id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17032 Mac multi-display crash chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. 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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""deploymentId"" : 240000460 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000012 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure_1B_1C_globalview.cxc > graphics silhouettes true > lighting soft > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_90195.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_90195.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_90196.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_90196.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_90196.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_90196.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_90197.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_90197.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available > mmaker #2/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_90195.pdb, chain B (#2), sequence alignment score = 1113.2 RMSD between 212 pruned atom pairs is 0.104 angstroms; (across all 212 pairs: 0.104) > mmaker #3/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_90196.pdb, chain B (#3), sequence alignment score = 1116.2 RMSD between 212 pruned atom pairs is 0.317 angstroms; (across all 212 pairs: 0.317) > mmaker #4/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_90196.pdb, chain B (#4), sequence alignment score = 1116.2 RMSD between 212 pruned atom pairs is 0.159 angstroms; (across all 212 pairs: 0.159) > mmaker #5/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_90197.pdb, chain B (#5), sequence alignment score = 1116.2 RMSD between 212 pruned atom pairs is 0.220 angstroms; (across all 212 pairs: 0.220) > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_74781.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_74781.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_74777.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_74777.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_74779.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_74779.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_74780.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_74780.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_74778.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_74778.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available > mmaker #6/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_74781.pdb, chain B (#6), sequence alignment score = 685.8 RMSD between 137 pruned atom pairs is 0.745 angstroms; (across all 206 pairs: 3.019) > mmaker #7/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_74777.pdb, chain B (#7), sequence alignment score = 690.6 RMSD between 139 pruned atom pairs is 0.790 angstroms; (across all 206 pairs: 2.958) > mmaker #8/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_74779.pdb, chain B (#8), sequence alignment score = 688.6 RMSD between 141 pruned atom pairs is 0.820 angstroms; (across all 206 pairs: 2.920) > mmaker #9/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_74780.pdb, chain B (#9), sequence alignment score = 685.6 RMSD between 141 pruned atom pairs is 0.771 angstroms; (across all 206 pairs: 2.932) > mmaker #10/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_74778.pdb, chain B (#10), sequence alignment score = 685.8 RMSD between 143 pruned atom pairs is 0.781 angstroms; (across all 206 pairs: 2.817) > select #1-5/A,B 16470 atoms, 16735 bonds, 2060 residues, 5 models selected > color sel light grey target acs > hide sel target a > show sel target c > select clear > select #1-5/C 1185 atoms, 1195 bonds, 150 residues, 5 models selected > hide sel target a > show sel target c > rainbow sel > select #5-10/A,B 19789 atoms, 20057 bonds, 2472 residues, 6 models selected > color sel wheat target acs > hide sel target a > show sel target c > select clear > select #6-10/C 1175 atoms, 1200 bonds, 145 residues, 5 models selected > rainbow sel > hide sel target a > show sel target c executed Figure_1B_1C_globalview.cxc > set bgColor white > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > ui tool show ""Side View"" > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure1A_global1.png.pdb > hide #4 models > hide #3 models > hide #2 models > hide #1 models > show #5 models > show #4 models > show #3 models > show #2 models > show #1 models > delete all > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure_1B_1C_globalview.cxc > set bgColor white > graphics silhouettes true > lighting soft > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_90195.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_90195.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_90196.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_90196.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_90196.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_90196.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/models/scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_90197.pdb Chain information for scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_90197.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available > mmaker #2/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_90195.pdb, chain B (#2), sequence alignment score = 1113.2 RMSD between 212 pruned atom pairs is 0.104 angstroms; (across all 212 pairs: 0.104) > mmaker #3/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_90196.pdb, chain B (#3), sequence alignment score = 1116.2 RMSD between 212 pruned atom pairs is 0.317 angstroms; (across all 212 pairs: 0.317) > mmaker #4/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_90196.pdb, chain B (#4), sequence alignment score = 1116.2 RMSD between 212 pruned atom pairs is 0.159 angstroms; (across all 212 pairs: 0.159) > mmaker #5/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_90197.pdb, chain B (#5), sequence alignment score = 1116.2 RMSD between 212 pruned atom pairs is 0.220 angstroms; (across all 212 pairs: 0.220) > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_74781.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_74781.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_74777.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_74777.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_74779.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_74779.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_74780.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_74780.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/models/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_74778.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_74778.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available > mmaker #6/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_74781.pdb, chain B (#6), sequence alignment score = 685.8 RMSD between 137 pruned atom pairs is 0.745 angstroms; (across all 206 pairs: 3.019) > mmaker #7/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_74777.pdb, chain B (#7), sequence alignment score = 690.6 RMSD between 139 pruned atom pairs is 0.790 angstroms; (across all 206 pairs: 2.958) > mmaker #8/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_74779.pdb, chain B (#8), sequence alignment score = 688.6 RMSD between 141 pruned atom pairs is 0.820 angstroms; (across all 206 pairs: 2.920) > mmaker #9/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_74780.pdb, chain B (#9), sequence alignment score = 685.6 RMSD between 141 pruned atom pairs is 0.771 angstroms; (across all 206 pairs: 2.932) > mmaker #10/A,B to #1/A,B Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_74778.pdb, chain B (#10), sequence alignment score = 685.8 RMSD between 143 pruned atom pairs is 0.781 angstroms; (across all 206 pairs: 2.817) > select #1-5/A,B 16470 atoms, 16735 bonds, 2060 residues, 5 models selected > color sel light grey target acs > hide sel target a > show sel target c > select clear > select #1-5/C 1185 atoms, 1195 bonds, 150 residues, 5 models selected > hide sel target a > show sel target c > rainbow sel > select #6-10/A,B 16495 atoms, 16710 bonds, 2060 residues, 5 models selected > color sel wheat target acs > hide sel target a > show sel target c > select clear > select #6-10/C 1175 atoms, 1200 bonds, 145 residues, 5 models selected > rainbow sel > hide sel target a > show sel target c executed Figure_1B_1C_globalview.cxc > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #2 models > show #2 models > hide #3 models > show #3 models > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure_1A_global1.png > width 1152 height 720 supersample 3 > hide #1 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > show #6 models > show #7 models > show #8 models > show #9 models > show #10 models > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure_1A_global2.png > width 1152 height 720 supersample 3 > select clear > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure_1A_global2.png > width 1152 height 720 supersample 3 > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #6 models > show #1 models > select #1/C 237 atoms, 239 bonds, 30 residues, 1 model selected > color sel orange > style sel ball Changed 237 atom styles > show sel atoms > color sel byhetero > select #1/C 237 atoms, 239 bonds, 30 residues, 1 model selected > hide sel atoms > select #1/C:23 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/C:@N,CA,C,O Expected an objects specifier or a keyword > select #1/C@N,CA,C,O 120 atoms, 119 bonds, 30 residues, 1 model selected > show sel atoms > hide sel cartoons > hide sel atoms > select #1/C 237 atoms, 