id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16825 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. 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All rights reserved. > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1342_mre11_1_500>_dimer_31aa5/predictions/hrad50_1-200_1101-1312_mre11_1_500_dimeres/models/rad50_rif2bat_trf2iDDR_analyse_250210.cxs Log from Mon Feb 10 16:14:30 2025 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/ALphaFold2_I2BC/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_48c50/predictions/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30/models/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_48c50/predictions/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30/models/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_85090.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_48c50/predictions/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30/models/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_85088.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_48c50/predictions/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30/models/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_85089.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_48c50/predictions/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30/models/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_85088.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_48c50/predictions/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30/models/scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_85090.pdb Chain information for scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Chain information for scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_85090.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available Chain information for scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_85088.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available Chain information for scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_85089.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available Chain information for scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_85088.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available Chain information for scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_85090.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure [Repeated 5 time(s)] > set bgColor white > mmaker #5 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_85088.pdb, chain B (#5), sequence alignment score = 1102.4 RMSD between 209 pruned atom pairs is 0.395 angstroms; (across all 210 pairs: 0.421) > mmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_85090.pdb, chain B (#2), sequence alignment score = 1102.4 RMSD between 210 pruned atom pairs is 0.149 angstroms; (across all 210 pairs: 0.149) > mmaker #3 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_85088.pdb, chain B (#3), sequence alignment score = 1102.4 RMSD between 210 pruned atom pairs is 0.294 angstroms; (across all 210 pairs: 0.294) > mmaker #4 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_85089.pdb, chain B (#4), sequence alignment score = 1102.4 RMSD between 210 pruned atom pairs is 0.291 angstroms; (across all 210 pairs: 0.291) > color /A cornflower blue > color /B cornflower blue > mmaker #6 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_85090.pdb, chain B (#6), sequence alignment score = 1102.4 RMSD between 210 pruned atom pairs is 0.263 angstroms; (across all 210 pairs: 0.263) > select /C 1422 atoms, 1434 bonds, 180 residues, 6 models selected > rainbow sel > close #6 > graphics silhouettes true > lighting soft > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_c46a6/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_19647.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_c46a6/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_19649.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_c46a6/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_19648.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_c46a6/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_4_seed_19647.pdb > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_c46a6/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_1_seed_19647.pdb Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_19649.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_19648.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_19647.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available Chain information for hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_19647.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure [Repeated 4 time(s)] > mmaker #7 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_19649.pdb, chain B (#7), sequence alignment score = 1085.2 RMSD between 212 pruned atom pairs is 0.153 angstroms; (across all 212 pairs: 0.153) > mmaker #8 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_19648.pdb, chain B (#8), sequence alignment score = 1088.2 RMSD between 212 pruned atom pairs is 0.256 angstroms; (across all 212 pairs: 0.256) > mmaker #6 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6), sequence alignment score = 686.3 RMSD between 138 pruned atom pairs is 0.755 angstroms; (across all 204 pairs: 2.900) > mmaker #7 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_19649.pdb, chain B (#7), sequence alignment score = 1085.2 RMSD between 212 pruned atom pairs is 0.153 angstroms; (across all 212 pairs: 0.153) > mmaker #8 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_19648.pdb, chain B (#8), sequence alignment score = 1088.2 RMSD between 212 pruned atom pairs is 0.256 angstroms; (across all 212 pairs: 0.256) > mmaker #9 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_19647.pdb, chain B (#9), sequence alignment score = 1075.6 RMSD between 205 pruned atom pairs is 0.391 angstroms; (across all 212 pairs: 0.720) > mmaker #10 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb, chain B (#6) with hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_19647.pdb, chain B (#10), sequence alignment score = 1081.6 RMSD between 200 pruned atom pairs is 0.444 angstroms; (across all 212 pairs: 0.872) > select #6-10/A/B 16495 atoms, 16710 bonds, 2060 residues, 5 models selected > ui tool show ""Color Actions"" > color sel royal blue > select clear > select #6-10/C 1175 atoms, 1200 bonds, 145 residues, 5 models selected > rainbow sel > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/Super_scRad50_rif2Bat_1_30_5bestStr.png > width 1152 height 812 supersample 3 > show #6 models > show #7 models > show #8 models > show #9 models > show #10 models > hide #1 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/Super_hRad50_trf2iDDR_448_478_5bestStr.png > width 1152 height 812 supersample 3 > select clear > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/Super_hRad50_trf2iDDR_448_478_5bestStr.png > width 1152 height 812 supersample 3 > hide #7 models > hide #8 models > hide #9 models > hide #10 models > show #1 models > hide #1 models > select #6/C 235 atoms, 240 bonds, 29 residues, 1 model selected > show sel atoms > show #1 models > select #1/C 237 atoms, 239 bonds, 30 residues, 1 model selected > show sel atoms > color #1/C gold > color #1/C green > color #6/C orange > style sel ball Changed 237 atom styles > color sel byhetero > select #6/C 235 atoms, 240 bonds, 29 residues, 1 model selected > style sel ball Changed 235 atom styles > color sel byhetero Alignment identifier is 6/C > renumber #6/C start 448 29 residues renumbered > select zone #1/C 4.0 #1/A/B residues true Selected 269 atoms > show sel atoms > hide #6 models > style sel ball Changed 269 atom styles > color sel byhetero > select zone #6/C 4.0 #6/A/B residues true Selected 235 atoms > show #6 models > hide #1 models > show sel atoms > style sel ball Changed 235 atom styles > color sel byhetero > renumber #1/A start 1 0 residues renumbered > renumber #1/B start 1101 210 residues renumbered > renumber #6/B start 1101 212 residues renumbered > select #6/A/B 3299 atoms, 3342 bonds, 412 residues, 1 model selected Alignment identifier is 6/A Alignment identifier is 6/B > ui mousemode right label > label #6/C:452 > label #6/B:1274 > label #6/B:1307 > label #6/B:1309 > label #6/B:1286 > label #6/C:452 > label #6/C:451 > label #6/B:1275 > label #6/B:1288 > ui mousemode right select > select #6/C:454@CB 1 atom, 1 residue, 1 model selected > view sel > ui tool show ""Side View"" > select #6/B:1290@NZ 1 atom, 1 residue, 1 model selected > ui mousemode right label > label #6/B:1290 > label #6/C:459 > label #6/C:460 > label #6/B:1301 > label #6/C:461 > label #6/B:1298 > ui mousemode right translate > ui mousemode right distance > distance #6/C:462@OE1 #6/B:1287@OH Distance between hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb #6/C GLU 462 OE1 and /B TYR 1287 OH: 2.800Å > ui mousemode right label > label #6/C:462 > label #6/B:1287 > label #6/A:46 > label delete residues > label #6/A:46 > label delete residues [Repeated 1 time(s)] > label #6/A:46 > label #6/C:462 > ui mousemode right translate > ui mousemode right label > label #6/C:464 > label #6/A:24 > label #6/C:470 > ui mousemode right distance > distance #6/C:464@NE1 #6/A:85@OE1 Distance between hrad50_monomer_1-200_1101-1312_trf2IDDR_448_478_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_19647.pdb #6/C TRP 464 NE1 and /A GLN 85 OE1: 3.304Å > ui mousemode right label > label #6/A:6 > label #6/A:83 > label #6/C:471 > label #6/A:95 > label #6/A:119 > label #6/A:117 > label #6/A:5 > show #1 models > label #6/A:34 > ui mousemode right translate > select #1,6/C 472 atoms, 479 bonds, 59 residues, 2 models selected > show sel atoms > hide sel atoms > select clear > select #1,6/A,B 6574 atoms, 6669 bonds, 822 residues, 2 models selected > hide sel atoms > select clear > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/super_rf2bat_trf2iddr_on_hRad50-scRad50.png > width 1152 height 812 supersample 3 > hide #1 models > show #1 models > hide #!6 models > select #1/C 237 atoms, 239 bonds, 30 residues, 1 model selected > show sel atoms > style sel ball Changed 237 atom styles > select zone #1/C 4.0 #/A/B residue t Expected an objects specifier or a keyword > select zone #1/C 4.0 #1/A/B residues true Selected 269 atoms > show sel atoms > style sel ball Changed 269 atom styles > color sel byhetero > select clear > ui mousemode right label > label #1/C:24 > label #1/B:1277 > label #1/A:33 > label #1/C:23 > label #1/B:1289 > label #1/B:1307 > show #!6 models > select #6/C 235 atoms, 240 bonds, 29 residues, 1 model selected > show sel atoms > label #1/C:17 > hide #!6 models > label #1/C:12 > label #1/B:1301 > label #1/C:11 > label #1/B:1302 > label #1/C:8 > label #1/A:119 > label #1/A:83 > label #1/A:81 > label #1/A:6 > label #1/A:5 > label #1/B:1266 > ui mousemode right translate > ui mousemode right select > ui mousemode right label > label #1/A:6 > label #1/A:93 > label #1/C:4 > label #1/C:5 > label #1/A:6 > label #1/C:7 > label #1/A:125 > select #6/C 235 atoms, 240 bonds, 29 residues, 1 model selected > select #1/C 237 atoms, 239 bonds, 30 residues, 1 model selected > hide sel atoms > select #1/A/B 3275 atoms, 3327 bonds, 410 residues, 1 model selected > hide sel atoms > ~label sel residues [Repeated 1 time(s)] > select #1/A/B/C 3512 atoms, 3566 bonds, 440 residues, 1 model selected > ~label sel residues > open > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1342_mre11_1_500>_dimer_31aa5/predictions/hrad50_1-200_1101-1312_mre11_1_500_dimeres/models/hrad50_1-200_1101-1312_mre11_1_500_dimeres_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_15394.pdb Chain information for hrad50_1-200_1101-1312_mre11_1_500_dimeres_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_15394.pdb #12 --- Chain | Description A B | No description available C D | No description available E F | No description available > hide sel atoms > hide #!11 models > hide #11.1 models > hide #1 models > show #1 models > hide sel atoms > select #12 14694 atoms, 14950 bonds, 1824 residues, 1 model selected > hide sel atoms > show sel cartoons Computing secondary structure > hide #1 models > mmaker #12/C to #1/A Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain A (#1) with hrad50_1-200_1101-1312_mre11_1_500_dimeres_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_15394.pdb, chain C (#12), sequence alignment score = 50.1 RMSD between 17 pruned atom pairs is 0.828 angstroms; (across all 55 pairs: 18.780) > show #1 models > hide #12 models > show #12 models > mmaker #12/C to #1/B Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain B (#1) with hrad50_1-200_1101-1312_mre11_1_500_dimeres_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_15394.pdb, chain C (#12), sequence alignment score = 689.1 RMSD between 113 pruned atom pairs is 0.801 angstroms; (across all 204 pairs: 3.649) > mmaker #12/A to #1/A Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scrad50_monomer_1_200_1100_1312_rif2Bat_1_30_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_85088.pdb, chain A (#1) with hrad50_1-200_1101-1312_mre11_1_500_dimeres_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_15394.pdb, chain A (#12), sequence alignment score = 632.4 RMSD between 160 pruned atom pairs is 0.787 angstroms; (across all 198 pairs: 2.110) > label #12/C:202 > ui mousemode right translate > hide #1 models > show #1 models > hide #1 models > hide #!12 models > show #!12 models > show #1 models > hide #1 models > show #1 models > hide #1 models > select #12/A:204-212 Nothing selected > select #12/A:204-212 Nothing selected > select #12/C:204-212 67 atoms, 68 bonds, 9 residues, 1 model selected > show sel atoms > style sel ball Changed 67 atom styles > color sel byhetero > select zone #12/C:204-212 4.0 #12/E/F Selected 12 atoms > show sel atoms > style sel ball Changed 12 atom styles > select zone #12/C:204-212 4.0 #12/E/F byresi Expected a keyword > select zone #12/C:204-212 4.0 #12/E/residue ti Expected a keyword > show sel atoms > select zone #12/C:204-212 4.0 #12/E/residue t Expected a keyword > show sel atoms > select zone #12/C:204-212 4.0 #12/E/F residues true Selected 26 atoms > show sel atoms > style sel ball Changed 26 atom styles > color sel byhetero > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > select #12/A/C 3299 atoms, 3342 bonds, 412 residues, 1 model selected > color sel cornlower blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel cornflower blue > 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 #12 14694 atoms, 14950 bonds, 1824 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 > select #12/C-D:1 18 atoms, 16 bonds, 2 residues, 1 model selected > select #12/C-D:1-2 36 atoms, 34 bonds, 4 residues, 1 model selected > renumber #1/C start 1101 30 residues renumbered > renumber #1/D start 1101 No residues specified > renumber #1/C start 1 30 residues renumbered > renumber #12/C start 1101 212 residues renumbered > renumber #12/D start 1101 212 residues renumbered > save > /Users/pc126390/Integrative_Modelling/Projet_scRad50_rif2BAT/ALphaFold2_I2BC/hrad50_1-200_1101-1342_mre11_1_500>_dimer_31aa5/predictions/hrad50_1-200_1101-1312_mre11_1_500_dimeres/models/rad50_rif2bat_trf2iDDR_analyse_250210.cxs ——— End of log from Mon Feb 10 16:14:30 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: 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: 11881.81.2 OS Loader Version: 11881.81.2 Software: System Software Overview: System Version: macOS 15.3 (24D60) Kernel Version: Darwin 24.3.0 Time since boot: 13 jours, 5 heures et 41 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 Cinema HD: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 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 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