id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17754 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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{ }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ { ""treatmentId"" : ""ccf01f2d-382e-4ccc-a332-b3f688bc9bbf"", ""experimentId"" : ""67f46b1a73932228c9baf274"", ""deploymentId"" : 400000001 } ] }, ""reportNotes"" : [ ""RIP register does not match crashing frame (0x0 vs 0x7FF89085EAE0)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7cyq 7cyq title: Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis [more info...] Chain information for 7cyq #1 --- Chain | Description | UniProt A | RNA-directed RNA polymerase | R1AB_SARS2 1-932 B D | Non-structural protein 8 | R1AB_SARS2 1-198 C | Non-structural protein 7 | R1AB_SARS2 1-83 E F | Helicase | R1AB_SARS2 1-601 G | Non-structural protein 9 | R1AB_SARS2 1-113 I | Primer | J | Template | Non-standard residues in 7cyq #1 --- GDP — guanosine-5'-diphosphate MG — magnesium ion ZN — zinc ion 16 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide atoms > show cartoons > color bychain > open 7n0d 7n0d title: Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex [more info...] Chain information for 7n0d #2 --- Chain | Description | UniProt A C E G | Non-structural protein 10 | R1AB_SARS2 1-139 B D F H | Proofreading exoribonuclease | R1AB_SARS2 1-527 I T | RNA (5'-R(*GP*GP*GP*GP*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*G)-3') | J P | RNA (5'-R(*CP*CP*CP*CP*C)-3') | K L | RNA (5'-R(*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') | Non-standard residues in 7n0d #2 --- 1N7 — chapso (2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium) MG — magnesium ion ZN — zinc ion > hide #!1 models > hide #!2 atoms > show #!2 cartoons > color #!2 bychain > combine #2 > matchmaker #3/D to #2/B 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 7n0d, chain B (#2) with copy of 7n0d, chain D (#3), sequence alignment score = 2582.4 RMSD between 507 pruned atom pairs is 0.498 angstroms; (across all 512 pairs: 0.593) > hide #!3 models > matchmaker #4/F to #2/B 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 7n0d, chain B (#2) with copy of 7n0d, chain F (#4), sequence alignment score = 2768.4 RMSD between 512 pruned atom pairs is 0.007 angstroms; (across all 512 pairs: 0.007) > hide #!4 models > matchmaker #5/H to #2/B 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 7n0d, chain B (#2) with copy of 7n0d, chain H (#5), sequence alignment score = 2582.4 RMSD between 507 pruned atom pairs is 0.498 angstroms; (across all 512 pairs: 0.593) > hide #!5 models > show #!3 models > show #!4 models > show #!5 models > select #2/A 957 atoms, 976 bonds, 8 pseudobonds, 133 residues, 2 models selected Drag select of 8 residues > select up 1135 atoms, 1152 bonds, 8 pseudobonds, 159 residues, 5 models selected > select up 15349 atoms, 15780 bonds, 8 pseudobonds, 1945 residues, 5 models selected Drag select of 6 residues > select up 16377 atoms, 16896 bonds, 8 pseudobonds, 2015 residues, 5 models selected > select up 18081 atoms, 18656 bonds, 8 pseudobonds, 2219 residues, 5 models selected > select up 18153 atoms, 18712 bonds, 8 pseudobonds, 2243 residues, 5 models selected > select up 87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected > select down 18153 atoms, 18712 bonds, 8 pseudobonds, 2243 residues, 5 models selected Drag select of 8 residues > select up 19559 atoms, 20282 bonds, 8 pseudobonds, 2309 residues, 5 models selected > select up 87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected > select down 19559 atoms, 20282 bonds, 8 pseudobonds, 2309 residues, 5 models selected Drag select of 2 residues > select up 20381 atoms, 21202 bonds, 8 pseudobonds, 2347 residues, 5 models selected > select up 87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected > select down 20381 atoms, 21202 bonds, 8 pseudobonds, 2347 residues, 5 models selected Drag select of 2 residues > select up 20581 atoms, 21420 bonds, 8 pseudobonds, 2357 residues, 5 models selected > select up 87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected > select down 20581 atoms, 21420 bonds, 8 pseudobonds, 2357 residues, 5 models selected > select ~sel & ##selected 66803 atoms, 68820 bonds, 509 pseudobonds, 8363 residues, 16 models selected > delete sel > show nucleic > style stick Changed 42422 atom styles > ~ribbon nucleic > hide protein-5 > ~ribbon protein-5 > hide #!3 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!5 models > combine #2 > delete protein > ~show nucleic > hide #!6 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > show :mg > color :mg green > set bgColor white > ui tool show ""Side View"" > color #!2,6 byhetero > save /Users/rnkirchdoerf/Desktop/7n0d_nsp1014_RNA.jpg width 769 height 772 > supersample 3 > close #3-6 > open 7kf4 Summary of feedback from opening 7kf4 fetched from pdb --- note | Fetching compressed mmCIF 7kf4 from http://files.rcsb.org/download/7kf4.cif 7kf4 title: Crystal structure from SARS-CoV-2 NendoU NSP15 [more info...] Chain information for 7kf4 #3 --- Chain | Description | UniProt A B C D E F | Uridylate-specific endoribonuclease | R1AB_SARS2 1-346 Non-standard residues in 7kf4 #3 --- CIT — citric acid 30 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > view #3 > hide > ribbon > delete #3/B-F > open 7bq7 7bq7 title: Crystal structure of 2019-nCoV nsp16-nsp10 complex [more info...] Chain information for 7bq7 #4 --- Chain | Description | UniProt A | 2'-O-methyltransferase | R1AB_SARS2 1-298 B | Non-structural protein 10 | R1AB_SARS2 1-139 Non-standard residues in 7bq7 #4 --- SAM — S-adenosylmethionine ZN — zinc ion > view #4 > color #4 bychain > ~ribbon #4/B > ~show > hide #!4 models > hide #3 models > hide #!2 models > show #!1 models > view #1 > ~ribbon #1/A-B,D-G > ~ribbon nucleic > view #1 > color #1 light grey > save /Users/rnkirchdoerf/Desktop/7cyq_nsp7.jpg width 1200 height 1205 > supersample 3 > ~ribbon #1 > ribbon #1/B > view #1/B > color #1/grey > color #1 grey > save /Users/rnkirchdoerf/Desktop/7cyq_nsp8.jpg width 1200 height 1205 > supersample 3 > ~ribbon #1 > ribbon #1/G > view #1 > color #1/dim grey > color #1 dim grey > save /Users/rnkirchdoerf/Desktop/7cyq_nsp9.png width 769 height 772 > supersample 3 transparentBackground true > ~ribbon #1 > ribbon #1/C > view #1 > color #1/C light grey > save /Users/rnkirchdoerf/Desktop/7cyq_nsp7.png width 1200 height 1205 > supersample 3 transparentBackground true > ~ribbon #1 > ribbon #1/B > view #1/B > color #1/B grey > ui tool show ""Side View"" > save /Users/rnkirchdoerf/Desktop/7cyq_nsp8.png width 1200 height 1205 > supersample 3 transparentBackground true > hide #!1 models > show #!2 models > ~ribbon #2/A > ~ribbon #2 > ribbon #2/A > view #2 > color #2 dark grey > color #2 black > save /Users/rnkirchdoerf/Desktop/7n0d_nsp10.png width 1200 height 1205 > supersample 3 transparentBackground true > hide #!2 models > show #!1 models > ~ribbon #1 > ribbon #1/A > view #1 > color #1/A goldenrod > lighting soft > save /Users/rnkirchdoerf/Desktop/7cyq_nsp12.png width 1200 height 1205 > supersample 3 transparentBackground true > ~ribbon #1 > ribbon #1/E > view #1 > color #1/E light green > hide pseudobonds > cartoon style thickness 0.5 > cartoon style thickness 0.8 > save /Users/rnkirchdoerf/Desktop/7cyq_nsp13.png width 1200 height 1205 > supersample 3 transparentBackground true > hide #!1 models > show #!2 models > view #2 > ~ribbon #2/A > ribbon #2/B > color #2/B light grey > view #2 > save /Users/rnkirchdoerf/Desktop/7n0d_nsp14.png width 1200 height 1205 > supersample 3 transparentBackground true > hide #!2 models > show #3 models > view #3 > ui tool show ""Color Actions"" > color #3 lime green > color #3 medium sea green > save /Users/rnkirchdoerf/Desktop/7kf4_nsp14.png width 1200 height 1205 > supersample 3 transparentBackground true > hide #3 models > show #!4 models > view #4 > color #4 bychain > select ~sel & ##selected Nothing selected > color #4 forest green > save /Users/rnkirchdoerf/Desktop/7bq7_nsp16.png width 1200 height 1205 > supersample 3 transparentBackground true > hide #!4 models > show #!1 models > view #1 > color #1/E yellow green > save /Users/rnkirchdoerf/Desktop/7cyq_nsp13.png width 1200 height 1205 > supersample 3 transparentBackground true > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_13_12_32_eav_nsp5_6/fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif"" Chain information for fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif #5 --- Chain | Description A | . > view #5 clip false > hide #!1 models > show #5 > rainbow #5 > color byhetero > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_1.cif"" Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_1.cif #6 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_2.cif"" Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_2.cif #7 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_3.cif"" Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_3.cif #8 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_4.cif"" Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_4.cif #9 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_0.cif"" Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_0.cif #10 --- Chain | Description A | . > matchmaker #7-10 to #6 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_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with fold_2025_05_21_08_34_shfv_nsp5_model_2.cif, chain A (#7), sequence alignment score = 865.4 RMSD between 163 pruned atom pairs is 0.468 angstroms; (across all 166 pairs: 0.573) Matchmaker fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with fold_2025_05_21_08_34_shfv_nsp5_model_3.cif, chain A (#8), sequence alignment score = 868.4 RMSD between 160 pruned atom pairs is 0.443 angstroms; (across all 166 pairs: 0.761) Matchmaker fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with fold_2025_05_21_08_34_shfv_nsp5_model_4.cif, chain A (#9), sequence alignment score = 865.4 RMSD between 161 pruned atom pairs is 0.442 angstroms; (across all 166 pairs: 0.621) Matchmaker fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with fold_2025_05_21_08_34_shfv_nsp5_model_0.cif, chain A (#10), sequence alignment score = 864.8 RMSD between 156 pruned atom pairs is 0.375 angstroms; (across all 166 pairs: 1.587) > matchmaker #6-10 to #5 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_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6), sequence alignment score = 311.1 RMSD between 85 pruned atom pairs is 0.891 angstroms; (across all 155 pairs: 4.763) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_34_shfv_nsp5_model_2.cif, chain A (#7), sequence alignment score = 321.9 RMSD between 86 pruned atom pairs is 0.911 angstroms; (across all 155 pairs: 4.587) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_34_shfv_nsp5_model_3.cif, chain A (#8), sequence alignment score = 318.3 RMSD between 87 pruned atom pairs is 0.892 angstroms; (across all 155 pairs: 4.682) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_34_shfv_nsp5_model_4.cif, chain A (#9), sequence alignment score = 321.9 RMSD between 83 pruned atom pairs is 0.886 angstroms; (across all 155 pairs: 4.690) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_34_shfv_nsp5_model_0.cif, chain A (#10), sequence alignment score = 314.7 RMSD between 85 pruned atom pairs is 0.899 angstroms; (across all 155 pairs: 5.107) > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > show #6 models > select #5:50-75 206 atoms, 211 bonds, 26 residues, 1 model selected > hide #6 models > select #6:50-75 201 atoms, 205 bonds, 26 residues, 1 model selected > hide #5 models > show #6 models > hide #6 models > show #5 models > close #7-10 > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_1.cif"" Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_1.cif #7 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_2.cif"" Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_2.cif #8 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_3.cif"" Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_3.cif #9 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_4.cif"" Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_4.cif #10 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_0.cif"" Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_0.cif #11 --- Chain | Description A | . > matchmaker #7-11 to #5 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_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7), sequence alignment score = 145.5 RMSD between 10 pruned atom pairs is 1.212 angstroms; (across all 168 pairs: 18.928) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment score = 145 RMSD between 19 pruned atom pairs is 1.055 angstroms; (across all 172 pairs: 17.976) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_3.cif, chain A (#9), sequence alignment score = 145.5 RMSD between 10 pruned atom pairs is 1.222 angstroms; (across all 168 pairs: 18.972) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_4.cif, chain A (#10), sequence alignment score = 145 RMSD between 22 pruned atom pairs is 1.085 angstroms; (across all 172 pairs: 17.958) Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_0.cif, chain A (#11), sequence alignment score = 145 RMSD between 15 pruned atom pairs is 1.479 angstroms; (across all 172 pairs: 16.979) > matchmaker #7 to #5 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_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7), sequence alignment score = 145.5 RMSD between 10 pruned atom pairs is 1.212 angstroms; (across all 168 pairs: 18.928) > matchmaker #8-11 to #7 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_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment score = 1541.1 RMSD between 290 pruned atom pairs is 0.452 angstroms; (across all 290 pairs: 0.452) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_08_43_sars2_nsp6_model_3.cif, chain A (#9), sequence alignment score = 1544.1 RMSD between 290 pruned atom pairs is 0.342 angstroms; (across all 290 pairs: 0.342) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_08_43_sars2_nsp6_model_4.cif, chain A (#10), sequence alignment score = 1541.1 RMSD between 273 pruned atom pairs is 0.334 angstroms; (across all 290 pairs: 1.134) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_08_43_sars2_nsp6_model_0.cif, chain A (#11), sequence alignment score = 1541.1 RMSD between 290 pruned atom pairs is 0.400 angstroms; (across all 290 pairs: 0.400) > hide #5 models > select clear > hide #8 models > hide #9 models > hide #10 models > hide #11 models > show #5 models > rainbow #7 > matchmaker #7 to #5 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_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7), sequence alignment score = 145.5 RMSD between 10 pruned atom pairs is 1.212 angstroms; (across all 168 pairs: 18.928) > ui tool show Matchmaker > matchmaker #8 to #5 ssFraction 0.8088 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.8088 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_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment score = 589.859 RMSD between 8 pruned atom pairs is 1.430 angstroms; (across all 170 pairs: 16.553) > matchmaker #8 to #5 ssFraction 0.8088 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.8088 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_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment score = 589.859 RMSD between 8 pruned atom pairs is 1.430 angstroms; (across all 170 pairs: 16.553) > hide #5 models > select #7:157 5 atoms, 4 bonds, 1 residue, 1 model selected > hide #7 models > select up 120 atoms, 121 bonds, 16 residues, 1 model selected > select up 2321 atoms, 2383 bonds, 290 residues, 1 model selected > select up 48150 atoms, 49268 bonds, 6157 residues, 11 models selected > select up 48150 atoms, 49268 bonds, 6157 residues, 11 models selected > select up 48150 atoms, 49268 bonds, 6157 residues, 11 models selected > close #8-11 > select clear > show #5 models > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_1.cif"" Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_1.cif #8 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_2.cif"" Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_2.cif #9 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_3.cif"" Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_3.cif #10 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_4.cif"" Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_4.cif #11 --- Chain | Description A | . > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri > nsp9 > grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_0.cif"" Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_0.cif #12 --- Chain | Description A | . > matchmaker #8-12 to #7 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_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_09_00_mhv_nsp6_model_1.cif, chain A (#8), sequence alignment score = 36 RMSD between 5 pruned atom pairs is 1.030 angstroms; (across all 101 pairs: 17.951) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_09_00_mhv_nsp6_model_2.cif, chain A (#9), sequence alignment score = 48.9 RMSD between 4 pruned atom pairs is 1.448 angstroms; (across all 99 pairs: 18.180) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_09_00_mhv_nsp6_model_3.cif, chain A (#10), sequence alignment score = 45.3 RMSD between 5 pruned atom pairs is 1.205 angstroms; (across all 99 pairs: 18.905) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_09_00_mhv_nsp6_model_4.cif, chain A (#11), sequence alignment score = 48.9 RMSD between 4 pruned atom pairs is 1.003 angstroms; (across all 99 pairs: 18.713) Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with fold_2025_05_21_09_00_mhv_nsp6_model_0.cif, chain A (#12), sequence alignment score = 48.9 RMSD between 4 pruned atom pairs is 1.450 angstroms; (across all 99 pairs: 18.091) > hide #5 models > show #7 models > hide #12 models > hide #11 models > hide #10 models > hide #9 models > hide #7 models > hide #8 models > show #9 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: Z14Z00105LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 34 days, 9 hours, 48 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-Clipper: 0.23.1 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX