id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18454 Crash on Mac waking from sleep bck243@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-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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All rights reserved. How to cite UCSF ChimeraX > open > /Users/bethanykolody/Downloads/folds_2025_08_15_22_11/sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0/fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif Chain information for fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif #1 --- Chain | Description A | . Computing secondary structure > set bgColor white > set bgColor black > color bfactor palette alphafold 29075 atoms, 4139 residues, atom bfactor range 18.5 to 87.1 > ui tool show ""Side View"" > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select clear > select /A:4122-4123 12 atoms, 11 bonds, 2 residues, 1 model selected > select /A:4122-4139 139 atoms, 138 bonds, 18 residues, 1 model selected > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-7 46 atoms, 46 bonds, 7 residues, 1 model selected > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-30 193 atoms, 195 bonds, 30 residues, 1 model selected > select /A:31 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:31-109 550 atoms, 553 bonds, 79 residues, 1 model selected > select /A:63-64 12 atoms, 11 bonds, 2 residues, 1 model selected > select /A:1-64 428 atoms, 432 bonds, 64 residues, 1 model selected > select /A:1-64 428 atoms, 432 bonds, 64 residues, 1 model selected > select /A:1-64 428 atoms, 432 bonds, 64 residues, 1 model selected > select /A:1-64 428 atoms, 432 bonds, 64 residues, 1 model selected > select clear > color bychain > rainbow > color bypolymer > rainbow > select /A:1-64 428 atoms, 432 bonds, 64 residues, 1 model selected > color #1 #76d6ffff > select /A:4043-4088 328 atoms, 331 bonds, 46 residues, 1 model selected > select /A:1-64 428 atoms, 432 bonds, 64 residues, 1 model selected > select /A:4043-4088 328 atoms, 331 bonds, 46 residues, 1 model selected > select /A:4139 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:4097-4139 312 atoms, 313 bonds, 43 residues, 1 model selected > select /A:3691-4139 3337 atoms, 3387 bonds, 449 residues, 1 model selected > set bgColor white > color #1 #0096ffff > select clear > select /A:3691-4139 3337 atoms, 3387 bonds, 449 residues, 1 model selected > select /A:3943 10 atoms, 10 bonds, 1 residue, 1 model selected > select /A:3943-4139 1405 atoms, 1419 bonds, 197 residues, 1 model selected > select /A:3943 10 atoms, 10 bonds, 1 residue, 1 model selected > select /A:3943-4139 1405 atoms, 1419 bonds, 197 residues, 1 model selected > select /A:3943 10 atoms, 10 bonds, 1 residue, 1 model selected > select /A:3943-4128 1318 atoms, 1332 bonds, 186 residues, 1 model selected > select /A:3991-3992 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:3991-4083 655 atoms, 663 bonds, 93 residues, 1 model selected > select /A:4089 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:4089 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:3993-3994 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:3993-4085 654 atoms, 662 bonds, 93 residues, 1 model selected > select /A:3999 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:3999-4089 640 atoms, 647 bonds, 91 residues, 1 model selected > select /A:4026 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4026-4080 400 atoms, 405 bonds, 55 residues, 1 model selected > select /A:4036-4037 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:4036-4087 377 atoms, 381 bonds, 52 residues, 1 model selected > select /A:4060-4061 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:4060-4074 114 atoms, 114 bonds, 15 residues, 1 model selected > select /A:4055 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:4055-4076 153 atoms, 154 bonds, 22 residues, 1 model selected > select /A:4078 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:4040-4078 279 atoms, 282 bonds, 39 residues, 1 model selected > select /A:4080-4081 17 atoms, 17 bonds, 2 residues, 1 model selected > select /A:4080-4084 39 atoms, 39 bonds, 5 residues, 1 model selected > select /A:4071 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:4071-4090 134 atoms, 135 bonds, 20 residues, 1 model selected > select /A:4079 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:4079-4093 111 atoms, 111 bonds, 15 residues, 1 model selected > select /A:4074 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4074-4093 136 atoms, 137 bonds, 20 residues, 1 model selected > select /A:4079-4080 14 atoms, 13 bonds, 2 residues, 1 model selected > select /A:4079-4093 111 atoms, 111 bonds, 15 residues, 1 model selected > select /A:4076 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4076-4091 111 atoms, 111 bonds, 16 residues, 1 model selected > select /A:4076 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4076-4139 459 atoms, 461 bonds, 64 residues, 1 model selected > select /A:4074 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4011-4074 457 atoms, 461 bonds, 64 residues, 1 model selected > select /A:4074 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:3931-4074 1026 atoms, 1036 bonds, 144 residues, 1 model selected > select /A:4074-4075 11 atoms, 11 bonds, 2 residues, 1 model selected > select /A:3883-4075 1404 atoms, 1425 bonds, 193 residues, 1 model selected > select /A:4075 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:3931-4075 1033 atoms, 1044 bonds, 145 residues, 1 model selected > select /A:3934 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:3934-4075 1009 atoms, 1020 bonds, 142 residues, 1 model selected > select /A:3985 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:3985-4075 642 atoms, 649 bonds, 91 residues, 1 model selected > select /A:3977 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:3977-4075 693 atoms, 700 bonds, 99 residues, 1 model selected > open 3HB2 Summary of feedback from opening 3HB2 fetched from pdb --- note | Fetching compressed mmCIF 3hb2 from http://files.rcsb.org/download/3hb2.cif 3hb2 title: PrtC methionine mutants: M226I [more info...] Chain information for 3hb2 #2 --- Chain | Description | UniProt P | Secreted protease C | PRTC_ERWCH 18-479 Non-standard residues in 3hb2 #2 --- CA — calcium ion CL — chloride ion ZN — zinc ion 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > color #2 #ff9300ff > ui tool show Matchmaker > matchmaker #!2 to #1 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 fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4 RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs: 34.548) > open 5K8G Summary of feedback from opening 5K8G fetched from pdb --- note | Fetching compressed mmCIF 5k8g from http://files.rcsb.org/download/5k8g.cif 5k8g title: Crystal structure of a putative peptide-binding domain of MpAFP [more info...] Chain information for 5k8g #3 --- Chain | Description | UniProt A | Antifreeze protein | A1YIY3_9GAMM 1-519 Non-standard residues in 5k8g #3 --- CA — calcium ion 11 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > matchmaker #!2-3 to #1 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 fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4 RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs: 34.548) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 5k8g, chain A (#3), sequence alignment score = 339.9 RMSD between 11 pruned atom pairs is 1.034 angstroms; (across all 441 pairs: 71.639) > hide #!3 models > open 2ML3 Summary of feedback from opening 2ML3 fetched from pdb --- note | Fetching compressed mmCIF 2ml3 from http://files.rcsb.org/download/2ml3.cif 2ml3 title: Solution Structure of AlgE6R3 subunit from the Azotobacter vinelandii Mannuronan C5-epimerase [more info...] Chain information for 2ml3 --- Chain | Description | UniProt 4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | Poly(beta-D-mannuronate) C5 epimerase 6 | ALGE6_AZOVI 2-181 > color #4 #ff2f92ff models > color #4 #00f900ff models > ui tool show Matchmaker > matchmaker #!2-3#!4.1-20 to #1 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 fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4 RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs: 34.548) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 5k8g, chain A (#3), sequence alignment score = 339.9 RMSD between 11 pruned atom pairs is 1.034 angstroms; (across all 441 pairs: 71.639) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.1), sequence alignment score = 197 RMSD between 18 pruned atom pairs is 1.221 angstroms; (across all 156 pairs: 14.254) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.2), sequence alignment score = 193.9 RMSD between 65 pruned atom pairs is 0.875 angstroms; (across all 148 pairs: 8.019) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.3), sequence alignment score = 191.3 RMSD between 16 pruned atom pairs is 1.159 angstroms; (across all 156 pairs: 14.128) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.4), sequence alignment score = 196.9 RMSD between 14 pruned atom pairs is 0.860 angstroms; (across all 156 pairs: 14.064) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.5), sequence alignment score = 191 RMSD between 16 pruned atom pairs is 1.100 angstroms; (across all 156 pairs: 14.326) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.6), sequence alignment score = 197 RMSD between 18 pruned atom pairs is 1.085 angstroms; (across all 156 pairs: 14.202) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.7), sequence alignment score = 193.2 RMSD between 18 pruned atom pairs is 1.129 angstroms; (across all 162 pairs: 14.207) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.8), sequence alignment score = 196.2 RMSD between 65 pruned atom pairs is 0.847 angstroms; (across all 155 pairs: 7.611) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.9), sequence alignment score = 202.2 RMSD between 71 pruned atom pairs is 0.938 angstroms; (across all 155 pairs: 7.359) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.10), sequence alignment score = 185.3 RMSD between 18 pruned atom pairs is 1.208 angstroms; (across all 156 pairs: 14.119) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.11), sequence alignment score = 190.9 RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs: 14.205) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.12), sequence alignment score = 191.3 RMSD between 18 pruned atom pairs is 1.203 angstroms; (across all 156 pairs: 14.161) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.13), sequence alignment score = 201.8 RMSD between 70 pruned atom pairs is 0.977 angstroms; (across all 161 pairs: 8.018) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.14), sequence alignment score = 184.9 RMSD between 17 pruned atom pairs is 1.250 angstroms; (across all 162 pairs: 14.301) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.15), sequence alignment score = 188.6 RMSD between 18 pruned atom pairs is 1.248 angstroms; (across all 156 pairs: 14.195) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.16), sequence alignment score = 187.2 RMSD between 16 pruned atom pairs is 1.178 angstroms; (across all 162 pairs: 14.338) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.17), sequence alignment score = 194.6 RMSD between 17 pruned atom pairs is 1.168 angstroms; (across all 156 pairs: 14.136) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.18), sequence alignment score = 190.9 RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs: 14.320) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.19), sequence alignment score = 184.9 RMSD between 17 pruned atom pairs is 1.190 angstroms; (across all 156 pairs: 14.240) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.20), sequence alignment score = 197.3 RMSD between 16 pruned atom pairs is 1.214 angstroms; (across all 156 pairs: 14.210) > hide #!2 models > hide #!4.20 models > hide #!4.19 models > hide #!4.18 models > hide #!4.17 models > hide #!4.16 models > hide #!4.15 models > hide #!4.14 models > hide #!4.13 models > hide #!4.12 models > hide #!4.11 models > hide #!4.10 models > hide #!4.9 models > hide #!4.7 models > hide #!4.8 models > hide #!4.6 models > hide #!4.5 models > hide #!4.4 models > hide #!4.3 models > hide #!4.2 models > hide #!4.1 models > show #!4.1 models > ui tool show ""Side View"" > color #4 #ff9300ff models > open > /Users/bethanykolody/Downloads/folds_2025_08_15_23_20/alg_like_domain_with_6_ca/fold_alg_like_domain_with_6_ca_model_0.cif Chain information for fold_alg_like_domain_with_6_ca_model_0.cif #5 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #5#!2-3#!4.1-20 to #1 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 fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with fold_alg_like_domain_with_6_ca_model_0.cif, chain A (#5), sequence alignment score = 473.2 RMSD between 91 pruned atom pairs is 0.620 angstroms; (across all 99 pairs: 2.322) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4 RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs: 34.548) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 5k8g, chain A (#3), sequence alignment score = 339.9 RMSD between 11 pruned atom pairs is 1.034 angstroms; (across all 441 pairs: 71.639) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.1), sequence alignment score = 197 RMSD between 18 pruned atom pairs is 1.221 angstroms; (across all 156 pairs: 14.254) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.2), sequence alignment score = 193.9 RMSD between 65 pruned atom pairs is 0.875 angstroms; (across all 148 pairs: 8.019) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.3), sequence alignment score = 191.3 RMSD between 16 pruned atom pairs is 1.159 angstroms; (across all 156 pairs: 14.128) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.4), sequence alignment score = 196.9 RMSD between 14 pruned atom pairs is 0.860 angstroms; (across all 156 pairs: 14.064) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.5), sequence alignment score = 191 RMSD between 16 pruned atom pairs is 1.100 angstroms; (across all 156 pairs: 14.326) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.6), sequence alignment score = 197 RMSD between 18 pruned atom pairs is 1.085 angstroms; (across all 156 pairs: 14.202) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.7), sequence alignment score = 193.2 RMSD between 18 pruned atom pairs is 1.129 angstroms; (across all 162 pairs: 14.207) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.8), sequence alignment score = 196.2 RMSD between 65 pruned atom pairs is 0.847 angstroms; (across all 155 pairs: 7.611) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.9), sequence alignment score = 202.2 RMSD between 71 pruned atom pairs is 0.938 angstroms; (across all 155 pairs: 7.359) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.10), sequence alignment score = 185.3 RMSD between 18 pruned atom pairs is 1.208 angstroms; (across all 156 pairs: 14.119) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.11), sequence alignment score = 190.9 RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs: 14.205) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.12), sequence alignment score = 191.3 RMSD between 18 pruned atom pairs is 1.203 angstroms; (across all 156 pairs: 14.161) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.13), sequence alignment score = 201.8 RMSD between 70 pruned atom pairs is 0.977 angstroms; (across all 161 pairs: 8.018) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.14), sequence alignment score = 184.9 RMSD between 17 pruned atom pairs is 1.250 angstroms; (across all 162 pairs: 14.301) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.15), sequence alignment score = 188.6 RMSD between 18 pruned atom pairs is 1.248 angstroms; (across all 156 pairs: 14.195) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.16), sequence alignment score = 187.2 RMSD between 16 pruned atom pairs is 1.178 angstroms; (across all 162 pairs: 14.338) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.17), sequence alignment score = 194.6 RMSD between 17 pruned atom pairs is 1.168 angstroms; (across all 156 pairs: 14.136) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.18), sequence alignment score = 190.9 RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs: 14.320) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.19), sequence alignment score = 184.9 RMSD between 17 pruned atom pairs is 1.190 angstroms; (across all 156 pairs: 14.240) Matchmaker fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif, chain A (#1) with 2ml3, chain A (#4.20), sequence alignment score = 197.3 RMSD between 16 pruned atom pairs is 1.214 angstroms; (across all 156 pairs: 14.210) > hide #1 models > color #5 #d783ffff ===== 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 > open > /Users/bethanykolody/Downloads/folds_2025_08_16_05_55/ricemega_all12creps_fn_pb_15730_l_63_rtx_cadhesin/fold_ricemega_all12creps_fn_pb_15730_l_63_rtx_cadhesin_model_0.cif Chain information for fold_ricemega_all12creps_fn_pb_15730_l_63_rtx_cadhesin_model_0.cif #1 --- Chain | Description A | . Computing secondary structure OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: MacBookPro18,2 Model Number: Z14Y0016GLL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 48 days, 7 hours, 40 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL S2722QC: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported DELL S2722QC: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 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 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 Window Toolkit duplicate all ChimeraX