id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16090 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 UTC) Description Last time you used ChimeraX it crashed. 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""b58fbb65b3eac789621057fafa5ec80ba5bfadb8"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/rnom/Desktop/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb > format pdb No such file/path: /Users/rnom/Desktop/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb > open /Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb > format pdb No such file/path: /Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb > open /Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb > format pdb No such file/path: /Users/rnom/Desktop/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb > open ""/Users/rnom/Desktop/論文化/for > figure/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb"" Chain information for hAC9-Gs_TM_trimmed_real_space_refined_026.pdb #1 --- Chain | Description A | No description available > set bgColor white > set bgColor #ffffff00 > open ""/Users/rnom/Desktop/論文化/for > figure/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb"" Chain information for hAC9-Gs_SD_trimmed_real_space_refined_025.pdb #2 --- Chain | Description A | No description available B | No description available > hide #!1 models > color #2 #43ecb5ff > color #2 #ec73c5ff > color #2 #ec5987ff > undo > hide #!2 models > show #!2 models > close #2 > close # Expected a models specifier or a keyword > open ""/Users/rnom/Desktop/論文化/for > figure/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb"" Chain information for hAC9-Gs_SD_trimmed_real_space_refined_025.pdb #2 --- Chain | Description A | No description available B | No description available > open ""/Users/rnom/Desktop/hAC/AC9 Hiroaki/pdb6r3q.ent"" pdb6r3q.ent title: The structure of A membrane adenylyl cyclase bound to an activated stimulatory G protein [more info...] Chain information for pdb6r3q.ent #3 --- Chain | Description | UniProt A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354 B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394 Non-standard residues in pdb6r3q.ent #3 --- GSP — 5'-guanosine-diphosphate-monothiophosphate MG — magnesium ion > matchmaker #2 to #3 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 pdb6r3q.ent, chain A (#3) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 1735.5 RMSD between 434 pruned atom pairs is 0.796 angstroms; (across all 443 pairs: 1.867) > show #!2-3 atoms > hide #!2-3 atoms > undo > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > color #1 #4ad7aeff > color #1 #1acdd7ff > color #1 #00d7ccff > color #1 #00d2d7ff > matchmaker #1 to #3 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 pdb6r3q.ent, chain A (#3) with hAC9-Gs_TM_trimmed_real_space_refined_026.pdb, chain A (#1), sequence alignment score = 1704.3 RMSD between 368 pruned atom pairs is 0.756 angstroms; (across all 418 pairs: 1.411) > color #!1,3 bychain > undo > graphics silhouettes true > show #!2 models > hide #!1 models > ui tool show ""Side View"" > view orient > view > close session > set bgColor white > open ""/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"" > ""/Users/rnom/Desktop/論文化/for > figure/AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb"" Chain information for SD_apo-coot-1.pdb #1 --- Chain | Description A | No description available Chain information for AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb #2 --- Chain | Description A | No description available > close session > open ""/Users/rnom/Desktop/論文化/for > figure/AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb"" Chain information for AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb #1 --- Chain | Description A | No description available > open ""/Users/rnom/Desktop/論文化/for figure/pdb6r3q.ent"" pdb6r3q.ent title: The structure of A membrane adenylyl cyclase bound to an activated stimulatory G protein [more info...] Chain information for pdb6r3q.ent #2 --- Chain | Description | UniProt A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354 B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394 Non-standard residues in pdb6r3q.ent #2 --- GSP — 5'-guanosine-diphosphate-monothiophosphate MG — magnesium ion > open ""/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"" Chain information for SD_apo-coot-1.pdb #3 --- Chain | Description A | No description available > hide #!2 models > hide #!3 models > dssp #1 > close #2-3 > open ""/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"" Chain information for SD_apo-coot-1.pdb #2 --- Chain | Description A | No description available > open ""/Users/rnom/Desktop/論文化/for figure/pdb6r3q.ent"" pdb6r3q.ent title: The structure of A membrane adenylyl cyclase bound to an activated stimulatory G protein [more info...] Chain information for pdb6r3q.ent #3 --- Chain | Description | UniProt A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354 B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394 Non-standard residues in pdb6r3q.ent #3 --- GSP — 5'-guanosine-diphosphate-monothiophosphate MG — magnesium ion > hide #!2 models > color #1 #20d7d1ff > matchmaker #1 to #3 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 pdb6r3q.ent, chain A (#3) with AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb, chain A (#1), sequence alignment score = 1600.8 RMSD between 360 pruned atom pairs is 0.770 angstroms; (across all 405 pairs: 1.583) > close #3 > open ""/Users/rnom/Desktop/論文化/for > figure/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb"" Chain information for hAC9-Gs_TM_trimmed_real_space_refined_026.pdb #3 --- Chain | Description A | No description available > close session > open ""/Users/rnom/Desktop/論文化/for > figure/hAC9-Gs_TM_trimmed_real_space_refined_026.pdb"" Chain information for hAC9-Gs_TM_trimmed_real_space_refined_026.pdb #1 --- Chain | Description A | No description available > open ""/Users/rnom/Desktop/論文化/for > figure/hAC9-Gs_SD_trimmed_real_space_refined_025.pdb"" Chain information for hAC9-Gs_SD_trimmed_real_space_refined_025.pdb #2 --- Chain | Description A | No description available B | No description available > color #1 #32d7b9ff > color #1 #3dd0d7ff > color #1 #15d7d2ff > open ""/Users/rnom/Desktop/論文化/for figure/pdb6r3q.ent"" pdb6r3q.ent title: The structure of A membrane adenylyl cyclase bound to an activated stimulatory G protein [more info...] Chain information for pdb6r3q.ent #3 --- Chain | Description | UniProt A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354 B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394 Non-standard residues in pdb6r3q.ent #3 --- GSP — 5'-guanosine-diphosphate-monothiophosphate MG — magnesium ion > matchmaker #1 to #3 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 pdb6r3q.ent, chain A (#3) with hAC9-Gs_TM_trimmed_real_space_refined_026.pdb, chain A (#1), sequence alignment score = 1704.3 RMSD between 368 pruned atom pairs is 0.756 angstroms; (across all 418 pairs: 1.411) > matchmaker #2 to #3 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 pdb6r3q.ent, chain A (#3) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 1735.5 RMSD between 434 pruned atom pairs is 0.796 angstroms; (across all 443 pairs: 1.867) > save ""/Users/rnom/Desktop/論文化/for figure/chimera hAC9Gs bAC9.pdb"" > open ""/Users/rnom/Desktop/論文化/for > figure/AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb"" Chain information for AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb #4 --- Chain | Description A | No description available > open ""/Users/rnom/Desktop/論文化/for figure/SD_apo-coot-1.pdb"" Chain information for SD_apo-coot-1.pdb #5 --- Chain | Description A | No description available > dssp #4 > color #5 #23ef16ff > color #5 #a0efa3ff > color #4 #18ec0dff > hide #!2 models > hide #!1 models > matchmaker #4 to #3 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 pdb6r3q.ent, chain A (#3) with AC9_TM_trimmed_real_space_refined_027_real_space_refined_028.pdb, chain A (#4), sequence alignment score = 1600.8 RMSD between 360 pruned atom pairs is 0.770 angstroms; (across all 405 pairs: 1.583) > matchmaker #5 to #3 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 pdb6r3q.ent, chain A (#3) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 1551 RMSD between 351 pruned atom pairs is 1.053 angstroms; (across all 421 pairs: 2.696) > hide #!3 models > show #!2 models > show #!1 models > save ""/Users/rnom/Desktop/論文化/for figure/hAC9Gs to hAC9 apo.pdb"" > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > hide #!1 models > hide #!2 models > show #!2 models > select #5/A:328 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/A:331 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 131 atoms, 131 bonds, 16 residues, 1 model selected > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > hide #!4 models > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.034141,0.43193,0.90126,-38.552,-0.97755,0.17318,-0.12003,241.88,-0.20792,-0.88512,0.41632,198.43 > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > view matrix models > #5,-0.037769,0.44792,0.89328,-39.356,-0.9722,0.19027,-0.13651,240.45,-0.23111,-0.8736,0.42828,199.11 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > view matrix models > #5,-0.01856,0.43326,0.90108,-40.644,-0.97179,0.20413,-0.11817,237.43,-0.23514,-0.87785,0.41725,200.92 > view matrix models > #5,0.018383,0.51801,0.85518,-51.68,-0.69803,0.61902,-0.35996,173.04,-0.71583,-0.59032,0.37296,231.14 > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > view matrix models > #5,0.0005245,0.38052,0.92477,-38.686,-0.97777,0.19412,-0.07932,236.46,-0.2097,-0.90417,0.37216,204.12 > view matrix models > #5,-0.030638,0.43233,0.90119,-39.032,-0.97431,0.18832,-0.12347,239.97,-0.2231,-0.88183,0.41546,200.01 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right rotate > select #2/B:129 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 80 atoms, 81 bonds, 9 residues, 1 model selected > select up 2518 atoms, 2574 bonds, 305 residues, 1 model selected > hide sel cartoons > select #2/B:199@CG 1 atom, 1 residue, 1 model selected > select #2/B:199@CG 1 atom, 1 residue, 1 model selected > select clear Drag select of 1 atoms Drag select of 147 atoms, 32 residues, 137 bonds > select #2/B:296@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 76 atoms, 75 bonds, 10 residues, 1 model selected > select up 2518 atoms, 2574 bonds, 305 residues, 1 model selected > hide sel cartoons > hide sel atoms Drag select of 5 atoms, 1 residues, 8 bonds > select clear Drag select of 39 atoms, 14 residues, 35 bonds Drag select of 4 atoms, 5 bonds > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > hide sel atoms > lighting soft > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting soft > lighting simple > graphics silhouettes false > graphics silhouettes true > view sel No displayed objects specified. > view sel No displayed objects specified. > select #2/A:1228 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 64 atoms, 64 bonds, 8 residues, 1 model selected > select up 1858 atoms, 1897 bonds, 231 residues, 1 model selected > select #5/A:1227 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:1228 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #5/A:1227 4 atoms, 3 bonds, 1 residue, 1 model selected Drag select of 6 residues > select up 85 atoms, 85 bonds, 12 residues, 1 model selected > select up 227 atoms, 229 bonds, 29 residues, 1 model selected > hide sel cartoons > hide sel atoms Drag select of 1 atoms > hide sel cartoons > hide sel atoms Drag select of 6 residues > select up 69 atoms, 55 bonds, 9 residues, 2 models selected > select up 2668 atoms, 2706 bonds, 344 residues, 2 models selected > hide sel cartoons Drag select of 24 residues > select up 249 atoms, 249 bonds, 31 residues, 2 models selected > select up 342 atoms, 342 bonds, 42 residues, 2 models selected > select down 249 atoms, 249 bonds, 31 residues, 2 models selected > hide sel cartoons > open ""/Users/rnom/Desktop/240617 > 解析関連/cryosparc_P78_J52_007_volume_map_sharp.mrc"" Opened cryosparc_P78_J52_007_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.79, shown at level 0.0733, step 2, values float32 > hide #!2 models > hide #!6 models > show #!6 models > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = -0.001662, steps = 96 shifted from previous position = 2.58 rotated from previous position = 5.11 degrees atoms outside contour = 3488, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.03600526 0.45927056 0.88756643 -47.55149952 -0.96150180 0.25803345 -0.09451466 229.92837055 -0.27242963 -0.84999370 0.45088004 199.48128659 Axis -0.38084979 0.58477367 -0.71623543 Axis point 60.90157452 223.33171648 0.00000000 Rotation angle (degrees) 97.32749762 Shift along axis 9.69047128 Drag select of 6 cryosparc_P78_J52_007_volume_map_sharp.mrc > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.93048,0.25148,-0.2664,6.1275,-0.27723,0.95872,-0.063269,47.421,0.23949,0.13272,0.96178,-43.103 > view matrix models > #6,0.45018,0.85133,0.26939,-73.984,-0.48171,0.48556,-0.72951,211.62,-0.75186,0.19865,0.62868,110.61 > view matrix models > #6,0.41223,0.54124,0.73289,-81.503,-0.2083,0.8391,-0.50252,104.83,-0.88695,0.054493,0.45864,165.98 > color #6 #b2b2b2af models > color #6 #b2b2b22d models > color #6 #acacac2d models > color #6 #acacac2e models > view matrix models > #6,0.2871,0.63523,0.71698,-76.369,-0.5901,0.70689,-0.38999,157.19,-0.75455,-0.31112,0.5778,183.86 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.07513, steps = 240 shifted from previous position = 9.46 rotated from previous position = 34.2 degrees atoms outside contour = 2065, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.98878045 0.14669790 -0.02815925 -14.93133511 -0.14492117 0.98778755 0.05721541 12.59098993 0.03620874 -0.05249260 0.99796465 -2.48024412 Axis -0.34482880 -0.20231829 -0.91660264 Axis point 85.52431162 96.86518788 0.00000000 Rotation angle (degrees) 9.15327141 Shift along axis 4.87476506 > view matrix models > #6,0.078253,0.58406,0.80793,-53.878,-0.64902,0.64501,-0.40341,174.25,-0.75674,-0.49279,0.42954,225.02 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.0777, steps = 96 shifted from previous position = 6.95 rotated from previous position = 6.42 degrees atoms outside contour = 2034, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.99772083 0.01841915 -0.06491441 4.18488356 -0.02420010 0.99569947 -0.08942545 11.91254364 0.06298810 0.09079257 0.99387585 -22.80120914 Axis 0.80073976 -0.56829293 -0.18936467 Axis point 0.00000000 257.79482173 126.52714719 Rotation angle (degrees) 6.46130668 Shift along axis 0.89893181 > view matrix models > #6,0.046323,0.60142,0.79759,-50.977,-0.65046,0.62414,-0.43285,180.55,-0.75813,-0.49875,0.42011,227.06 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.0777, steps = 68 shifted from previous position = 1.89 rotated from previous position = 2.18 degrees atoms outside contour = 2034, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.99772940 0.01835985 -0.06479944 4.18259708 -0.02415752 0.99566196 -0.08985357 11.94320014 0.06286864 0.09121494 0.99384474 -22.83666976 Axis 0.80262984 -0.56591956 -0.18846853 Axis point 0.00000000 257.01253906 126.19234231 Rotation angle (degrees) 6.47657686 Shift along axis 0.90218026 > view matrix models > #6,-0.10361,0.63925,0.76198,-33.088,-0.57517,0.58651,-0.57025,191.8,-0.81145,-0.49735,0.30691,246.52 > view matrix models > #6,0.00059231,0.62064,0.78409,-46.23,-0.78696,0.48408,-0.38258,210.33,-0.61701,-0.61682,0.48871,217.05 > view matrix models > #6,-0.38948,0.43995,0.80917,23.562,-0.92101,-0.19261,-0.33859,311.15,0.00689,-0.87713,0.48021,174.1 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.1415, steps = 256 shifted from previous position = 10.7 rotated from previous position = 53.6 degrees atoms outside contour = 1033, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.99999125 0.00227039 0.00351385 -0.40477670 -0.00227859 0.99999469 0.00232871 0.11727871 -0.00350854 -0.00233670 0.99999111 0.74862997 Axis -0.48700357 0.73303847 -0.47484958 Axis point 203.25802129 0.00000000 125.73379773 Rotation angle (degrees) 0.27444303 Shift along axis -0.07238913 > show #!2 models > matchmaker #5 to #2 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 hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2) with SD_apo-coot-1.pdb, chain A (#5), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > undo > view matrix models > #6,0.28316,0.63549,0.71831,-76.062,-0.58937,0.70616,-0.39241,157.47,-0.75661,-0.31224,0.5745,184.64 > view matrix models > #6,0.082155,0.30908,0.94748,-34.162,-0.48044,0.84521,-0.23406,107.39,-0.87317,-0.43598,0.21794,256.37 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05886, steps = 132 shifted from previous position = 4.85 rotated from previous position = 6.48 degrees atoms outside contour = 2338, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.62396070 0.75885718 -0.18657124 -22.89073700 -0.74126437 0.65033448 0.16610897 125.99194015 0.24738669 0.03465314 0.96829695 -41.79708916 Axis -0.08388200 -0.27690868 -0.95722797 Axis point 128.66236222 93.14297026 0.00000000 Rotation angle (degrees) 51.58915812 Shift along axis 7.04120229 > view matrix models > #6,0.016458,0.4504,0.89267,-38.25,-0.040171,0.89237,-0.44951,70.679,-0.99906,-0.028461,0.03278,239.72 > view matrix models > #6,0.10908,0.50046,0.85886,-52.572,-0.063432,0.86576,-0.49642,82.468,-0.99201,-0.00032921,0.12618,224.44 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.10908,0.50046,0.85886,-61.111,-0.063432,0.86576,-0.49642,83.85,-0.99201,-0.00032921,0.12618,225.11 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05192, steps = 64 shifted from previous position = 3.11 rotated from previous position = 3.75 degrees atoms outside contour = 2448, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.28788878 0.93592299 -0.20289948 -0.89561999 -0.79229189 0.35178264 0.49852033 132.41035783 0.53795316 0.01723720 0.84279848 -55.58520203 Axis -0.24796477 -0.38169914 -0.89040398 Axis point 102.16520782 78.90961022 0.00000000 Rotation angle (degrees) 76.04056030 Shift along axis -0.82555257 > view matrix models > #6,0.10908,0.50046,0.85886,-67.052,-0.063432,0.86576,-0.49642,86.515,-0.99201,-0.00032921,0.12618,222.62 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05319, steps = 100 shifted from previous position = 3.72 rotated from previous position = 8.8 degrees atoms outside contour = 2399, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.42604160 0.88779422 -0.17409761 -18.66873133 -0.76978287 0.45683169 0.44580168 120.71375853 0.47531346 -0.05591270 0.87803808 -37.53274104 Axis -0.27125586 -0.35110925 -0.89618221 Axis point 95.80100050 84.08897101 0.00000000 Rotation angle (degrees) 67.63808831 Shift along axis -3.68354021 > view matrix models > #6,0.10908,0.50046,0.85886,-65.246,-0.063432,0.86576,-0.49642,83.733,-0.99201,-0.00032921,0.12618,226.79 > view matrix models > #6,0.10908,0.50046,0.85886,-65.453,-0.063432,0.86576,-0.49642,84.767,-0.99201,-0.00032921,0.12618,225.08 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.1415, steps = 296 shifted from previous position = 8.21 rotated from previous position = 67.6 degrees atoms outside contour = 1032, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.99999107 0.00228442 0.00355335 -0.40872594 -0.00229289 0.99999454 0.00237990 0.11395914 -0.00354789 -0.00238802 0.99999085 0.76072823 Axis -0.49147968 0.73199928 -0.47183131 Axis point 204.16680335 0.00000000 125.86171639 Rotation angle (degrees) 0.27791855 Shift along axis -0.07463689 > view matrix models > #6,0.10908,0.50046,0.85886,-60.387,-0.063432,0.86576,-0.49642,82.945,-0.99201,-0.00032921,0.12618,226.42 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.07771, steps = 168 shifted from previous position = 3.38 rotated from previous position = 6.67 degrees atoms outside contour = 2031, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.99772712 0.01834223 -0.06483939 4.18748969 -0.02413117 0.99568029 -0.08965731 11.92606966 0.06291478 0.09101818 0.99385986 -22.83065082 Axis 0.80186453 -0.56699190 -0.18850322 Axis point 0.00000000 257.49363072 126.30050427 Rotation angle (degrees) 6.46865321 Shift along axis 0.89946561 > undo > show #!2 models > matchmaker #2 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 SD_apo-coot-1.pdb, chain A (#5) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > hide #!2 models > view matrix models > #6,0.10908,0.50046,0.85886,-65.456,-0.063432,0.86576,-0.49642,84.744,-0.99201,-0.00032921,0.12618,225.05 > show #!2 models > view matrix models > #6,0.10908,0.50046,0.85886,-76.713,-0.063432,0.86576,-0.49642,73.417,-0.99201,-0.00032921,0.12618,212.87 > undo > hide #!2 models > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.1415, steps = 72 shifted from previous position = 3.4 rotated from previous position = 6.67 degrees atoms outside contour = 1032, contour level = 0.073323 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J52_007_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.99999093 0.00230189 0.00358227 -0.41272768 -0.00231046 0.99999447 0.00239007 0.11282165 -0.00357675 -0.00239832 0.99999072 0.76598986 Axis -0.49010819 0.73275135 -0.47209047 Axis point 203.71185785 0.00000000 126.21838261 Rotation angle (degrees) 0.27989268 Shift along axis -0.07666508 > show #!2 models > matchmaker #2 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 SD_apo-coot-1.pdb, chain A (#5) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > matchmaker #2 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 SD_apo-coot-1.pdb, chain A (#5) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > open /Users/rnom/Desktop/pdb6r3q.ent pdb6r3q.ent title: The structure of A membrane adenylyl cyclase bound to an activated stimulatory G protein [more info...] Chain information for pdb6r3q.ent #7 --- Chain | Description | UniProt A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354 B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394 Non-standard residues in pdb6r3q.ent #7 --- GSP — 5'-guanosine-diphosphate-monothiophosphate MG — magnesium ion > open /Users/rnom/Desktop/pdb6r3q.ent pdb6r3q.ent title: The structure of A membrane adenylyl cyclase bound to an activated stimulatory G protein [more info...] Chain information for pdb6r3q.ent #8 --- Chain | Description | UniProt A | adenylyl cyclase family member (ACY-1)-LIKE | E1BM79_BOVIN 1-1354 B | adenylate cyclase-stimulating G α protein | GNAS2_BOVIN 1-394 Non-standard residues in pdb6r3q.ent #8 --- GSP — 5'-guanosine-diphosphate-monothiophosphate MG — magnesium ion > open /Users/rnom/Downloads/pdb7pdd.ent pdb7pdd.ent title: Focus refinement of soluble domain of adenylyl cyclase 9 In complex with darpin C4 and mant-GTP [more info...] Chain information for pdb7pdd.ent #9 --- Chain | Description | UniProt A | adenylate cyclase 9 | E1BM79_BOVIN 1-1354 B | darpin C4 | > hide #!7 models > show #!7 models > hide #!7 models > close #7-9 > open ""/Users/rnom/Desktop/bAC9 model,map/7pd4.pdb"" 7pd4.pdb title: Structure of adenylyl cyclase 9 In complex with mant-GTP [more info...] Chain information for 7pd4.pdb #7 --- Chain | Description | UniProt A | adenylate cyclase 9 | E1BM79_BOVIN 1-1354 > close #7 > close #6 > open ""/Users/rnom/Desktop/論文化/for figure/hAC9 model, > map/AC9_SD/cryosparc_P78_J60_005_volume_map_sharp.mrc"" Opened cryosparc_P78_J60_005_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.79, shown at level 0.0635, step 2, values float32 Drag select of 6 cryosparc_P78_J60_005_volume_map_sharp.mrc > view matrix models #6,1,0,0,-74.685,0,1,0,-17.294,0,0,1,38.859 > view matrix models #6,1,0,0,-39.269,0,1,0,-8.0412,0,0,1,50.854 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.35591,-0.12873,0.92561,-43.424,-0.19238,0.95916,0.20736,-1.3276,-0.91451,-0.25187,0.31661,274.91 > view matrix models > #6,0.48889,-0.012202,0.87226,-69.56,-0.66365,0.64376,0.38097,80.254,-0.56617,-0.76513,0.30663,299.11 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.48889,-0.012202,0.87226,-43.821,-0.66365,0.64376,0.38097,87.914,-0.56617,-0.76513,0.30663,246.02 > hide #!2 models > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.0576, steps = 428 shifted from previous position = 28.2 rotated from previous position = 39.2 degrees atoms outside contour = 2267, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.06418813 -0.63318352 0.77133554 125.15384509 0.98007258 0.18559561 0.07079547 -29.17775390 -0.18798302 0.75142059 0.63247884 -40.82598727 Axis 0.34090378 0.48049258 0.80802939 Axis point 86.99326752 71.42481315 0.00000000 Rotation angle (degrees) 93.37487970 Shift along axis -4.34287326 > color #6 #b2b2b242 models > color #6 #b2b2b256 models > color #6 #b2b2b257 models > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.0576, steps = 40 shifted from previous position = 0.00397 rotated from previous position = 0.00954 degrees atoms outside contour = 2268, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.06409108 -0.63308705 0.77142279 125.14551701 0.98007015 0.18557860 0.07087379 -29.18300725 -0.18802884 0.75150607 0.63236365 -40.82295833 Axis 0.34090967 0.48056249 0.80798533 Axis point 86.99033611 71.41488258 0.00000000 Rotation angle (degrees) 93.38145894 Shift along axis -4.34529269 > view matrix models > #6,0.48889,-0.012202,0.87226,-51.712,-0.66365,0.64376,0.38097,85.631,-0.56617,-0.76513,0.30663,234.53 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.35647,-0.18819,0.91516,-16.718,-0.70197,0.59246,0.39526,95.599,-0.61657,-0.78331,0.079095,268.44 > view matrix models > #6,0.66049,-0.18784,0.72696,-34.362,-0.7226,0.10399,0.6834,130.2,-0.20397,-0.97668,-0.067049,257.75 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.66049,-0.18784,0.72696,-40.357,-0.7226,0.10399,0.6834,129.13,-0.20397,-0.97668,-0.067049,251.05 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05396, steps = 184 shifted from previous position = 9.99 rotated from previous position = 20.5 degrees atoms outside contour = 2262, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.56092550 -0.53166240 0.63458465 201.89721759 0.77848791 -0.59951514 0.18584449 70.92659522 0.28163658 0.59826139 0.75017608 -86.01878073 Axis 0.29081299 0.24887895 0.92384364 Axis point 98.35061172 92.69261318 0.00000000 Rotation angle (degrees) 134.84023198 Shift along axis -3.10143294 > view matrix models > #6,0.66049,-0.18784,0.72696,-40.006,-0.7226,0.10399,0.6834,128.66,-0.20397,-0.97668,-0.067049,259.81 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.07375, steps = 232 shifted from previous position = 6.85 rotated from previous position = 17.9 degrees atoms outside contour = 1943, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.74629259 -0.54301442 0.38494508 251.38648943 0.65642579 -0.69620280 0.29052858 97.88167330 0.11023863 0.46950720 0.87601966 -57.75740346 Axis 0.14393778 0.22092380 0.96461111 Axis point 112.39700349 100.93081789 0.00000000 Rotation angle (degrees) 141.55799490 Shift along axis 2.09497277 > view matrix models > #6,0.66049,-0.18784,0.72696,-38.776,-0.7226,0.10399,0.6834,129.55,-0.20397,-0.97668,-0.067049,250.64 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.07513, steps = 88 shifted from previous position = 2.87 rotated from previous position = 9.69 degrees atoms outside contour = 1985, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.76523589 -0.60093746 0.23084237 269.35421235 0.64371868 -0.71784510 0.26518800 97.23918505 0.00634766 0.35152892 0.93615551 -35.85225341 Axis 0.06810921 0.17709050 0.98183506 Axis point 118.23408164 100.87294714 0.00000000 Rotation angle (degrees) 140.66586681 Shift along axis 0.36463841 > view matrix models > #6,0.66049,-0.18784,0.72696,-40.452,-0.7226,0.10399,0.6834,127.55,-0.20397,-0.97668,-0.067049,252.82 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.07115, steps = 124 shifted from previous position = 1.89 rotated from previous position = 5.79 degrees atoms outside contour = 2038, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.70690984 -0.64672681 0.28639645 264.38204486 0.70462141 -0.67914550 0.20559683 92.23937195 0.06153988 0.34713949 0.93579219 -37.95810671 Axis 0.10277413 0.16326837 0.98121400 Axis point 115.58274225 102.94958249 0.00000000 Rotation angle (degrees) 136.47979439 Shift along axis 4.98638149 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.65374,-0.23032,0.72082,-33.367,-0.66445,0.28113,0.69244,96.043,-0.36212,-0.93162,0.030747,256.1 > view matrix models > #6,-0.091081,-0.58969,0.80248,98.695,0.19546,0.77957,0.59504,-67.002,-0.97647,0.21105,0.044259,182.84 > view matrix models > #6,-0.089335,-0.62056,0.77906,105.1,0.37864,0.7023,0.60283,-80.908,-0.92122,0.34884,0.17223,143.7 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.04426, steps = 196 shifted from previous position = 13 rotated from previous position = 6.14 degrees atoms outside contour = 2570, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.75444757 -0.45385825 0.47415352 36.22522290 0.63281065 0.69473638 -0.34189478 -8.73132935 -0.17423994 0.55799108 0.81134851 -20.04509765 Axis 0.57954025 0.41757530 0.69983138 Axis point 41.59126644 53.07478525 0.00000000 Rotation angle (degrees) 50.93023294 Shift along axis 3.31979897 > view matrix models > #6,-0.13448,-0.56943,0.81097,100.59,0.3635,0.733,0.57496,-79.925,-0.92184,0.37211,0.10841,147.79 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05375, steps = 124 shifted from previous position = 4.4 rotated from previous position = 9.21 degrees atoms outside contour = 2359, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.68545093 -0.56994047 0.45312789 64.51164247 0.72041859 0.62113553 -0.30852507 -16.92140215 -0.10561291 0.53792055 0.83635363 -30.44505651 Axis 0.51573359 0.34043699 0.78620704 Axis point 64.33106263 74.45184289 0.00000000 Rotation angle (degrees) 55.14719991 Shift along axis 3.57403211 > view matrix models > #6,-0.72884,-0.4357,0.52816,189.48,0.26423,0.53266,0.80403,-66.523,-0.63165,0.72556,-0.2731,107.11 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05499, steps = 76 shifted from previous position = 1.92 rotated from previous position = 6.74 degrees atoms outside contour = 2435, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.90184778 -0.37893425 -0.20755581 76.64071143 0.27337981 0.87247868 -0.40502399 20.03740715 0.33456548 0.30852842 0.89043594 -63.34038632 Axis 0.64376387 -0.48909947 0.58851490 Axis point 0.00000000 205.20654040 -12.40597061 Rotation angle (degrees) 33.65587279 Shift along axis 2.26147457 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.05498, steps = 48 shifted from previous position = 0.0248 rotated from previous position = 0.144 degrees atoms outside contour = 2437, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 0.90282527 -0.37671180 -0.20735180 76.24688757 0.27166607 0.87346854 -0.40404239 20.04831489 0.33332281 0.30844923 0.89092928 -63.22447310 Axis 0.64496256 -0.48943014 0.58692541 Axis point 0.00000000 205.07134507 -11.86871488 Rotation angle (degrees) 33.52846202 Shift along axis 2.25608804 > view matrix models > #6,0.78289,0.60399,0.14926,-95.549,-0.0941,-0.1222,0.98804,44.015,0.61501,-0.78757,-0.038829,121.5 > view matrix models > #6,0.79504,0.48543,0.3637,-105.3,-0.18787,-0.37305,0.90859,97.445,0.57673,-0.79069,-0.2054,145.16 > view matrix models > #6,0.75975,0.17454,0.62635,-89.244,-0.35135,-0.70035,0.62134,192.66,0.54711,-0.69213,-0.47077,165.37 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #6,0.75975,0.17454,0.62635,-77.794,-0.35135,-0.70035,0.62134,175.36,0.54711,-0.69213,-0.47077,152.26 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.1606, steps = 148 shifted from previous position = 12.6 rotated from previous position = 18.4 degrees atoms outside contour = 901, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.99401473 0.00323811 0.10919811 241.20741140 0.01958709 -0.97808088 0.20730208 212.87036962 0.10747585 0.20820019 0.97216337 -35.66515130 Axis 0.05455038 0.10460789 0.99301634 Axis point 121.14214835 108.81363402 0.00000000 Rotation angle (degrees) 179.52833707 Shift along axis 0.00979704 > show #!2 models > matchmaker #2 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 SD_apo-coot-1.pdb, chain A (#5) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > hide #!2 models > select add #5 3488 atoms, 3546 bonds, 4 pseudobonds, 438 residues, 4 models selected > select subtract #5 2 models selected > view matrix models > #6,0.75975,0.17454,0.62635,-76.501,-0.35135,-0.70035,0.62134,176.77,0.54711,-0.69213,-0.47077,151.6 > fitmap #5 inMap #6 Fit molecule SD_apo-coot-1.pdb (#5) to map cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) using 3488 atoms average map value = 0.1606, steps = 64 shifted from previous position = 2.01 rotated from previous position = 0.00868 degrees atoms outside contour = 900, contour level = 0.063498 Position of SD_apo-coot-1.pdb (#5) relative to cryosparc_P78_J60_005_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.99400449 0.00322052 0.10929184 241.20055875 0.01961108 -0.97810542 0.20718397 212.88014700 0.10756618 0.20808512 0.97217802 -35.66997391 Axis 0.05459652 0.10454880 0.99302002 Axis point 121.13853906 108.81896286 0.00000000 Rotation angle (degrees) 179.52713907 Shift along axis 0.00407661 > ui mousemode right ""rotate selected models"" > show #!2 models > matchmaker #2 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 SD_apo-coot-1.pdb, chain A (#5) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > hide #!6 models > select add #5 3488 atoms, 3546 bonds, 4 pseudobonds, 438 residues, 4 models selected > select subtract #5 2 models selected > hide #!5 models > show #!5 models > hide #!2 models > show #!6 models > show #!2 models > hide #!2 models > hide #!5 models > show #!5 models > hide #!6 models > show #!2 models > show #!6 models > hide #!6 models > open ""/Users/rnom/Desktop/論文化/for figure/hAC9+Gs > model,map/AC9-Gs_SD/J242_004_volume_map_sharp_trimmed.mrc"" Opened J242_004_volume_map_sharp_trimmed.mrc as #7, grid size 292,292,292, pixel 0.79, shown at level 0.139, step 2, values float32 > surface dust #7 size 7.9 > color #7 #ffffb249 models > color #7 #ffffb255 models > color #7 #ffffb254 models > color #7 #3fffd854 models > color #7 #b9ffe654 models > color #7 #b5fffe54 models Drag select of 7 J242_004_volume_map_sharp_trimmed.mrc > view matrix models > #7,-0.8589,0.26683,-0.43714,248.52,0.18053,-0.64104,-0.74598,270.23,-0.47927,-0.71964,0.50242,207.77 > view matrix models > #7,-0.82962,0.29912,-0.47144,246.23,0.21869,-0.60282,-0.76732,264.41,-0.51371,-0.73969,0.4347,223.58 > view matrix models > #7,-0.80378,0.35561,-0.47694,237.55,0.19334,-0.60203,-0.77471,268.32,-0.56263,-0.71491,0.41515,229.23 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.80378,0.35561,-0.47694,248.83,0.19334,-0.60203,-0.77471,252.08,-0.56263,-0.71491,0.41515,183.45 > hide #!5 models > view matrix models > #7,-0.80378,0.35561,-0.47694,232.19,0.19334,-0.60203,-0.77471,243.96,-0.56263,-0.71491,0.41515,190.06 > fitmap #2 inMap #7 Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms average map value = 0.06654, steps = 140 shifted from previous position = 4.85 rotated from previous position = 8.55 degrees atoms outside contour = 5130, contour level = 0.13875 Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates: Matrix rotation and translation 0.96348241 -0.19216888 -0.18647455 65.93026295 0.17408753 0.97867059 -0.10907527 -5.75243065 0.20345803 0.07262921 0.97638610 -28.99043090 Axis 0.32160957 -0.69016487 0.64825900 Axis point 198.07460760 -0.00000000 303.76792232 Rotation angle (degrees) 16.40901215 Shift along axis 6.38062155 > view matrix models > #7,-0.80378,0.35561,-0.47694,224.8,0.19334,-0.60203,-0.77471,241.87,-0.56263,-0.71491,0.41515,176.06 > fitmap #2 inMap #7 Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms average map value = 0.0704, steps = 192 shifted from previous position = 5.17 rotated from previous position = 10.5 degrees atoms outside contour = 5081, contour level = 0.13875 Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates: Matrix rotation and translation 0.97942469 -0.13254196 -0.15218381 38.51969094 0.14397435 0.98733166 0.06669018 -36.35623404 0.14141664 -0.08722857 0.98609964 -4.17941113 Axis -0.35655192 -0.68012380 0.64054848 Axis point 92.77975956 0.00000000 260.05114793 Rotation angle (degrees) 12.46501192 Shift along axis 8.31535466 > view matrix models > #7,-0.80378,0.35561,-0.47694,216.63,0.19334,-0.60203,-0.77471,247.94,-0.56263,-0.71491,0.41515,179.48 > view matrix models > #7,-0.80378,0.35561,-0.47694,220.74,0.19334,-0.60203,-0.77471,246.96,-0.56263,-0.71491,0.41515,176.92 > view matrix models > #7,-0.80378,0.35561,-0.47694,218.99,0.19334,-0.60203,-0.77471,246.07,-0.56263,-0.71491,0.41515,185.98 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.82508,0.32047,-0.46534,223.85,0.16231,-0.65444,-0.73849,250.58,-0.5412,-0.68484,0.48795,169.84 > fitmap #2 inMap #7 Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms average map value = 0.5312, steps = 116 shifted from previous position = 5.95 rotated from previous position = 13.2 degrees atoms outside contour = 831, contour level = 0.13875 Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates: Matrix rotation and translation 0.99999999 0.00007070 0.00007818 -0.02645356 -0.00007069 0.99999999 -0.00007378 0.01482179 -0.00007818 0.00007378 0.99999999 0.00013710 Axis 0.57344071 0.60765315 -0.54947558 Axis point -42.11207468 0.00000000 292.61736079 Rotation angle (degrees) 0.00737159 Shift along axis -0.00623838 > view matrix models > #7,-0.67891,-0.043491,-0.73294,285.69,0.54975,-0.6918,-0.46817,171.57,-0.48669,-0.72077,0.49358,166.76 > view matrix models > #7,-0.80853,0.23973,-0.5374,241.21,0.25647,-0.67838,-0.68849,235.27,-0.52962,-0.6945,0.48701,169.71 > fitmap #2 inMap #7 Fit molecule hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) to map J242_004_volume_map_sharp_trimmed.mrc (#7) using 6416 atoms average map value = 0.5312, steps = 80 shifted from previous position = 2.32 rotated from previous position = 6.3 degrees atoms outside contour = 829, contour level = 0.13875 Position of hAC9-Gs_SD_trimmed_real_space_refined_025.pdb (#2) relative to J242_004_volume_map_sharp_trimmed.mrc (#7) coordinates: Matrix rotation and translation 0.99999999 -0.00000079 0.00013980 -0.02856000 0.00000083 0.99999996 -0.00026357 0.04123823 -0.00013980 0.00026357 0.99999995 -0.01486838 Axis 0.88342705 0.46856092 0.00270438 Axis point 0.00000000 56.37836338 167.02643506 Rotation angle (degrees) 0.01709426 Shift along axis -0.00594827 > show #!5 models > hide #!5 models > hide #!7 models > show #!5 models > view matrix models > #7,-0.80853,0.23973,-0.5374,241.21,0.25647,-0.67838,-0.68849,235.27,-0.52962,-0.6945,0.48701,169.71 > matchmaker #2 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 SD_apo-coot-1.pdb, chain A (#5) with hAC9-Gs_SD_trimmed_real_space_refined_025.pdb, chain A (#2), sequence alignment score = 2132.5 RMSD between 406 pruned atom pairs is 0.921 angstroms; (across all 438 pairs: 1.891) > show #!2,5 atoms > hide #!2,5 atoms > select #2/A:326 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #5/A:1028 5 atoms, 4 bonds, 1 residue, 1 model selected > hide #!5 models > select #2/A:1028 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:1025 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:326 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms ===== Log before crash end ===== Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/rnom/Desktop/240617 解析関連/240617 hAC9 phenix/240617 hAC9 whole > P78J52.pdb"" format pdb Chain information for 240617 hAC9 whole P78J52.pdb #1 --- Chain | Description A | No description available OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: 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: MacBookPro17,1 Model Number: MYDC2J/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 13日 20時間 52分 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LCD-MF235XD: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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: 1.6.3 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 ChimeraX-AtomicLibrary: 14.0.5 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: 1.2.4 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-ColorActions: 1.0.4 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: 1.8rc202405202242 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: 1.2.3 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-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 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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: 1.13.4 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-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: 3.0.4 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: 1.16.4 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 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 4.51.0 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: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 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: 3.0.43 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 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Window Toolkit duplicate all ChimeraX