239 bonds, 30 residues, 1 model selected > show sel cartoons > show #6 models > show #7 models > hide #7 models > show #8 models > hide #8 models > show #9 models > hide #9 models > show #10 models > hide #10 models > hide #6 models > select #1/C:25-30 44 atoms, 43 bonds, 6 residues, 1 model selected > hide sel cartoons > select zone #1/C:23 4.0 #1/A,B Selected 3 atoms > select zone #1/C:23 4.0 #1/A,B residues true Selected 27 atoms > show sel atoms > style sel ball Changed 27 atom styles > select #1/A,B 3294 atoms, 3347 bonds, 412 residues, 1 model selected Alignment identifier is 1/A Alignment identifier is 1/B > select #1/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:1-3 19 atoms, 18 bonds, 3 residues, 1 model selected > renumber #1/B start 1101 212 residues renumbered > renumber #1-5/B start 1101 848 residues renumbered > hide #1 models > show #6 models > select #6/A,B 3299 atoms, 3342 bonds, 412 residues, 1 model selected Alignment identifier is 6/A Alignment identifier is 6/B > renumber #6-10/B start 1101 1060 residues renumbered > select #6/C 235 atoms, 240 bonds, 29 residues, 1 model selected Alignment identifier is 6/C > select zone #1/C:23 4.0 #1/A,B residues true Selected 27 atoms > hide #6 models > show #1 models > label sel text ""{0.name} {0.number}{0.insertion_code}"" > graphics silhouettes false > graphics silhouettes true > lighting soft > ui mousemode right ""move label"" > ui mousemode right label > label #1/C:23 > ui mousemode right ""move label"" > select #1/C:23 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel orange target l > show #2 models > hide #2 models > show #2 models > hide #2 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #5 models > ui mousemode right translate > select zone #1/C:23 4.5 #1/A,B residues true Selected 27 atoms > show sel atoms > select clear > save > ""/Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure > 1B_2I23_around.png"" width 1152 height 720 supersample 3 > hide #!1 models > show #5 models > hide #5 models > show #6 models > renumber #6-10/C start 449 145 residues renumbered > select #6.C:453,465 Expected an objects specifier or a keyword > select #6/C:453,465 28 atoms, 30 bonds, 2 residues, 1 model selected > show sel atoms > color #1/C lawn green > color #1/C lawn green target ac > color #6/C lawn green target ac > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select zone #6/C:453 Missing or invalid ""range"" argument: Expected a number > select zone #6/C: Missing or invalid ""near"" argument: only initial part ""#6/C"" of atom specifier valid > select zone #6/C:453 4.0 #6/A,B residues true Selected 57 atoms > show sel atoms > style sel ball Changed 57 atom styles > label sel text ""{0.name} {0.number}{0.insertion_code}"" > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!6 models > show #!6 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #6:C:453 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel atoms > style sel ball Changed 14 atom styles > select #6:C1271,1288 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #6/A,B:1271,1288 20 atoms, 18 bonds, 2 residues, 1 model selected > hide sel atoms > ~label sel residues > select #6/C 235 atoms, 240 bonds, 29 residues, 1 model selected > show sel cartoons > ui mousemode right ""move label"" > select #6/C:453 14 atoms, 15 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel forest green target l > select clear > save > ""/Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure > 1B_3_W453_around.png"" width 1152 height 720 supersample 3 > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure1_BC.cxs > show #7 models > show #8 models > show #9 models > show #10 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #6 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_001_alphafold2_multimer_v3_model_2_seed_74781.json > color bfactor #6 palette alphafold 3534 atoms, 441 residues, atom bfactor range 30.4 to 98.4 > hide #7 models > hide #8 models > hide #9 models > hide #10 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #7 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_002_alphafold2_multimer_v3_model_2_seed_74777.json > color bfactor #7 palette alphafold 3534 atoms, 441 residues, atom bfactor range 29.4 to 98.4 > show #7 models > show #8 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #8 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_003_alphafold2_multimer_v3_model_2_seed_74779.json > color bfactor #8 palette alphafold 3534 atoms, 441 residues, atom bfactor range 28.1 to 98.4 > show #9 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #9 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_004_alphafold2_multimer_v3_model_2_seed_74780.json > color bfactor #9 palette alphafold 3534 atoms, 441 residues, atom bfactor range 28.9 to 98.4 > show #10 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #10 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_005_alphafold2_multimer_v3_model_2_seed_74778.json > color bfactor #10 palette alphafold 3534 atoms, 441 residues, atom bfactor range 28.9 to 98.4 > color #6-10/A,B wheat target c > color #6-10/A,B wheat target ca > ui mousemode right translate > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hRad50_Trf2_IDDR_pLDDT_IDDR.png > width 1152 height 720 supersample 3 > select #6-10:453 70 atoms, 75 bonds, 5 residues, 5 models selected > show sel atoms > select #6-10:449-453 215 atoms, 225 bonds, 25 residues, 5 models selected > select #6-10:449-452 145 atoms, 145 bonds, 20 residues, 5 models selected > hide sel cartoons > ui mousemode right ""move label"" > save > ""/Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure > 1B_W453_around_pLDDT.png"" width 1152 height 720 supersample 3 > ui mousemode right translate > save > ""/Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Papier_rif2BAT_2025/Figure > 1B_hRad50_Trf2IDDR_pLDDT.png"" width 1152 height 720 supersample 3 > hide #!6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > show #!1 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_001_alphafold2_multimer_v3_model_2_seed_74781.json Structure scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb #1 does not match PAE matrix size 441.The structure has 442 polymer residues and 0 non-polymer atoms This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error. > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1312_trf2IDDR_448_478_25st_88f42/predictions/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478/scores/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_scores_rank_001_alphafold2_multimer_v3_model_2_seed_74781.json Structure scRad50_1_200_1101_1312_scRif2BAT_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_90197.pdb #1 does not match PAE matrix size 441.The structure has 442 polymer residues and 0 non-polymer atoms This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error. > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/scores/scRad50_1_200_1101_1312_scRif2BAT_1_30_scores_rank_001_alphafold2_multimer_v3_model_1_seed_90197.json > color bfactor #1 palette alphafold 3531 atoms, 442 residues, atom bfactor range 31.7 to 98.1 > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/scores/scRad50_1_200_1101_1312_scRif2BAT_1_30_scores_rank_002_alphafold2_multimer_v3_model_1_seed_90195.json > color bfactor #2 palette alphafold 3531 atoms, 442 residues, atom bfactor range 33.6 to 97.9 > alphafold pae #2 colorDomains true > color bfactor #2 palette alphafold 3531 atoms, 442 residues, atom bfactor range 33.6 to 97.9 > show #2 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #3 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/scores/scRad50_1_200_1101_1312_scRif2BAT_1_30_scores_rank_003_alphafold2_multimer_v3_model_5_seed_90196.json > color bfactor #3 palette alphafold 3531 atoms, 442 residues, atom bfactor range 34.3 to 97.9 > show #3 models > show #4 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #4 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/scores/scRad50_1_200_1101_1312_scRif2BAT_1_30_scores_rank_004_alphafold2_multimer_v3_model_1_seed_90196.json > color bfactor #4 palette alphafold 3531 atoms, 442 residues, atom bfactor range 32.7 to 97.9 > show #5 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #5 file > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scRad50_1_200_1101_1312_scRif2BAT_1_30_25st_2f3b3/predictions/scRad50_1_200_1101_1312_scRif2BAT_1_30/scores/scRad50_1_200_1101_1312_scRif2BAT_1_30_scores_rank_005_alphafold2_multimer_v3_model_2_seed_90197.json > color bfactor #5 palette alphafold 3531 atoms, 442 residues, atom bfactor range 32.5 to 98.2 > select #1-5/A/B 16470 atoms, 16735 bonds, 2060 residues, 5 models selected > color sel light grey target ac > select clear > hide #5 models > show #5 models > select #1-5/C:26-30 175 atoms, 170 bonds, 25 residues, 5 models selected > hide sel cartoons > hide #5 models > show #5 models > hide #4 models > show #4 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Figure1B_scRad50_Rif2BAT_pLDDT.png > width 964 height 720 supersample 3 > select #1-5/C:23 40 atoms, 35 bonds, 5 residues, 5 models selected > show sel atoms > hide #4 models > show #4 models > hide #3 models > ui mousemode right ""move label"" > select clear > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/Figure1B_scRad50_Rif2Bat_pLDDT_zoom.png > width 964 height 720 supersample 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Max OpenGL vendor: Apple Python: 3.11.4 Locale: fr_FR.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,5 Model Number: Z1FV000H9FN/A Chip: Apple M4 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 21 jours, 1 heure et 58 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Platform duplicate all ChimeraX