #!2 models > show #!2 models > select clear > graphics silhouettes true > lighting flat > lighting soft > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > interfaces #!1 & ~solvent 2 buried areas: C D 2572, C B 306 > show sel atoms > sequence chain #1/B Alignment identifier is 1/B > select clear > sequence chain #1/C Alignment identifier is 1/C > select #1/C 995 atoms, 1007 bonds, 130 residues, 1 model selected > hide sel surfaces > show sel surfaces > select clear > show #!2 models > hide #!1 models > interfaces #!2 & ~solvent 1 buried areas: C D 2688 > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!5 models > hide #!4 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > sequence chain #5/C Alignment identifier is 5/C > select #5/C:1-2 14 atoms, 13 bonds, 2 residues, 1 model selected > select #5/C 995 atoms, 1007 bonds, 130 residues, 1 model selected > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > interfaces #!1 & ~solvent 2 buried areas: C D 2572, C B 306 > sequence chain #1/C Alignment identifier is 1/C > view sel > select clear > save > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/Superposition_1.cxs > close session > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899 > /ranked_0.pdb"" Chain information for ranked_0.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899 > /ranked_1.pdb"" Chain information for ranked_1.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899 > /ranked_2.pdb"" Chain information for ranked_2.pdb #3 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899 > /ranked_3.pdb"" Chain information for ranked_3.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899 > /ranked_4.pdb"" Chain information for ranked_4.pdb #5 --- Chain | Description B | No description available C | No description available D | No description available > graphics silhouettes true > lighting soft > set bgColor white > ui tool show Matchmaker > matchmaker #2-5 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 ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2), sequence alignment score = 644.6 RMSD between 111 pruned atom pairs is 0.427 angstroms; (across all 130 pairs: 4.915) Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3), sequence alignment score = 637.4 RMSD between 110 pruned atom pairs is 0.482 angstroms; (across all 130 pairs: 3.326) Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4), sequence alignment score = 645.2 RMSD between 99 pruned atom pairs is 0.592 angstroms; (across all 130 pairs: 3.344) Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5), sequence alignment score = 648.2 RMSD between 103 pruned atom pairs is 0.520 angstroms; (across all 130 pairs: 4.495) > select #*/B 1550 atoms, 1555 bonds, 200 residues, 5 models selected > color sel red > select #*/C 4975 atoms, 5035 bonds, 650 residues, 5 models selected > color sel forest green > select #*/D 4880 atoms, 4955 bonds, 630 residues, 5 models selected > color sel cornflower blue > select clear > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > interfaces #1 & ~solvent 2 buried areas: C D 2522, D B 395 > sequence chain #1/B Alignment identifier is 1/B > sequence chain #1/C Alignment identifier is 1/C > sequence chain #1/D Alignment identifier is 1/D > select add #1 2281 atoms, 2309 bonds, 296 residues, 1 model selected > show sel cartoons > select clear > show sel atoms > select clear Drag select of 1 atoms, 3 residues > select clear > show #2 models > hide #2 models > show #3 models > hide #1 models Drag select of 13 residues > select clear > hide #3 models > show #3 models > show #1 models > hide #3 models > show #3 models > hide #1 models > show #1 models > hide #1 models > hide #3 models > show #2 models > sequence chain #1/B,D Chains must have same sequence > interfaces #2 & ~solvent 2 buried areas: C D 2532, D B 402 > interfaces #2 & ~solvent 2 buried areas: C D 2532, D B 402 > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/D Alignment identifier is 2/D > hide #2 models > show #3 models > interfaces #3 & ~solvent 2 buried areas: C D 2579, C B 571 > select clear > interfaces #3 & ~solvent 2 buried areas: C D 2579, C B 571 > sequence chain #3/D Alignment identifier is 3/D > sequence chain #3/C Alignment identifier is 3/C > sequence chain #3/B Alignment identifier is 3/B > hide #3 models > show #4 models > show #3 models > hide #3 models > interfaces #4 & ~solvent 3 buried areas: C D 2656, D B 401, C B 304 > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/c Alignment identifier is 4/C > sequence chain #4/d Alignment identifier is 4/D > hide #4 models > show #5 models > interfaces #5 & ~solvent 3 buried areas: C D 2616, C B 447, D B 305 > sequence chain #5/b Alignment identifier is 5/B > sequence chain #5/c Alignment identifier is 5/C > sequence chain #5/d Alignment identifier is 5/D > save > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/2_Q9UNS1_958-997_and_P04908_and_P06899 > /Superposition_2.cxs"" > close session > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /ranked_0.pdb"" Chain information for ranked_0.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /ranked_2.pdb"" Chain information for ranked_2.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /ranked_3.pdb"" Chain information for ranked_3.pdb #3 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /ranked_4.pdb"" Chain information for ranked_4.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /ranked_1.pdb"" Chain information for ranked_1.pdb #5 --- Chain | Description B | No description available C | No description available D | No description available > graphics silhouettes true > lighting soft > set bgColor white > ui tool show Matchmaker > matchmaker #2-5 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 ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#2), sequence alignment score = 636.8 RMSD between 97 pruned atom pairs is 0.546 angstroms; (across all 130 pairs: 25.033) Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#3), sequence alignment score = 638.6 RMSD between 88 pruned atom pairs is 0.349 angstroms; (across all 130 pairs: 6.007) Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#4), sequence alignment score = 644.6 RMSD between 92 pruned atom pairs is 0.421 angstroms; (across all 130 pairs: 5.996) Matchmaker ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#5), sequence alignment score = 633.8 RMSD between 96 pruned atom pairs is 0.419 angstroms; (across all 130 pairs: 10.208) > select #*/B 1600 atoms, 1615 bonds, 190 residues, 5 models selected > color sel orange red > color sel red > select #*/C 4975 atoms, 5035 bonds, 650 residues, 5 models selected > color sel forest green > select #*/D 4880 atoms, 4955 bonds, 630 residues, 5 models selected > color sel cornflower blue > select clear > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #3 models > show #3 models > interfaces ~solvent 82 buried areas: #4/C #3/C 5562, #3/C #5/C 5105, #1/D #2/D 5011, #4/D #1/D 4972, #4/D #3/D 4877, #4/C #1/C 4869, #4/D #2/D 4869, #3/C #1/C 4855, #3/D #2/D 4770, #4/C #5/C 4710, #1/C #5/C 4691, #1/C #2/C 4664, #3/C #2/C 4602, #5/C #2/C 4563, #4/C #2/C 4377, #3/D #1/D 4336, #5/D #2/D 3843, #1/D #5/D 3835, #3/D #5/D 3830, #4/D #5/D 3813, #3/C #3/D 2687, #3/C #1/D 2679, #3/C #5/D 2666, #3/C #4/D 2662, #2/C #5/D 2660, #3/C #2/D 2655, #2/C #3/D 2649, #2/C #1/D 2640, #4/C #3/D 2639, #4/C #1/D 2634, #5/C #1/D 2627, #5/C #3/D 2627, #2/C #4/D 2625, #4/C #4/D 2622, #2/C #2/D 2622, #5/C #4/D 2615, #4/C #2/D 2613, #4/C #5/D 2601, #5/C #2/D 2601, #5/C #5/D 2595, #1/C #3/D 2570, #1/C #1/D 2568, #1/C #4/D 2559, #1/C #2/D 2550, #1/C #5/D 2540, #4/B #5/B 1116, #4/C #4/B 752, #4/B #3/B 734, #1/C #4/B 721, #3/C #4/B 717, #5/C #4/B 709, #2/C #4/B 689, #3/B #2/B 687, #4/C #5/B 682, #3/B #5/B 667, #3/C #5/B 661, #1/C #5/B 652, #5/C #5/B 647, #2/C #5/B 645, #4/D #2/B 599, #1/D #2/B 577, #2/D #2/B 565, #3/D #2/B 530, #4/C #1/B 492, #4/C #3/B 485, #5/C #1/B 477, #2/C #3/B 474, #5/D #2/B 471, #1/C #1/B 461, #1/C #3/B 451, #5/C #3/B 446, #2/C #1/B 445, #3/C #3/B 445, #3/D #4/B 422, #3/C #1/B 409, #4/D #4/B 360, #4/D #3/B 356, #1/D #3/B 335, #3/D #3/B 327, #2/D #3/B 320, #1/B #2/B 320, #1/D #4/B 308 > hide #5 models > hide #4 models > hide #3 models > hide #2 models > sequence chain #1/B Alignment identifier is 1/B > sequence chain #1/C Alignment identifier is 1/C > sequence chain #1/D Alignment identifier is 1/D > sequence chain #12D Missing or invalid ""chains"" argument: invalid chains specifier > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > sequence chain #2/D Alignment identifier is 2/D > hide #1 models > show #2 models > hide #2 models > sequence chain #3/* Chains must have same sequence > sequence chain #3/B Alignment identifier is 3/B > sequence chain #3/C Alignment identifier is 3/C > sequence chain #3/D Alignment identifier is 3/D > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/C Alignment identifier is 4/C > sequence chain #4/D Alignment identifier is 4/D > show #4 models > hide #4 models > show #5 models > sequence chain #5/B Alignment identifier is 5/B > sequence chain #5/C Alignment identifier is 5/C > sequence chain #5/D Alignment identifier is 5/D > save > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /Superposition_3.cxs"" > close session > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899 > /ranked_0.pdb"" Chain information for ranked_0.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899 > /ranked_1.pdb"" Chain information for ranked_1.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899 > /ranked_2.pdb"" Chain information for ranked_2.pdb #3 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899 > /ranked_3.pdb"" Chain information for ranked_3.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/4_Q9UNS1_634-711_and_P04908_and_P06899 > /ranked_4.pdb"" Chain information for ranked_4.pdb #5 --- Chain | Description B | No description available C | No description available D | No description available > set bgColor white > graphics silhouettes true > lighting soft > ui tool show Matchmaker > matchmaker #2-5 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 ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2), sequence alignment score = 645.2 RMSD between 101 pruned atom pairs is 0.688 angstroms; (across all 130 pairs: 2.629) Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3), sequence alignment score = 645.2 RMSD between 99 pruned atom pairs is 0.414 angstroms; (across all 130 pairs: 4.625) Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4), sequence alignment score = 641.6 RMSD between 96 pruned atom pairs is 0.550 angstroms; (across all 130 pairs: 3.664) Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5), sequence alignment score = 645.2 RMSD between 96 pruned atom pairs is 0.599 angstroms; (across all 130 pairs: 3.471) > select #*/B 3200 atoms, 3240 bonds, 390 residues, 5 models selected > color sel red > select #*/C 4975 atoms, 5035 bonds, 650 residues, 5 models selected > color sel forest green > select #*/D 4880 atoms, 4955 bonds, 630 residues, 5 models selected > color sel cornflower blue > select clear > hide #2 models > hide #3 models > hide #4 models > hide #5 models > show #5 models > show #4 models > show #3 models > show #2 models > interfaces ~solvent 95 buried areas: #2/C #4/C 5693, #3/C #4/C 5654, #5/C #4/C 5603, #3/C #2/C 5511, #1/C #2/C 5438, #2/C #5/C 5402, #3/C #5/C 5330, #2/D #5/D 5251, #5/D #4/D 5195, #1/C #5/C 5134, #1/C #4/C 5031, #1/C #3/C 4947, #2/D #4/D 4871, #1/D #4/D 4539, #3/D #2/D 4362, #1/D #3/D 4329, #1/D #5/D 4292, #1/D #2/D 4271, #3/D #4/D 4228, #3/D #5/D 4158, #5/C #4/D 2581, #3/C #4/D 2576, #5/C #2/D 2575, #5/C #3/D 2575, #3/C #3/D 2569, #3/C #2/D 2568, #5/C #5/D 2559, #5/C #1/D 2556, #3/C #5/D 2555, #3/C #1/D 2547, #2/C #4/D 2545, #2/C #2/D 2539, #2/C #3/D 2538, #4/C #4/D 2537, #4/C #2/D 2534, #1/C #4/D 2532, #4/C #3/D 2529, #1/C #2/D 2528, #1/C #3/D 2524, #2/C #5/D 2524, #2/C #1/D 2523, #4/C #5/D 2520, #4/C #1/D 2515, #1/C #5/D 2515, #1/C #1/D 2513, #5/B #4/B 2251, #2/B #4/B 2236, #2/B #5/B 2213, #1/B #3/B 2176, #3/B #2/B 1661, #1/B #5/B 1373, #1/B #4/B 1360, #3/B #4/B 1306, #1/B #2/B 1145, #2/D #4/B 804, #3/B #5/B 757, #4/D #4/B 722, #5/D #4/B 717, #3/D #4/B 656, #5/D #3/B 639, #4/D #3/B 620, #2/D #3/B 609, #1/D #4/B 593, #3/C #5/B 562, #5/C #5/B 561, #2/C #5/B 545, #4/C #5/B 539, #3/D #3/B 530, #1/C #5/B 515, #5/C #1/B 506, #1/D #3/B 504, #2/D #5/B 488, #3/D #5/B 483, #5/C #3/B 480, #1/C #1/B 480, #2/C #1/B 477, #4/D #5/B 474, #5/D #5/B 471, #1/D #5/B 465, #3/C #1/B 458, #4/C #1/B 450, #2/C #3/B 433, #1/C #3/B 431, #4/C #3/B 428, #2/D #1/B 416, #3/C #3/B 413, #5/D #1/B 410, #4/D #1/B 397, #1/D #1/B 336, #3/D #1/B 334, #5/C #4/B 332, #4/C #4/B 325, #3/C #4/B 324, #1/C #4/B 314, #2/C #4/B 310 > hide #2 models > hide #3 models > hide #4 models > hide #5 models > sequence chain #1/B Alignment identifier is 1/B > interfaces select & #1 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > interfaces #1 & ~solvent 3 buried areas: C D 2513, C B 480, D B 336 > sequence chain #1/C Alignment identifier is 1/C > sequence chain #1/D Alignment identifier is 1/D > hide #1 models > show #2 models > interfaces #2 & ~solvent 1 buried areas: C D 2539 > hide #2 models > show #3 models > interfaces #3 & ~solvent 3 buried areas: C D 2569, D B 530, C B 413 > sequence chain #3/b Alignment identifier is 3/B > sequence chain #3/c Alignment identifier is 3/C > sequence chain #3/d Alignment identifier is 3/D > hide #3 models > show #4 models > interfaces #4 & ~solvent 3 buried areas: C D 2537, D B 722, C B 325 > sequence chain #3/d Alignment identifier is 3/D > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/c Alignment identifier is 4/C > sequence chain #4/d Alignment identifier is 4/D > hide #4 models > show #5 models > interfaces #5 & ~solvent 3 buried areas: C D 2559, C B 561, D B 471 > sequence chain #5/b Alignment identifier is 5/B > sequence chain #5/c Alignment identifier is 5/C > sequence chain #5/d Alignment identifier is 5/D > close session > open > ""/Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/3_Q9UNS1_654-691_and_P04908_and_P06899 > /Superposition_3.cxs"" format session opened ChimeraX session > show #1 models > interfaces select & #1,5 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > interfaces #1,5 & ~solvent 10 buried areas: #1/C #5/C 4691, #1/D #5/D 3835, #5/C #1/D 2627, #5/C #5/D 2595, #1/C #1/D 2568, #1/C #5/D 2540, #1/C #5/B 652, #5/C #5/B 647, #5/C #1/B 477, #1/C #1/B 461 > hide #5 models > interfaces #1 & ~solvent 2 buried areas: C D 2568, C B 461 > sequence chain #1/B Alignment identifier is 1/B > sequence chain #1/C Alignment identifier is 1/C > sequence chain #1/D Alignment identifier is 1/D > hide #1 models > show #2 models > interfaces #2 & ~solvent 2 buried areas: C D 2622, D B 565 > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > sequence chain #2/D Alignment identifier is 2/D > hide #2 models > show #3 models > interfaces #3 & ~solvent 3 buried areas: C D 2687, C B 445, D B 327 > sequence chain #3/B Alignment identifier is 3/B > sequence chain #3/C Alignment identifier is 3/C > sequence chain #3/D Alignment identifier is 3/D > hide #3 models > show #4 models > interfaces #4 & ~solvent 3 buried areas: C D 2622, C B 752, D B 360 > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/C Alignment identifier is 4/C > sequence chain #4/D Alignment identifier is 4/D > show #5 models > hide #4 models > interfaces #5 & ~solvent 2 buried areas: C D 2595, C B 647 > sequence chain #5/B Alignment identifier is 5/B > sequence chain #5/C Alignment identifier is 5/C > sequence chain #5/D Alignment identifier is 5/D > close session > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_1.pdb Chain information for ranked_1.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_2.pdb Chain information for ranked_2.pdb #3 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_3.pdb Chain information for ranked_3.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/ranked_4.pdb Chain information for ranked_4.pdb #5 --- Chain | Description B | No description available C | No description available D | No description available > set bgColor white > graphics silhouettes true > lighting soft > ui tool show Matchmaker > matchmaker #2-5 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 ranked_0.pdb, chain C (#1) with ranked_1.pdb, chain C (#2), sequence alignment score = 637.4 RMSD between 98 pruned atom pairs is 0.443 angstroms; (across all 130 pairs: 23.512) Matchmaker ranked_0.pdb, chain C (#1) with ranked_2.pdb, chain C (#3), sequence alignment score = 645.2 RMSD between 93 pruned atom pairs is 0.320 angstroms; (across all 130 pairs: 20.678) Matchmaker ranked_0.pdb, chain C (#1) with ranked_3.pdb, chain C (#4), sequence alignment score = 644.6 RMSD between 108 pruned atom pairs is 0.557 angstroms; (across all 130 pairs: 3.918) Matchmaker ranked_0.pdb, chain C (#1) with ranked_4.pdb, chain C (#5), sequence alignment score = 648.2 RMSD between 92 pruned atom pairs is 0.406 angstroms; (across all 130 pairs: 23.947) > select #*/B 2375 atoms, 2400 bonds, 300 residues, 5 models selected > color sel red > select #*/C 4975 atoms, 5035 bonds, 650 residues, 5 models selected > color sel forest green > select #*/D 4880 atoms, 4955 bonds, 630 residues, 5 models selected > color sel cornflower blue > select clear > hide #5 models > hide #4 models > hide #3 models > hide #2 models > interfaces #1 & ~solvent 1 buried areas: C D 2533 > show #2 models > hide #1 models > interfaces #2 & ~solvent 2 buried areas: C D 2585, D B 460 > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > sequence chain #2/D Alignment identifier is 2/D > hide #2 models > show #3 models > interfaces #3 & ~solvent 2 buried areas: C D 2576, D B 328 > sequence chain #3/B Alignment identifier is 3/B > sequence chain #3/D Alignment identifier is 3/D > hide #3 models > show #4 models > interfaces #4 & ~solvent 2 buried areas: C D 2640, C B 382 > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/C Alignment identifier is 4/C > hide #4 models > show #5 models > interfaces #5 & ~solvent 3 buried areas: C D 2600, C B 677, D B 387 > sequence chain #5/B Alignment identifier is 5/B > sequence chain #5/C Alignment identifier is 5/C > sequence chain #5/D Alignment identifier is 5/D > hide #5 models > show #2 models > interfaces #2 & ~solvent 2 buried areas: C D 2585, D B 460 > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/D Alignment identifier is 2/D > save > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/5_Q9UNS1_1148-1207_and_P04908_and_P06899/Superposition_5.cxs > close session > open > /Users/hld575/Documents/OtherProjects/Collaborations/Thorkell/TIM_Histones/1_Q9UNS1_1168-1187_and_P04908_and_P06899/Superposition_1.cxs > format session opened ChimeraX session > interfaces #!1 & ~solvent 2 buried areas: C D 2572, C B 306 > show #!2 models > hide #!1 models > interfaces #!2 & ~solvent 1 buried areas: C D 2688 > hide #!2 models > show #!3 models > interfaces #!3 & ~solvent 1 buried areas: C D 2675 > hide #!3 models > show #!4 models > interfaces #!4 & ~solvent 2 buried areas: C D 2612, D B 376 > show #!1 models > hide #!4 models > hide #!1 models > show #!5 models > interfaces #!5 & ~solvent 2 buried areas: C D 2590, C B 360 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11C0001ADK/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5.2 (22G91) Kernel Version: Darwin 22.6.0 Time since boot: 23 days, 21 hours, 8 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX