id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15657 Qt fatal error: Failed to initialize graphics backend for OpenGL chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Qt fatal error: Failed to initialize graphics backend for OpenGL. Fatal Python error: Aborted Current thread 0x0000000202915240 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 861 in rapid_access_shown File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 198 in build File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 722 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util (total: 45) 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All rights reserved. > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtCENH3-nuc_Tal1_EVADE.cxs Log from Tue Jul 2 13:03:40 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_0.cif Chain information for fold_cc_hsch3_nuc_601_model_0.cif #1 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_1.cif Chain information for fold_cc_hsch3_nuc_601_model_1.cif #2 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_2.cif Chain information for fold_cc_hsch3_nuc_601_model_2.cif #3 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_3.cif Chain information for fold_cc_hsch3_nuc_601_model_3.cif #4 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_hsch3_nuc_601/fold_cc_hsch3_nuc_601_model_4.cif Chain information for fold_cc_hsch3_nuc_601_model_4.cif #5 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > hide #2 models > hide #3 models > hide #4 models > hide #5 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K Alignment identifier is 1/K > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K Alignment identifier is 1/K > ui tool show ""Show Sequence Viewer"" > sequence chain #1/J Alignment identifier is 1/J > ui tool show ""Show Sequence Viewer"" > sequence chain #1/I Alignment identifier is 1/I > select #1/I:426 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/I:426-537 908 atoms, 921 bonds, 112 residues, 1 model selected > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_cc_short_ch3_nuc_601/fold_cc_short_ch3_nuc_601_model_0.cif Chain information for fold_cc_short_ch3_nuc_601_model_0.cif #6 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > ui tool show ""Show Sequence Viewer"" > sequence chain #6/I Alignment identifier is 6/I > hide #1 models > select #6/I:62-112 427 atoms, 433 bonds, 51 residues, 1 model selected > select #6/I:57-112 461 atoms, 467 bonds, 56 residues, 1 model selected > hide #6 models > show #1 models > select #1/I:537-538 15 atoms, 14 bonds, 2 residues, 1 model selected > select #1/I:517-538 189 atoms, 193 bonds, 22 residues, 1 model selected > select #1/I 7502 atoms, 7630 bonds, 943 residues, 1 model selected > 1-425 Unknown command: 1-425 > select #1/I 7502 atoms, 7630 bonds, 943 residues, 1 model selected > 1:425 Unknown command: 1:425 > select #1/I 7502 atoms, 7630 bonds, 943 residues, 1 model selected > 1 425 Unknown command: 1 425 > select #1/I 7502 atoms, 7630 bonds, 943 residues, 1 model selected > 425 Unknown command: 425 > select #1/I: 425 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/I: 1-425 3372 atoms, 3429 bonds, 425 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #1/I: 538--943 Nothing selected > select #1/I: 538-943 3222 atoms, 3278 bonds, 406 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #1/I:517-538 189 atoms, 193 bonds, 22 residues, 1 model selected > select #1/I:538 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/I:522-538 149 atoms, 153 bonds, 17 residues, 1 model selected > select #1/E,F 2244 atoms, 2296 bonds, 278 residues, 1 model selected > show #6 models > ui tool show Matchmaker > matchmaker #6/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_cc_short_ch3_nuc_601_model_0.cif, chain E (#6), sequence alignment score = 601.8 RMSD between 97 pruned atom pairs is 0.254 angstroms; (across all 139 pairs: 15.946) > ui tool show Matchmaker > matchmaker #6/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_cc_short_ch3_nuc_601_model_0.cif, chain F (#6), sequence alignment score = 601.8 RMSD between 97 pruned atom pairs is 0.258 angstroms; (across all 139 pairs: 16.298) > matchmaker #6/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_cc_short_ch3_nuc_601_model_0.cif, chain F (#6), sequence alignment score = 601.8 RMSD between 97 pruned atom pairs is 0.258 angstroms; (across all 139 pairs: 16.298) > select clear > select #1/I 7502 atoms, 7630 bonds, 943 residues, 1 model selected > color sel red > select #1/A-H 7742 atoms, 7864 bonds, 990 residues, 1 model selected > color sel light gray > select #1/E,F 2244 atoms, 2296 bonds, 278 residues, 1 model selected > color sel light sea green > select #1/J,K 6931 atoms, 7774 bonds, 338 residues, 1 model selected > color sel light gray > select #6/J,K 6931 atoms, 7774 bonds, 338 residues, 1 model selected > color sel light gray > select #6/A-H 7742 atoms, 7864 bonds, 990 residues, 1 model selected > color sel light gray > select #6/E,F 2244 atoms, 2296 bonds, 278 residues, 1 model selected > color sel lime > select #6/I 909 atoms, 922 bonds, 112 residues, 1 model selected > color sel orange > hide #6 models > show #6 models > select add #1 23084 atoms, 24190 bonds, 2383 residues, 2 models selected > select add #6 37757 atoms, 39828 bonds, 3711 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear > select #1/I: 1-425 3372 atoms, 3429 bonds, 425 residues, 1 model selected > hide sel cartoons > select #1/I: 538-943 3222 atoms, 3278 bonds, 406 residues, 1 model selected > hide sel cartoons > save > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/HsCENH3-nuc_CCfull_CC426-537.cxs > open /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/6mup.pdb 6mup.pdb title: Cenp-A nucleosome bound by two copies of cenp-C(Cd) and two copies cenp-N(NT) [more info...] Chain information for 6mup.pdb #7 --- Chain | Description | UniProt A E | histone H3-like centromeric protein A | CENPA_HUMAN 38-139 B F | histone H4 | H4_HUMAN 8-101 C G | histone H2A/L | H2A1C_HUMAN 13-117 D H | histone H2B type 2-F | H2B2F_HUMAN 33-124 I | DNA (147-mer) | J | DNA (147-mer) | K L | centromere protein C | CENPC_HUMAN 518-537 M N | centromere protein N | CENPN_HUMAN 1-212 > open /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/6se6.pdb 6se6.pdb title: CLASS2 : cenp-A nucleosome In complex with cenp-C central region [more info...] Chain information for 6se6.pdb #8 --- Chain | Description | UniProt A E | histone H3-like centromeric protein A | CENPA_HUMAN 1-140 B F | histone H4 | H4_HUMAN 0-102 C G | histone H2A type 2-A | H2A2A_HUMAN 0-129 D H | histone H2B type 1-C/E/F/G/I | H2B1C_HUMAN 0-125 I | DNA (145-mer) | J | DNA (145-mer) | V | centromere protein C | CENPC_HUMAN 426-537 > select #7/A,E 1623 atoms, 1653 bonds, 203 residues, 1 model selected > select add #7 15803 atoms, 16702 bonds, 2 pseudobonds, 1518 residues, 2 models selected > select add #8 27871 atoms, 29582 bonds, 2 pseudobonds, 2579 residues, 3 models selected > hide sel atoms > show sel cartoons > color (#8#!7 & sel) light gray > select #7/A,E 1623 atoms, 1653 bonds, 203 residues, 1 model selected > color sel forest green > select #8/A,E 1624 atoms, 1654 bonds, 196 residues, 1 model selected > color sel forest green > ui tool show Matchmaker > matchmaker #7/A to #6/E pairing ss Parameters --- Chain pairing | ss 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_cc_short_ch3_nuc_601_model_0.cif, chain E (#6) with 6mup.pdb, chain A (#7), sequence alignment score = 440.4 RMSD between 90 pruned atom pairs is 0.526 angstroms; (across all 102 pairs: 1.235) > matchmaker #7/A to #6/E pairing ss Parameters --- Chain pairing | ss 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_cc_short_ch3_nuc_601_model_0.cif, chain E (#6) with 6mup.pdb, chain A (#7), sequence alignment score = 440.4 RMSD between 90 pruned atom pairs is 0.526 angstroms; (across all 102 pairs: 1.235) > select #7/K,L 343 atoms, 351 bonds, 39 residues, 1 model selected > color sel magenta > select clear > hide #8 models > save > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/HsCENH3-nuc_CCfull_CC426-537.cxs > hide #2-5 target m > close #2-5 > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601/fold_ch3_nuc_601_model_0.cif Chain information for fold_ch3_nuc_601_model_0.cif #2 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . > ui tool show Matchmaker > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_hsch3_nuc_601/fold_hsch3_nuc_601_model_0.cif Chain information for fold_hsch3_nuc_601_model_0.cif #3 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . > hide #6 models > hide #!7 models > hide #1 models > select #2,3 30170 atoms, 32104 bonds, 2784 residues, 2 models selected > color sel light gray > hide sel atoms > show sel cartoons > select #2,3/E,F 4996 atoms, 5098 bonds, 632 residues, 2 models selected > color sel cyan > show #1 models > ui tool show Matchmaker > matchmaker #2/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_model_0.cif, chain E (#2), sequence alignment score = 96.8 RMSD between 50 pruned atom pairs is 0.967 angstroms; (across all 89 pairs: 14.355) > matchmaker #3/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 118.7 RMSD between 50 pruned atom pairs is 1.037 angstroms; (across all 90 pairs: 13.968) > matchmaker #3/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 118.7 RMSD between 50 pruned atom pairs is 1.037 angstroms; (across all 90 pairs: 13.968) > select add #3 17425 atoms, 18440 bonds, 1682 residues, 2 models selected > select add #2 30170 atoms, 32104 bonds, 2784 residues, 2 models selected > select subtract #3 15497 atoms, 16466 bonds, 1456 residues, 1 model selected > select subtract #2 Nothing selected > hide #2 models > hide #3 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > ui tool show Matchmaker > matchmaker #2/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_model_0.cif, chain E (#2), sequence alignment score = 233.6 RMSD between 86 pruned atom pairs is 0.451 angstroms; (across all 114 pairs: 17.583) > matchmaker #2/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_model_0.cif, chain F (#2), sequence alignment score = 233.6 RMSD between 86 pruned atom pairs is 0.453 angstroms; (across all 114 pairs: 16.825) > matchmaker #2/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_model_0.cif, chain F (#2), sequence alignment score = 233.6 RMSD between 86 pruned atom pairs is 0.453 angstroms; (across all 114 pairs: 16.825) > show #3 models > hide #1 models > ui tool show Matchmaker > matchmaker #3/F to #2/F pairing ss Parameters --- Chain pairing | ss 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_ch3_nuc_601_model_0.cif, chain F (#2) with fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 320.9 RMSD between 80 pruned atom pairs is 0.461 angstroms; (across all 134 pairs: 35.917) > matchmaker #3/F to #2/F pairing ss Parameters --- Chain pairing | ss 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_ch3_nuc_601_model_0.cif, chain F (#2) with fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 320.9 RMSD between 80 pruned atom pairs is 0.461 angstroms; (across all 134 pairs: 35.917) > hide #2 models > show #1 models > save > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtvsHsCENH3-nuc_CCfull_CC426-537.cxs > hide #3 models > show #3 models > hide #1 models > show #1 models > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_atcc_full/fold_ch3_nuc_601_atcc_full_model_0.cif Chain information for fold_ch3_nuc_601_atcc_full_model_0.cif #4 --- Chain | Description A B | . C D | . E F | . G H | . I | . J | . K | . > select #4 21050 atoms, 22126 bonds, 2161 residues, 1 model selected > color sel light gray > select #4/E,f 2752 atoms, 2802 bonds, 354 residues, 1 model selected > select #4/E,F 2752 atoms, 2802 bonds, 354 residues, 1 model selected > color sel cyan > select #4 21050 atoms, 22126 bonds, 2161 residues, 1 model selected > hide sel atoms > show sel cartoons > select #4/K 3484 atoms, 3911 bonds, 169 residues, 1 model selected > select #4/I 5553 atoms, 5660 bonds, 705 residues, 1 model selected > color sel yellow > ui tool show Matchmaker > matchmaker #4/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs: 15.366) > matchmaker #4/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs: 14.027) > matchmaker #4/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs: 14.027) > ui tool show Matchmaker > matchmaker #4/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs: 14.027) > matchmaker #3/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.210 angstroms; (across all 139 pairs: 24.773) > matchmaker #3/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs: 24.430) > matchmaker #3/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs: 24.430) > hide #4 models > select add #4 21050 atoms, 22126 bonds, 2161 residues, 1 model selected > select subtract #4 Nothing selected > ui tool show Matchmaker > matchmaker #3/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs: 24.430) > matchmaker #3/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.210 angstroms; (across all 139 pairs: 24.773) > select #1/E 1122 atoms, 1148 bonds, 139 residues, 1 model selected > select #3/E 1122 atoms, 1148 bonds, 139 residues, 1 model selected > hide #3 models > show #3 models > hide #1 models > show #1 models > ui tool show Matchmaker > matchmaker #3/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs: 24.430) > matchmaker #3/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs: 24.430) > ui tool show Matchmaker > matchmaker #3/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 118.7 RMSD between 50 pruned atom pairs is 1.037 angstroms; (across all 90 pairs: 13.968) > ui tool show Matchmaker > matchmaker #3/F to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 118.7 RMSD between 49 pruned atom pairs is 1.012 angstroms; (across all 90 pairs: 13.942) > matchmaker #3/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain E (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.222 angstroms; (across all 139 pairs: 24.430) > matchmaker #3/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_hsch3_nuc_601_model_0.cif, chain F (#3), sequence alignment score = 604.8 RMSD between 8 pruned atom pairs is 1.210 angstroms; (across all 139 pairs: 24.773) > matchmaker #3/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain A (#3), sequence alignment score = 578.1 RMSD between 106 pruned atom pairs is 0.202 angstroms; (across all 129 pairs: 4.154) > matchmaker #3/B to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain B (#3), sequence alignment score = 578.1 RMSD between 106 pruned atom pairs is 0.202 angstroms; (across all 129 pairs: 4.327) > matchmaker #3/B to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_hsch3_nuc_601_model_0.cif, chain B (#3), sequence alignment score = 578.1 RMSD between 106 pruned atom pairs is 0.202 angstroms; (across all 129 pairs: 4.327) > select add #3 14673 atoms, 15638 bonds, 1328 residues, 1 model selected > select subtract #3 Nothing selected > show #4 models > hide #3 models > hide #1 models > show #3 models > hide #3 models > show #1 models > ui tool show Matchmaker > matchmaker #4/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 103.6 RMSD between 48 pruned atom pairs is 0.938 angstroms; (across all 96 pairs: 18.224) > matchmaker #4/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 103.6 RMSD between 48 pruned atom pairs is 0.938 angstroms; (across all 96 pairs: 18.224) > ui tool show Matchmaker > matchmaker #4/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs: 15.366) > ui tool show Matchmaker > matchmaker #4/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs: 14.027) > matchmaker #4/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs: 14.027) > ui tool show Matchmaker > matchmaker #4/E to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain E (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.440 angstroms; (across all 135 pairs: 14.027) > matchmaker #4/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs: 15.366) > matchmaker #4/F to #1/E pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain E (#1) with fold_ch3_nuc_601_atcc_full_model_0.cif, chain F (#4), sequence alignment score = 308 RMSD between 85 pruned atom pairs is 0.426 angstroms; (across all 135 pairs: 15.366) > save > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtvsHsCENH3-nuc_CCfull_CC426-537.cxs > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_tal1_dimer/fold_tal1_dimer_model_0.cif Chain information for fold_tal1_dimer_model_0.cif #5 --- Chain | Description A B | . > close #5 > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_tal1_integrase_long_dimer/fold_tal1_integrase_long_dimer_model_0.cif Chain information for fold_tal1_integrase_long_dimer_model_0.cif #5 --- Chain | Description A | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_evade_integrase_long_dimer/fold_evade_integrase_long_dimer_model_0.cif Chain information for fold_evade_integrase_long_dimer_model_0.cif #9 --- Chain | Description A | . > hide #1 models > hide #4 models > ui tool show Matchmaker > matchmaker #9/A to #5/A pairing ss Parameters --- Chain pairing | ss 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_tal1_integrase_long_dimer_model_0.cif, chain A (#5) with fold_evade_integrase_long_dimer_model_0.cif, chain A (#9), sequence alignment score = 2141.7 RMSD between 249 pruned atom pairs is 0.422 angstroms; (across all 510 pairs: 28.859) > matchmaker #9/A to #5/A pairing ss Parameters --- Chain pairing | ss 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_tal1_integrase_long_dimer_model_0.cif, chain A (#5) with fold_evade_integrase_long_dimer_model_0.cif, chain A (#9), sequence alignment score = 2141.7 RMSD between 249 pruned atom pairs is 0.422 angstroms; (across all 510 pairs: 28.859) > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A Alignment identifier is 5/A > select #5/A:55-56 16 atoms, 16 bonds, 2 residues, 1 model selected > select #5/A:55-108 419 atoms, 432 bonds, 54 residues, 1 model selected > select #5/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:56-310 2057 atoms, 2111 bonds, 255 residues, 1 model selected > select #5/A:6-56 381 atoms, 389 bonds, 51 residues, 1 model selected > select #5/A:6-107 778 atoms, 799 bonds, 102 residues, 1 model selected > select #5/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:56-496 3542 atoms, 3633 bonds, 441 residues, 1 model selected > select #5/A:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #5/A:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer/fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif #10 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > select add #10 24217 atoms, 25406 bonds, 2550 residues, 2 models selected > select add #5 28445 atoms, 29738 bonds, 3082 residues, 2 models selected > select subtract #5 24129 atoms, 25314 bonds, 2540 residues, 1 model selected > hide sel atoms > show sel cartoons > color sel light gray > select #3/K Nothing selected > select #10/K 3447 atoms, 3863 bonds, 169 residues, 1 model selected > select #10/I,J 8632 atoms, 8848 bonds, 1084 residues, 1 model selected > color sel hot pink > hide #9 models > color sel cornflower blue > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #10/I Alignment identifier is 10/I > select #10/I:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #10/I:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > select #5/A:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #5/A:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > select #10/I:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #10/I:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > hide #5 models > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/E,F 2752 atoms, 2802 bonds, 354 residues, 1 model selected > color sel lime > select clear > show #5 models > hide #10 models > select #5/A:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #5/A:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > show #10 models > hide #5 models > select add #5 4316 atoms, 4424 bonds, 542 residues, 1 model selected > select subtract #5 Nothing selected > select #10/I:481-482 18 atoms, 19 bonds, 2 residues, 1 model selected > select #10/I:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > show #5 models > hide #10 models > select #5/A:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #5/A:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > show #10 models > hide #5 models > select add #5 4316 atoms, 4424 bonds, 542 residues, 1 model selected > select subtract #5 Nothing selected > select #10/I:481 11 atoms, 11 bonds, 1 residue, 1 model selected > select #10/I:481-490 88 atoms, 92 bonds, 10 residues, 1 model selected > select #10/I:490-491 18 atoms, 17 bonds, 2 residues, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #10 24129 atoms, 25314 bonds, 2540 residues, 1 model selected > select subtract #10 Nothing selected > select > #10/I:59-68,74-80,88-90,92-98,155-172,186-189,191-199,212-235,240-256,260-262,267-272,294-296,349-354,359-372,484-486,490-492,513-523,531-536,538-541 1335 atoms, 1350 bonds, 158 residues, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > show #4 models > hide #10 models > select add #10 24129 atoms, 25314 bonds, 2540 residues, 1 model selected > select subtract #10 Nothing selected > show #1 models > hide #4 models > show #!7 models > hide #!7 models > show #4 models > show #10 models > hide #4 models > hide #10 models > hide #1 models > show #5 models > show #9 models > show #10 models > hide #9 models > hide #5 models > show #5 models > hide #10 models > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A Alignment identifier is 5/A > color #5 #9437ffff > select #5/A:479-481 28 atoms, 28 bonds, 3 residues, 1 model selected > select #5/A:479-481 28 atoms, 28 bonds, 3 residues, 1 model selected > select #5/A:480 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:480-492 116 atoms, 121 bonds, 13 residues, 1 model selected > color #5 #ff2600ff > color #5 #531b93ff > color #5 #9437ffff > color #5 #d783ffff > color sel red > select clear > show #10 models > hide #5 models > ui tool show ""Show Sequence Viewer"" > sequence chain #10/I Alignment identifier is 10/I > select #10/I:480 9 atoms, 8 bonds, 1 residue, 1 model selected > select #10/I:480-492 116 atoms, 121 bonds, 13 residues, 1 model selected > color sel red > show #5 models > show #1 models > hide #1 models > ui tool show Matchmaker > matchmaker #10/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain A (#10), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.214 angstroms; (across all 122 pairs: 4.250) > matchmaker #10/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain A (#10), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.214 angstroms; (across all 122 pairs: 4.250) > show #1 models > ui tool show Matchmaker > matchmaker #10/E to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain E (#10), sequence alignment score = 93.8 RMSD between 50 pruned atom pairs is 0.979 angstroms; (across all 89 pairs: 14.792) > matchmaker #10/B to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain B (#10), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.226 angstroms; (across all 122 pairs: 4.155) > matchmaker #10/B to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain B (#10), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.226 angstroms; (across all 122 pairs: 4.155) > hide #5 models > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/I 7502 atoms, 7630 bonds, 943 residues, 1 model selected > color sel orange > select #10/I 4316 atoms, 4424 bonds, 542 residues, 1 model selected > ui tool show Matchmaker > matchmaker #5/A to #10/I pairing ss Parameters --- Chain pairing | ss 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_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain I (#10) with fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5), sequence alignment score = 2729.1 RMSD between 235 pruned atom pairs is 0.452 angstroms; (across all 542 pairs: 53.406) > matchmaker #5/A to #10/I pairing ss Parameters --- Chain pairing | ss 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_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain I (#10) with fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5), sequence alignment score = 2729.1 RMSD between 235 pruned atom pairs is 0.452 angstroms; (across all 542 pairs: 53.406) > matchmaker #5/A to #10/I pairing ss Parameters --- Chain pairing | ss 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_ch3_nuc_601_tal1_int_long_dimer_model_0.cif, chain I (#10) with fold_tal1_integrase_long_dimer_model_0.cif, chain A (#5), sequence alignment score = 2729.1 RMSD between 235 pruned atom pairs is 0.452 angstroms; (across all 542 pairs: 53.406) > hide #1 models > show #5 models > select clear > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_evade_int_long_dimer/fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif Chain information for fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif #11 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > select add #11 23779 atoms, 24954 bonds, 2476 residues, 1 model selected > hide sel atoms > show sel cartoons > ui tool show Matchmaker > matchmaker #11/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif, chain A (#11), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.193 angstroms; (across all 122 pairs: 4.436) > matchmaker #11/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_evade_int_long_dimer_model_0.cif, chain A (#11), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.193 angstroms; (across all 122 pairs: 4.436) > select subtract #11 Nothing selected > show #1 models > select add #11 23779 atoms, 24954 bonds, 2476 residues, 1 model selected > color sel light gray > select #11/E,F 2752 atoms, 2802 bonds, 354 residues, 1 model selected > color sel lime > hide #1 models > hide #11 models > show #11 models > hide #11 models > show #11 models > hide #11 models > show #11 models > hide #5 models > hide #10 models > select #11/I,J 8282 atoms, 8488 bonds, 1020 residues, 1 model selected > color sel magenta > select clear > show #10 models > select #11/I 4141 atoms, 4244 bonds, 510 residues, 1 model selected > select #10/I 4316 atoms, 4424 bonds, 542 residues, 1 model selected > select #10/J 4316 atoms, 4424 bonds, 542 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel cartoons > select #11/J 4141 atoms, 4244 bonds, 510 residues, 1 model selected > select #11/I 4141 atoms, 4244 bonds, 510 residues, 1 model selected > hide sel cartoons > select #11/J 4141 atoms, 4244 bonds, 510 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #11/J Alignment identifier is 11/J > color sel cyan > select #11/J:455 11 atoms, 10 bonds, 1 residue, 1 model selected > select #11/J:455-459 49 atoms, 48 bonds, 5 residues, 1 model selected > select #11/J:460 11 atoms, 11 bonds, 1 residue, 1 model selected > select #11/J:455-460 60 atoms, 60 bonds, 6 residues, 1 model selected > color sel hot pink > select #11/J:458 9 atoms, 8 bonds, 1 residue, 1 model selected > select #11/J:458 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > set bgColor white > lighting soft > lighting simple > lighting soft > lighting full > lighting shadows false > graphics silhouettes true > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > select #5/A:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:490 11 atoms, 10 bonds, 1 residue, 1 model selected > style #10-11 stick Changed 47908 atom styles > show #10-11 atoms > undo > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/I:490 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > show sel atoms > lighting full > select clear > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_0.cif Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_0.cif #12 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > select add #12 24125 atoms, 25310 bonds, 2540 residues, 1 model selected > hide sel atoms > show sel cartoons > color sel light gray > ui tool show Matchmaker > matchmaker #12/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_0.cif, chain A (#12), sequence alignment score = 446.8 RMSD between 102 pruned atom pairs is 0.234 angstroms; (across all 122 pairs: 4.401) > select subtract #12 Nothing selected > select add #10 24129 atoms, 25314 bonds, 2540 residues, 1 model selected > select subtract #10 Nothing selected > select add #11 23779 atoms, 24954 bonds, 2476 residues, 1 model selected > select subtract #11 Nothing selected > hide #11 models > select #12/J 4314 atoms, 4422 bonds, 542 residues, 1 model selected > select #12/I 4314 atoms, 4422 bonds, 542 residues, 1 model selected > select add #12 24125 atoms, 25310 bonds, 2540 residues, 1 model selected > select subtract #12 Nothing selected > select add #10 24129 atoms, 25314 bonds, 2540 residues, 1 model selected > hide #10 models > select subtract #10 Nothing selected > select add #12 24125 atoms, 25310 bonds, 2540 residues, 1 model selected > show #10 models > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_1.cif Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_1.cif #13 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_2.cif Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_2.cif #14 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif #15 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_ch3_nuc_601_tal1_int_long_dimer_r892k/fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif Chain information for fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif #16 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > select subtract #12 Nothing selected > select add #13 24125 atoms, 25310 bonds, 2540 residues, 1 model selected > select add #14 48250 atoms, 50620 bonds, 5080 residues, 2 models selected > select add #15 72375 atoms, 75930 bonds, 7620 residues, 3 models selected > select add #16 96500 atoms, 101240 bonds, 10160 residues, 4 models selected > hide sel atoms > show sel cartoons > ui tool show Matchmaker > matchmaker #13/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_1.cif, chain A (#13), sequence alignment score = 437.8 RMSD between 102 pruned atom pairs is 0.222 angstroms; (across all 122 pairs: 4.382) > matchmaker #14/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_2.cif, chain A (#14), sequence alignment score = 434.2 RMSD between 102 pruned atom pairs is 0.229 angstroms; (across all 122 pairs: 4.676) > matchmaker #15/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif, chain A (#15), sequence alignment score = 423.4 RMSD between 102 pruned atom pairs is 0.282 angstroms; (across all 122 pairs: 4.897) > matchmaker #16/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif, chain A (#16), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.224 angstroms; (across all 122 pairs: 4.142) > matchmaker #16/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_4.cif, chain A (#16), sequence alignment score = 436 RMSD between 102 pruned atom pairs is 0.224 angstroms; (across all 122 pairs: 4.142) > hide #13 models > hide #14 models > hide #15 models > select subtract #13 72375 atoms, 75930 bonds, 7620 residues, 3 models selected > select subtract #14 48250 atoms, 50620 bonds, 5080 residues, 2 models selected > select subtract #15 24125 atoms, 25310 bonds, 2540 residues, 1 model selected > hide #16 models > select subtract #16 Nothing selected > show #16 models > hide #12 models > show #15 models > hide #16 models > ui tool show Matchmaker > matchmaker #15/B to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif, chain B (#15), sequence alignment score = 423.4 RMSD between 102 pruned atom pairs is 0.287 angstroms; (across all 122 pairs: 4.662) > matchmaker #15/B to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_ch3_nuc_601_tal1_int_long_dimer_r892k_model_3.cif, chain B (#15), sequence alignment score = 423.4 RMSD between 102 pruned atom pairs is 0.287 angstroms; (across all 122 pairs: 4.662) > show #14 models > hide #15 models > show #13 models > hide #14 models > show #12 models > hide #13 models > show #11 models > hide #12 models > hide #11 models > show #11 models > hide #10 models > show #10 models > show #12 models > hide #11 models > show #11 models > hide #12 models > hide #10 models > select #11/A 966 atoms, 978 bonds, 131 residues, 1 model selected > select #11/A,B 1932 atoms, 1956 bonds, 262 residues, 1 model selected > color sel red > hide #11 models > show #11 models > show #9 models > hide #9 models > show #10 models > hide #10 models > hide #11 models > show #10 models > save > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtCENH3-nuc_Tal1_EVADE.cxs > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_h3_nuc_601_tal1_int_long_dimer/fold_h3_nuc_601_tal1_int_long_dimer_model_0.cif Chain information for fold_h3_nuc_601_tal1_int_long_dimer_model_0.cif #17 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > select add #12 26057 atoms, 27266 bonds, 2802 residues, 2 models selected > select add #11 47904 atoms, 50264 bonds, 5016 residues, 2 models selected > select subtract #12 23779 atoms, 24954 bonds, 2476 residues, 1 model selected > select subtract #11 Nothing selected > select add #17 23509 atoms, 24672 bonds, 2456 residues, 1 model selected > hide sel atoms > show sel cartoons > color sel light gray > select #11/I,J 8282 atoms, 8488 bonds, 1020 residues, 1 model selected > close #13-16 > select #17/I,J 8632 atoms, 8848 bonds, 1084 residues, 1 model selected > color sel hot pink > select #17/E,F 2132 atoms, 2160 bonds, 270 residues, 1 model selected > color sel cornflower blue > ui tool show Matchmaker No reference and/or match structure/chain chosen > matchmaker #17/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_h3_nuc_601_tal1_int_long_dimer_model_0.cif, chain A (#17), sequence alignment score = 441.4 RMSD between 102 pruned atom pairs is 0.238 angstroms; (across all 122 pairs: 4.370) > select clear > select #17/J 4316 atoms, 4424 bonds, 542 residues, 1 model selected > select #17/I 4316 atoms, 4424 bonds, 542 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #17/B:112 8 atoms, 7 bonds, 1 residue, 1 model selected > open > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/fold_h3_nuc_601_evade_int_long_dimer/fold_h3_nuc_601_evade_int_long_dimer_model_0.cif Chain information for fold_h3_nuc_601_evade_int_long_dimer_model_0.cif #13 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K | . L | . > select add #17 23509 atoms, 24672 bonds, 2456 residues, 1 model selected > select add #13 46668 atoms, 48984 bonds, 4848 residues, 2 models selected > select subtract #17 23159 atoms, 24312 bonds, 2392 residues, 1 model selected > hide sel atoms > show sel cartoons > color sel light gray > ui tool show Matchmaker > matchmaker #13/A to #1/A pairing ss Parameters --- Chain pairing | ss 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_cc_hsch3_nuc_601_model_0.cif, chain A (#1) with fold_h3_nuc_601_evade_int_long_dimer_model_0.cif, chain A (#13), sequence alignment score = 450.4 RMSD between 102 pruned atom pairs is 0.222 angstroms; (across all 122 pairs: 4.421) > show #11 models > hide #10 models > hide #17 models > select #13/I 4141 atoms, 4244 bonds, 510 residues, 1 model selected > hide sel cartoons > select #13/A,B 1932 atoms, 1956 bonds, 262 residues, 1 model selected > hide #11 models > show #11 models > select add #13 23159 atoms, 24312 bonds, 2392 residues, 1 model selected > select subtract #13 Nothing selected > hide #11 models > show #11 models > hide #13 models > select #13/A,B 1932 atoms, 1956 bonds, 262 residues, 1 model selected > select #11/A,B 1932 atoms, 1956 bonds, 262 residues, 1 model selected > color sel light gray > select clear > show #13 models > select #11/E,F 2752 atoms, 2802 bonds, 354 residues, 1 model selected > color sel cornflower blue > show #17 models > hide #11 models > select add #11 23779 atoms, 24954 bonds, 2476 residues, 1 model selected > select subtract #11 Nothing selected > hide #17 models > show #17 models > show #11 models > hide #11 models > show #11 models > hide #11 models > select #11/E,F 2752 atoms, 2802 bonds, 354 residues, 1 model selected > color #13,17 lime > show #11 models > hide #13 models > hide #17 models > undo [Repeated 7 time(s)] > hide #17 models > hide #13 models > show #13 models > show #11 models > hide #13 models > show #10 models > hide #11 models > show #11 models > select #11/E,F 2752 atoms, 2802 bonds, 354 residues, 1 model selected > color sel lime > hide #10 models > hide #11 models > show #11 models > select clear > show #12 models > hide #11 models > show #11 models > hide #11 models > show #13 models > hide #12 models > select #13/E,F 2132 atoms, 2160 bonds, 270 residues, 1 model selected > color sel cornflower blue > select #17/E,F 2132 atoms, 2160 bonds, 270 residues, 1 model selected > color #13 cornflower blue > show #17 models > hide #17 models > select #17/E,F 2132 atoms, 2160 bonds, 270 residues, 1 model selected > show #17 models > hide #13 models > show #13 models > hide #17 models > select add #17 23509 atoms, 24672 bonds, 2456 residues, 1 model selected > select subtract #17 Nothing selected > select #13 23159 atoms, 24312 bonds, 2392 residues, 1 model selected > color sel light gray > select #13/E,F 2132 atoms, 2160 bonds, 270 residues, 1 model selected > color sel cornflower blue > select add #13 23159 atoms, 24312 bonds, 2392 residues, 1 model selected > select subtract #13 Nothing selected > show #17 models > hide #13 models > show #13 models > hide #17 models > select #13/I 4141 atoms, 4244 bonds, 510 residues, 1 model selected > select #13/J 4141 atoms, 4244 bonds, 510 residues, 1 model selected > color sel orange > show #17 models > select add #13 23159 atoms, 24312 bonds, 2392 residues, 1 model selected > select subtract #13 Nothing selected > hide #17 models > show #17 models > hide #17 models > show #17 models > show #12 models > hide #13 models > hide #12 models > show #10 models > show #13 models > show #9 models > hide #17 models > hide #10 models > hide #9 models > show #11 models > show #17 models > hide #17 models > save > /Users/AkihisaOsakabe/Documents/研究/プロジェクト/塚原さん_Tal1/AF3/AtCENH3-nuc_Tal1_EVADE.cxs ——— End of log from Tue Jul 2 13:03:40 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11C000D7J/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 2分 2秒 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 DELL P2419HC: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 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1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect assigned normal Window Toolkit Tom Goddard all ChimeraX