id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20080 Crash on Mac waking from sleep chengtao.xu@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000001f34f2140 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 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, 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UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260302 update/STAND-Cas3.cxs"" Log from Mon Mar 2 20:22:33 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/xuchengtao/Documents/Building models undergoing/20250505 I-E > apo/RealSpaceRefine_2/MERGE_real_space_refined_002.pdb"" Chain information for MERGE_real_space_refined_002.pdb #1 --- Chain | Description A | No description available B | No description available C D E F G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available > show atoms > save /Users/xuchengtao/Desktop/image477.png supersample 3 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for MERGE_real_space_refined_002.pdb_A SES surface #1.1: minimum, -13.00, mean -0.41, maximum 14.96 Coulombic values for MERGE_real_space_refined_002.pdb_B SES surface #1.2: minimum, -22.09, mean -10.50, maximum -0.21 Coulombic values for MERGE_real_space_refined_002.pdb_C SES surface #1.3: minimum, -18.27, mean -1.74, maximum 15.13 Coulombic values for MERGE_real_space_refined_002.pdb_D SES surface #1.4: minimum, -19.65, mean -1.75, maximum 13.73 Coulombic values for MERGE_real_space_refined_002.pdb_E SES surface #1.5: minimum, -29.28, mean -1.67, maximum 27.70 Coulombic values for MERGE_real_space_refined_002.pdb_F SES surface #1.6: minimum, -20.31, mean -1.66, maximum 19.52 Coulombic values for MERGE_real_space_refined_002.pdb_G SES surface #1.7: minimum, -19.25, mean -1.74, maximum 16.40 Coulombic values for MERGE_real_space_refined_002.pdb_H SES surface #1.8: minimum, -15.94, mean -1.67, maximum 15.97 Coulombic values for MERGE_real_space_refined_002.pdb_I SES surface #1.9: minimum, -23.17, mean -1.54, maximum 15.21 Coulombic values for MERGE_real_space_refined_002.pdb_J SES surface #1.10: minimum, -20.01, mean 0.54, maximum 12.18 Coulombic values for MERGE_real_space_refined_002.pdb_K SES surface #1.11: minimum, -19.21, mean 0.51, maximum 12.49 Coulombic values for MERGE_real_space_refined_002.pdb_L SES surface #1.12: minimum, -21.10, mean 2.18, maximum 14.79 To also show corresponding color key, enter the above coulombic command and add key true > hide atoms > hide #!1 models > open ""/Users/xuchengtao/Documents/Building models undergoing/20250830 I-E > STAND/merged_251009_real_space_refined_006_real_space_refined_002_best.pdb"" Chain information for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb #2 --- Chain | Description A | No description available B | No description available C D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available > mmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker MERGE_real_space_refined_002.pdb, chain H (#1) with merged_251009_real_space_refined_006_real_space_refined_002_best.pdb, chain J (#2), sequence alignment score = 2446.3 RMSD between 329 pruned atom pairs is 0.567 angstroms; (across all 500 pairs: 4.870) > coulombic #!2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_A SES surface #2.2: minimum, -22.89, mean -2.13, maximum 12.44 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_B SES surface #2.3: minimum, -19.22, mean -1.57, maximum 17.26 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_C SES surface #2.4: minimum, -17.81, mean -1.38, maximum 17.52 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_D SES surface #2.5: minimum, -19.84, mean -1.44, maximum 17.37 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_E SES surface #2.6: minimum, -25.54, mean -1.07, maximum 15.87 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_F SES surface #2.7: minimum, -30.85, mean -1.04, maximum 16.78 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_G SES surface #2.8: minimum, -12.95, mean 1.67, maximum 12.27 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_H SES surface #2.9: minimum, -11.77, mean 2.20, maximum 12.43 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_I SES surface #2.10: minimum, -16.36, mean -0.43, maximum 13.84 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_J SES surface #2.11: minimum, -18.88, mean -1.15, maximum 12.85 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_K SES surface #2.12: minimum, -13.74, mean 2.48, maximum 15.14 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_L SES surface #2.13: minimum, -15.05, mean -7.76, maximum -0.49 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_M SES surface #2.14: minimum, -22.56, mean -10.24, maximum -1.10 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_N SES surface #2.15: minimum, -23.46, mean -11.85, maximum -2.57 To also show corresponding color key, enter the above coulombic command and add key true > hide #!2 atoms > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > set bgColor white > hide #!2 models > open 5u0a 5u0a title: CRISPR RNA-guided surveillance complex [more info...] Chain information for 5u0a #3 --- Chain | Description | UniProt A | CRISPR-associated protein, Cse3 family | Q47PJ5_THEFY 1-232 C | CRISPR-associated protein, Cse1 family | Q47PJ1_THEFY 1-549 D E F G H I | CRISPR-associated protein, Cse4 family | Q47PJ3_THEFY 1-373 J L | Cse2 | Q47PJ2_THEFY 1-244 K | crRNA | M | Target Strand | N | CRISPR-associated protein, Cas5e family | Q47PJ4_THEFY 1-254 O | Nontarget Strand | > open 5u07 Summary of feedback from opening 5u07 fetched from pdb --- note | Fetching compressed mmCIF 5u07 from http://files.rcsb.org/download/5u07.cif 5u07 title: CRISPR RNA-guided surveillance complex [more info...] Chain information for 5u07 #4 --- Chain | Description | UniProt A | CRISPR-associated protein, Cse3 family | Q47PJ5_THEFY 1-232 B J | Cse2 | Q47PJ2_THEFY 1-244 C | CRISPR-associated protein, Cse1 family | Q47PJ1_THEFY 1-549 D E F G H I | CRISPR-associated protein, Cse4 family | Q47PJ3_THEFY 1-373 K | crRNA | M | Target Strand | N | CRISPR-associated protein, Cas5e family | Q47PJ4_THEFY 1-254 O | Nontarget Strand | > close #3-4 > open 6c66 6c66 title: CRISPR RNA-guided surveillance complex, pre-nicking [more info...] Chain information for 6c66 #3 --- Chain | Description | UniProt A | CRISPR-associated protein, Cse1 family | Q47PJ1_THEFY 1-549 B C D E F H | CRISPR-associated protein, Cse4 family | Q47PJ3_THEFY 1-373 G | CRISPR-associated helicase, Cas3 family | Q47PJ0_THEFY 1-944 I K | Uncharacterized protein | Q47PJ2_THEFY 1-244 J | crRNA | L | Target strand | M | CRISPR-associated protein, Cas5e family | Q47PJ4_THEFY 1-254 N | Nontarget strand | O | CRISPR-associated protein, Cse3 family | Q47PJ5_THEFY 1-232 Non-standard residues in 6c66 #3 --- FE — Fe (III) ion > hide #!3 atoms > show #!3 cartoons > open 5u0a 5u0a title: CRISPR RNA-guided surveillance complex [more info...] Chain information for 5u0a #4 --- Chain | Description | UniProt A | CRISPR-associated protein, Cse3 family | Q47PJ5_THEFY 1-232 C | CRISPR-associated protein, Cse1 family | Q47PJ1_THEFY 1-549 D E F G H I | CRISPR-associated protein, Cse4 family | Q47PJ3_THEFY 1-373 J L | Cse2 | Q47PJ2_THEFY 1-244 K | crRNA | M | Target Strand | N | CRISPR-associated protein, Cas5e family | Q47PJ4_THEFY 1-254 O | Nontarget Strand | > mmaker #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 6c66, chain A (#3) with 5u0a, chain C (#4), sequence alignment score = 2681.6 RMSD between 494 pruned atom pairs is 0.680 angstroms; (across all 503 pairs: 0.759) > hide #!3-4 atoms > show #!3-4 cartoons > color #3 #aea7d9ff > color #3 #9a7fd9ff > color #4 #d99b26ff > open 5u07 5u07 title: CRISPR RNA-guided surveillance complex [more info...] Chain information for 5u07 #5 --- Chain | Description | UniProt A | CRISPR-associated protein, Cse3 family | Q47PJ5_THEFY 1-232 B J | Cse2 | Q47PJ2_THEFY 1-244 C | CRISPR-associated protein, Cse1 family | Q47PJ1_THEFY 1-549 D E F G H I | CRISPR-associated protein, Cse4 family | Q47PJ3_THEFY 1-373 K | crRNA | M | Target Strand | N | CRISPR-associated protein, Cas5e family | Q47PJ4_THEFY 1-254 O | Nontarget Strand | > mmaker #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 6c66, chain A (#3) with 5u07, chain C (#5), sequence alignment score = 2643.2 RMSD between 346 pruned atom pairs is 0.711 angstroms; (across all 493 pairs: 4.435) > hide #!3-5 atoms > show #!3-5 cartoons > color #5 #daef4fff > color #5 #e2ef3dff > hide #!3 models > hide #!4 models > hide #!5 models > show #!3 models > show #!4 models > hide #3.3 models > select add #3 36255 atoms, 37323 bonds, 154 pseudobonds, 4419 residues, 4 models selected > cartoon style (#!3 & sel) modeHelix tube sides 20 > select subtract #3 Nothing selected > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!5 models > hide #!3 models > show #!1 models > mmaker #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 6c66, chain D (#3) with merged_251009_real_space_refined_006_real_space_refined_002_best.pdb, chain A (#2), sequence alignment score = 642.7 RMSD between 188 pruned atom pairs is 0.867 angstroms; (across all 346 pairs: 12.930) > mmaker #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 6c66, chain E (#3) with MERGE_real_space_refined_002.pdb, chain D (#1), sequence alignment score = 606.6 RMSD between 185 pruned atom pairs is 0.990 angstroms; (across all 346 pairs: 12.902) > hide #!1,5 surfaces > show #!1,5 cartoons > color #1 #6dd704ff > hide #!1 models > show #!2 models > hide #!2,5 surfaces > show #!2,5 cartoons > ui mousemode right ""translate selected models"" > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 2 models selected > view matrix models > #2,-0.48483,0.11946,0.86641,124.78,-0.80986,-0.43537,-0.39316,399.14,0.33024,-0.89229,0.30783,199.59 > view matrix models > #2,-0.68354,0.34322,0.64419,152.49,-0.50999,-0.85596,-0.085086,373.16,0.5222,-0.38669,0.76012,34.977 > view matrix models > #2,-0.8264,0.032948,0.56212,229.58,0.38482,-0.69574,0.60652,123.1,0.41107,0.71754,0.56228,-80.726 > view matrix models > #2,-0.67696,-0.21964,0.70248,224.71,0.73486,-0.25516,0.62838,5.6857,0.041232,0.94162,0.33414,-27.481 > view matrix models > #2,-0.67696,-0.21964,0.70248,201.56,0.73486,-0.25516,0.62838,5.095,0.041232,0.94162,0.33414,-35.053 > view matrix models > #2,-0.76144,0.21092,0.61296,164.15,0.60086,-0.12518,0.78949,-17.024,0.24326,0.96945,-0.031416,-16.775 > view matrix models > #2,-0.76144,0.21092,0.61296,155.29,0.60086,-0.12518,0.78949,-14.55,0.24326,0.96945,-0.031416,-10.835 > view matrix models > #2,-0.76144,0.21092,0.61296,148.4,0.60086,-0.12518,0.78949,-20.284,0.24326,0.96945,-0.031416,-14.737 > select up 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 16 models selected > select up 156107 atoms, 160499 bonds, 12 pseudobonds, 19239 residues, 20 models selected > mmaker #2/j to #5/c 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 5u07, chain C (#5) with merged_251009_real_space_refined_006_real_space_refined_002_best.pdb, chain J (#2), sequence alignment score = 461.8 RMSD between 136 pruned atom pairs is 1.168 angstroms; (across all 444 pairs: 6.173) > hide #!2 models > select subtract #2 124229 atoms, 127708 bonds, 15296 residues, 30 models selected > select add #3 124229 atoms, 127708 bonds, 154 pseudobonds, 15296 residues, 19 models selected > select add #4 124229 atoms, 127708 bonds, 287 pseudobonds, 15296 residues, 21 models selected > select subtract #4 95306 atoms, 97896 bonds, 154 pseudobonds, 11823 residues, 18 models selected > select subtract #3 59051 atoms, 60573 bonds, 7404 residues, 14 models selected > select add #5 59051 atoms, 60573 bonds, 83 pseudobonds, 7404 residues, 16 models selected > select subtract #5 31370 atoms, 32136 bonds, 4001 residues, 13 models selected > select subtract #1 12 models selected > show #!1 models > mmaker #1/H to #5/c 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 5u07, chain C (#5) with MERGE_real_space_refined_002.pdb, chain H (#1), sequence alignment score = 501.2 RMSD between 130 pruned atom pairs is 1.203 angstroms; (across all 431 pairs: 5.956) > hide #!1 models > show #!4 models > hide #!5 models > hide #!4 models > show #!1 models > hide #!1 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!5 models > show #!4 models > hide #!4 models > show #!1 models > cartoon style #1,5 modeHelix tube sides 20 > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 2 models selected > select subtract #2 14 models selected > select add #1 31370 atoms, 32136 bonds, 4001 residues, 1 model selected > view matrix models > #1,-0.68389,0.14022,0.71598,145.54,0.65296,-0.32016,0.6864,30.077,0.32548,0.93693,0.1274,-24.34 > view matrix models > #1,-0.68322,0.076069,0.72624,152.85,0.67328,-0.31937,0.66686,29.637,0.28266,0.94457,0.16698,-24.476 > view matrix models > #1,-0.66129,0.07846,0.74601,147.11,0.69996,-0.29304,0.65129,24.392,0.26971,0.95288,0.13886,-20.369 > view matrix models > #1,-0.66129,0.07846,0.74601,144.95,0.69996,-0.29304,0.65129,19.609,0.26971,0.95288,0.13886,-19.863 > mmaker #1/H to #5/c 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 5u07, chain C (#5) with MERGE_real_space_refined_002.pdb, chain H (#1), sequence alignment score = 501.2 RMSD between 130 pruned atom pairs is 1.203 angstroms; (across all 431 pairs: 5.956) > hide #!5 models > mmaker #1/H:365-400 to #5/c:412-445 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 5u07, chain C (#5) with MERGE_real_space_refined_002.pdb, chain H (#1), sequence alignment score = 74.8 RMSD between 30 pruned atom pairs is 0.880 angstroms; (across all 33 pairs: 1.238) > select up 31370 atoms, 32136 bonds, 4001 residues, 13 models selected > select up 31370 atoms, 32136 bonds, 4001 residues, 13 models selected > select up 31370 atoms, 32136 bonds, 4001 residues, 13 models selected > mmaker #1/H to #5/c 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 5u07, chain C (#5) with MERGE_real_space_refined_002.pdb, chain H (#1), sequence alignment score = 501.2 RMSD between 130 pruned atom pairs is 1.203 angstroms; (across all 431 pairs: 5.956) > hide #!5 models > show #!4 models > select subtract #1 12 models selected > hide #!1 models > show #!2 models > mmaker #2 to #4 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 5u0a, chain H (#4) with merged_251009_real_space_refined_006_real_space_refined_002_best.pdb, chain B (#2), sequence alignment score = 663.9 RMSD between 249 pruned atom pairs is 0.899 angstroms; (across all 345 pairs: 5.423) > hide #!2 models > show #!3 models > show #!5 models > hide #!4 models > hide #!5 models > show #!1 models > show #!2 models > cartoon style #1-2#3.1-2#!3 modeHelix tube sides 20 > hide #!1 models > hide #!2 models > show #!2 models > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20250113 AF predictions/stand.pdb"" Chain information for stand.pdb #6 --- Chain | Description A | No description available Computing secondary structure > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > cartoon style sel modeHelix tube sides 20 > select subtract #6 Nothing selected > hide #6 models > hide #!2 models > hide #!3 models > show #!4 models > coulombic #!4 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: 5u0a #4/A VAL 8 5u0a #4/A ARG 41 5u0a #4/A GLU 57 5u0a #4/A GLU 61 5u0a #4/A LEU 62 5u0a #4/A GLN 67 5u0a #4/A ARG 73 5u0a #4/A LEU 96 5u0a #4/A TYR 104 5u0a #4/A ILE 106 5u0a #4/A THR 111 5u0a #4/A LEU 114 5u0a #4/A LEU 140 5u0a #4/A TRP 149 5u0a #4/A GLU 159 5u0a #4/A LEU 160 5u0a #4/A LEU 161 5u0a #4/A SER 162 5u0a #4/A ILE 183 5u0a #4/A ARG 189 5u0a #4/A PHE 190 5u0a #4/A GLU 193 5u0a #4/A ILE 196 5u0a #4/A ASP 198 5u0a #4/C GLN 84 5u0a #4/C LYS 93 5u0a #4/C HIS 127 5u0a #4/C ILE 233 5u0a #4/C LEU 234 5u0a #4/C ILE 236 5u0a #4/C LEU 254 5u0a #4/C THR 359 5u0a #4/C VAL 364 5u0a #4/C THR 420 5u0a #4/C ASP 487 5u0a #4/I TYR 14 5u0a #4/I ASP 248 5u0a #4/L ASP 216 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 5u0a_A SES surface #4.3: minimum, -11.24, mean 2.59, maximum 19.50 Coulombic values for 5u0a_C SES surface #4.4: minimum, -22.80, mean -1.09, maximum 14.95 Coulombic values for 5u0a_D SES surface #4.5: minimum, -14.41, mean -2.25, maximum 14.14 Coulombic values for 5u0a_E SES surface #4.6: minimum, -16.21, mean -1.22, maximum 17.68 Coulombic values for 5u0a_F SES surface #4.7: minimum, -16.74, mean -1.28, maximum 14.64 Coulombic values for 5u0a_G SES surface #4.8: minimum, -16.31, mean -1.25, maximum 15.05 Coulombic values for 5u0a_H SES surface #4.9: minimum, -23.69, mean -1.26, maximum 15.79 Coulombic values for 5u0a_I SES surface #4.10: minimum, -18.58, mean -0.60, maximum 15.32 Coulombic values for 5u0a_J SES surface #4.11: minimum, -15.75, mean 1.75, maximum 14.73 Coulombic values for 5u0a_K SES surface #4.12: minimum, -23.18, mean -11.48, maximum -2.36 Coulombic values for 5u0a_L SES surface #4.13: minimum, -10.27, mean 2.38, maximum 17.74 Coulombic values for 5u0a_M SES surface #4.14: minimum, -21.24, mean -10.53, maximum -1.03 Coulombic values for 5u0a_N SES surface #4.15: minimum, -13.34, mean 1.07, maximum 15.94 Coulombic values for 5u0a_O SES surface #4.16: minimum, -19.08, mean -9.14, maximum -1.26 To also show corresponding color key, enter the above coulombic command and add key true > hide #!4 models > show #!5 models > coulombic #!5 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: 5u07 #5/A THR 5 5u07 #5/A LEU 11 5u07 #5/A TYR 104 5u07 #5/A ILE 106 5u07 #5/A GLU 118 5u07 #5/A THR 121 5u07 #5/A GLN 122 5u07 #5/A TRP 149 5u07 #5/A GLU 159 5u07 #5/A LEU 161 5u07 #5/A ILE 183 5u07 #5/A LEU 223 5u07 #5/B SER 18 5u07 #5/B ARG 28 5u07 #5/B GLN 159 5u07 #5/C ASP 21 5u07 #5/C ASN 89 5u07 #5/C LEU 246 5u07 #5/C ASN 304 5u07 #5/C ASP 337 5u07 #5/C HIS 343 5u07 #5/C TYR 344 5u07 #5/C GLU 346 5u07 #5/C ARG 351 5u07 #5/C THR 359 5u07 #5/C GLN 363 5u07 #5/E GLU 141 5u07 #5/E HIS 220 5u07 #5/E ASP 331 5u07 #5/F ASP 331 5u07 #5/F LEU 346 5u07 #5/G ARG 289 5u07 #5/I TRP 43 5u07 #5/J ARG 16 5u07 #5/J SER 18 5u07 #5/J LYS 19 5u07 #5/J LEU 20 5u07 #5/J ILE 21 5u07 #5/J VAL 22 5u07 #5/J ASN 23 5u07 #5/J GLU 24 5u07 #5/J ARG 28 5u07 #5/J VAL 84 5u07 #5/J GLN 159 5u07 #5/J GLN 167 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 5u07_A SES surface #5.3: minimum, -10.89, mean 4.41, maximum 23.10 Coulombic values for 5u07_B SES surface #5.4: minimum, -11.50, mean 2.14, maximum 12.93 Coulombic values for 5u07_C SES surface #5.5: minimum, -24.66, mean -1.35, maximum 13.42 Coulombic values for 5u07_D SES surface #5.6: minimum, -17.90, mean -1.85, maximum 12.61 Coulombic values for 5u07_E SES surface #5.7: minimum, -16.00, mean -0.79, maximum 17.13 Coulombic values for 5u07_F SES surface #5.8: minimum, -17.86, mean -1.16, maximum 15.32 Coulombic values for 5u07_G SES surface #5.9: minimum, -17.10, mean -1.41, maximum 15.89 Coulombic values for 5u07_H SES surface #5.10: minimum, -18.26, mean -1.19, maximum 14.41 Coulombic values for 5u07_I SES surface #5.11: minimum, -18.03, mean -0.37, maximum 14.81 Coulombic values for 5u07_J SES surface #5.12: minimum, -11.18, mean 1.17, maximum 12.29 Coulombic values for 5u07_K SES surface #5.13: minimum, -23.10, mean -11.41, maximum -2.29 Coulombic values for 5u07_M SES surface #5.14: minimum, -20.42, mean -10.05, maximum -0.97 Coulombic values for 5u07_N SES surface #5.15: minimum, -12.62, mean 0.72, maximum 13.88 Coulombic values for 5u07_O SES surface #5.16: minimum, -18.75, mean -9.22, maximum -0.59 To also show corresponding color key, enter the above coulombic command and add key true > hide #!5 models > show #!3 models > coulombic #!3 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: 6c66 #3/A THR 80 6c66 #3/A LYS 88 6c66 #3/A LYS 93 6c66 #3/A ARG 97 6c66 #3/A GLN 100 6c66 #3/A ASP 356 6c66 #3/A LYS 543 6c66 #3/B THR 62 6c66 #3/B ARG 63 6c66 #3/B ILE 66 6c66 #3/B ILE 69 6c66 #3/B LYS 71 6c66 #3/B ARG 72 6c66 #3/B GLU 75 6c66 #3/B ASP 79 6c66 #3/B ASP 81 6c66 #3/B ARG 88 6c66 #3/B LEU 119 6c66 #3/B ILE 124 6c66 #3/B LEU 127 6c66 #3/B ASP 132 6c66 #3/B ARG 135 6c66 #3/B ASP 136 6c66 #3/B ILE 150 6c66 #3/B LEU 151 6c66 #3/B THR 157 6c66 #3/B ARG 163 6c66 #3/B ASN 164 6c66 #3/B GLU 176 6c66 #3/B LEU 177 6c66 #3/B SER 218 6c66 #3/B ARG 233 6c66 #3/B ASP 240 6c66 #3/B ARG 241 6c66 #3/D THR 157 6c66 #3/D ASN 236 6c66 #3/E GLU 105 6c66 #3/G SER 219 6c66 #3/G THR 629 6c66 #3/G PHE 944 6c66 #3/I GLU 158 6c66 #3/N DA 21 6c66 #3/O GLN 47 6c66 #3/O ARG 59 6c66 #3/O ARG 113 6c66 #3/O ARG 123 6c66 #3/O ARG 141 6c66 #3/O SER 151 6c66 #3/O ASN 156 6c66 #3/O ILE 183 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6c66_A SES surface #3.4: minimum, -19.83, mean -1.72, maximum 13.57 Coulombic values for 6c66_B SES surface #3.5: minimum, -22.52, mean -2.41, maximum 13.13 Coulombic values for 6c66_C SES surface #3.6: minimum, -15.96, mean -1.16, maximum 15.98 Coulombic values for 6c66_D SES surface #3.7: minimum, -16.61, mean -0.99, maximum 15.30 Coulombic values for 6c66_E SES surface #3.8: minimum, -15.78, mean -0.82, maximum 16.29 Coulombic values for 6c66_F SES surface #3.9: minimum, -15.28, mean -1.13, maximum 15.29 Coulombic values for 6c66_G SES surface #3.10: minimum, -21.54, mean -2.52, maximum 15.14 Coulombic values for 6c66_H SES surface #3.11: minimum, -15.59, mean -0.67, maximum 14.48 Coulombic values for 6c66_I SES surface #3.12: minimum, -19.93, mean 1.56, maximum 15.48 Coulombic values for 6c66_J SES surface #3.13: minimum, -22.95, mean -11.34, maximum -2.12 Coulombic values for 6c66_K SES surface #3.14: minimum, -14.43, mean 1.67, maximum 15.87 Coulombic values for 6c66_L SES surface #3.15: minimum, -21.32, mean -10.47, maximum -1.18 Coulombic values for 6c66_M SES surface #3.16: minimum, -14.78, mean 0.86, maximum 15.12 Coulombic values for 6c66_N SES surface #3.17: minimum, -20.28, mean -9.24, maximum -1.60 Coulombic values for 6c66_O SES surface #3.18: minimum, -16.26, mean 1.89, maximum 18.57 To also show corresponding color key, enter the above coulombic command and add key true > hide #3.4 models > show #3.4 models > hide #3.5 models > hide #3.7 models > hide #3.6 models > hide #3.8 models > hide #3.9 models > hide #3.10 models > show #3.10 models > hide #3.11 models > hide #3.12 models > hide #3.13 models > hide #3.14 models > hide #3.15 models > hide #3.16 models > hide #3.17 models > hide #3.18 models > close #3.5-9 > close #3.11-18 > hide #!3 models > show #!4 models > hide #4.3 models > hide #4.4 models > show #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.14 models > hide #4.16 models > hide #4.15 models > show #4.15 models > hide #4.13 models > hide #4.15 models > close #4.5-16 > close #4.3 > hide #!4 models > show #!5 models > hide #5.3 models > hide #5.4 models > hide #5.5 models > show #5.5 models > hide #5.6 models > close #5.6-16 > show #!4 models > hide #!5 models > hide #!4 models > show #!3 models > hide #3.4 models > show #3.4 models > hide #3.10 models > show #3.10 models > hide #3.10 models > hide #3.4 models > show #3.10 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #3.10 models > show #3.10 models > hide #!3 models > show #!2 models > show #6 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models #6,1,0,0,122.96,0,1,0,117.82,0,0,1,91.796 > view matrix models #6,1,0,0,103.22,0,1,0,140.29,0,0,1,119.36 > view matrix models > #6,0.77583,-0.39524,0.49181,103.4,-0.020375,-0.79477,-0.60657,151.89,0.63061,0.46057,-0.62466,123.15 > view matrix models > #6,0.77547,0.20699,0.59649,99.89,0.59313,-0.56266,-0.57585,150.47,0.21642,0.80035,-0.5591,121.21 > view matrix models > #6,0.85592,0.49119,-0.16167,101.34,0.50171,-0.86454,0.029505,149.71,-0.12528,-0.10636,-0.9864,127.6 > view matrix models > #6,0.075994,0.93407,0.3489,97.217,0.96773,0.015218,-0.25152,146.17,-0.24025,0.35676,-0.90278,124.91 > view matrix models > #6,0.67367,0.46645,0.57323,98.659,0.25505,0.58126,-0.77272,145.39,-0.69363,0.66676,0.27261,118.85 > view matrix models > #6,0.67559,-0.72601,-0.12842,107.52,0.70374,0.68694,-0.18129,142.48,0.21983,0.0321,0.97501,119.25 > view matrix models > #6,0.64957,-0.51832,0.55624,103.81,0.66033,0.74723,-0.074844,141.77,-0.37685,0.41592,0.82764,117.95 > view matrix models > #6,0.64957,-0.51832,0.55624,85.554,0.66033,0.74723,-0.074844,140.09,-0.37685,0.41592,0.82764,100.82 > show sel atoms > view matrix models > #6,0.65539,-0.58731,0.47491,86.102,0.62852,0.77277,0.088278,139.4,-0.41884,0.24063,0.8756,101.28 > hide sel atoms > view matrix models > #6,0.62232,-0.61919,0.47888,86.257,0.69823,0.71565,0.017952,139.95,-0.35382,0.3232,0.8777,100.83 > view matrix models > #6,0.62232,-0.61919,0.47888,83.162,0.69823,0.71565,0.017952,124.7,-0.35382,0.3232,0.8777,129.61 > view matrix models > #6,0.62232,-0.61919,0.47888,83.754,0.69823,0.71565,0.017952,129.48,-0.35382,0.3232,0.8777,154.51 > view matrix models > #6,0.64671,-0.63996,0.41499,79.366,0.66796,0.73786,0.096923,137.28,-0.36824,0.21452,0.90465,150.09 > view matrix models > #6,0.5968,-0.61071,0.52044,78.817,0.73801,0.67236,-0.057314,138.2,-0.31492,0.41829,0.85197,149.23 > view matrix models > #6,0.5968,-0.61071,0.52044,78.369,0.73801,0.67236,-0.057314,141.93,-0.31492,0.41829,0.85197,146.23 > hide #6 models > select subtract #6 Nothing selected > hide #!2 models > show #!3 models > hide #3.10 models > select #3/G 6469 atoms, 6620 bonds, 15 pseudobonds, 834 residues, 3 models selected > color (#!3 & sel) cyan > color (#!3 & sel) light sea green > select add #3 36255 atoms, 37323 bonds, 154 pseudobonds, 4419 residues, 5 models selected > select subtract #3 2 models selected > show #6 models > hide #6 models > show #!2 models > color #2 #bab71bff > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 2 models selected > view matrix models > #2,-0.71597,0.25826,0.64861,136.83,0.51165,-0.43798,0.73918,46.435,0.47498,0.86109,0.18144,-56.76 > view matrix models > #2,-0.71597,0.25826,0.64861,128.98,0.51165,-0.43798,0.73918,50.86,0.47498,0.86109,0.18144,-63.181 > view matrix models > #2,-0.71597,0.25826,0.64861,131.81,0.51165,-0.43798,0.73918,48.752,0.47498,0.86109,0.18144,-60.289 > view matrix models > #2,-0.65814,0.15681,0.73639,125.74,0.68127,-0.29233,0.67113,12.828,0.32051,0.94337,0.085562,-36.359 > view matrix models > #2,-0.65814,0.15681,0.73639,126.35,0.68127,-0.29233,0.67113,11.849,0.32051,0.94337,0.085562,-32.971 > hide #!2 models > select subtract #2 14 models selected > show #!4 models > hide #!3 models > show #!2 models > hide #4.4 models > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 2 models selected > view matrix models > #2,-0.65814,0.15681,0.73639,125.51,0.68127,-0.29233,0.67113,9.7539,0.32051,0.94337,0.085562,-33.909 > view matrix models > #2,-0.64817,0.13471,0.74949,125.42,0.70471,-0.26684,0.6574,4.6243,0.28855,0.95428,0.078026,-29.809 > view matrix models > #2,-0.64817,0.13471,0.74949,126.8,0.70471,-0.26684,0.6574,3.3912,0.28855,0.95428,0.078026,-25.751 > view matrix models > #2,-0.64817,0.13471,0.74949,127.71,0.70471,-0.26684,0.6574,1.5303,0.28855,0.95428,0.078026,-29.323 > view matrix models > #2,-0.67296,0.059034,0.73732,143.94,0.70786,-0.23783,0.66511,-4.1983,0.21462,0.96951,0.11826,-26.521 > view matrix models > #2,-0.67296,0.059034,0.73732,147.22,0.70786,-0.23783,0.66511,-3.687,0.21462,0.96951,0.11826,-21.742 > view matrix models > #2,-0.62718,0.090911,0.77355,130.9,0.72148,-0.30636,0.62097,10.462,0.29344,0.94756,0.12655,-31.119 > view matrix models > #2,-0.64068,-0.093598,0.76208,161.1,0.72549,-0.39877,0.56093,31.688,0.2514,0.91226,0.32339,-47.695 > view matrix models > #2,-0.67864,-0.0098439,0.7344,158.39,0.62806,-0.52616,0.57332,62.399,0.38077,0.85033,0.36326,-63.047 > undo [Repeated 1 time(s)] > view matrix models > #2,-0.62718,0.090911,0.77355,129.54,0.72148,-0.30636,0.62097,9.708,0.29344,0.94756,0.12655,-31.121 > view matrix models > #2,-0.62718,0.090911,0.77355,128.71,0.72148,-0.30636,0.62097,8.562,0.29344,0.94756,0.12655,-32.588 > view matrix models > #2,-0.62718,0.090911,0.77355,128.69,0.72148,-0.30636,0.62097,8.3743,0.29344,0.94756,0.12655,-32.921 > view matrix models > #2,-0.62718,0.090911,0.77355,130.02,0.72148,-0.30636,0.62097,7.7485,0.29344,0.94756,0.12655,-33.783 > view matrix models > #2,-0.61954,0.096077,0.77907,127.39,0.73021,-0.29364,0.6169,5.2248,0.28803,0.95108,0.11176,-31.425 > view matrix models > #2,-0.61954,0.096077,0.77907,127.53,0.73021,-0.29364,0.6169,4.9436,0.28803,0.95108,0.11176,-31.982 > view matrix models > #2,-0.60169,0.10709,0.79152,121.61,0.72969,-0.32934,0.59924,12.663,0.32485,0.93812,0.12002,-36.59 > hide #!4 models > select subtract #2 14 models selected > hide #!2 models > show #!3 models > select add #3 36255 atoms, 37323 bonds, 154 pseudobonds, 4419 residues, 4 models selected > select subtract #3 2 models selected > show #6 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.5968,-0.61071,0.52044,78.442,0.73801,0.67236,-0.057314,140.17,-0.31492,0.41829,0.85197,147.86 > view matrix models > #6,0.56985,-0.6304,0.52713,82.896,0.76488,0.64139,-0.059811,147.2,-0.30039,0.43727,0.84768,147.14 > view matrix models > #6,0.56985,-0.6304,0.52713,82.385,0.76488,0.64139,-0.059811,147.09,-0.30039,0.43727,0.84768,147.55 > view matrix models > #6,0.53453,-0.67432,0.50948,82.686,0.80238,0.59425,-0.055329,147.31,-0.26545,0.43837,0.8587,147.49 > view matrix models > #6,0.53453,-0.67432,0.50948,82.286,0.80238,0.59425,-0.055329,149.71,-0.26545,0.43837,0.8587,146.37 > hide #6 models > show #6 models > view matrix models > #6,0.53453,-0.67432,0.50948,81.89,0.80238,0.59425,-0.055329,150.06,-0.26545,0.43837,0.8587,143.18 > view matrix models > #6,0.56181,-0.67168,0.48293,81.974,0.80094,0.58772,-0.11433,150.32,-0.20703,0.45103,0.86816,143.07 > view matrix models > #6,0.5949,-0.64475,0.48,81.841,0.78498,0.59448,-0.17435,150.52,-0.17294,0.48051,0.85977,142.95 > view matrix models > #6,0.59302,-0.64605,0.48057,81.845,0.78693,0.5914,-0.17603,150.54,-0.17048,0.48256,0.85911,142.94 > view matrix models > #6,0.59302,-0.64605,0.48057,78.272,0.78693,0.5914,-0.17603,140.29,-0.17048,0.48256,0.85911,145.56 > view matrix models > #6,0.59302,-0.64605,0.48057,84.268,0.78693,0.5914,-0.17603,139.63,-0.17048,0.48256,0.85911,139.96 > hide #6 models > show #6 models > hide #6 models > show #6 models > view matrix models > #6,0.6029,-0.62883,0.491,84.137,0.7809,0.59119,-0.20173,139.73,-0.16342,0.50505,0.84748,139.89 > view matrix models > #6,0.6029,-0.62883,0.491,83.164,0.7809,0.59119,-0.20173,140.01,-0.16342,0.50505,0.84748,139.16 > hide #!3 models > show #!3 models > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #6 models > select #3/G 6469 atoms, 6620 bonds, 15 pseudobonds, 834 residues, 3 models selected > style sel stick Changed 6469 atom styles > show sel atoms > color sel byhetero > select #3/A 4053 atoms, 4175 bonds, 1 pseudobond, 511 residues, 2 models selected > style sel stick Changed 4053 atom styles > show sel atoms > color sel byhetero > select add #3 36255 atoms, 37323 bonds, 154 pseudobonds, 4419 residues, 5 models selected > select subtract #3 2 models selected > hide #!3 models > show #!2 models > show #6 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.6029,-0.62883,0.491,83.426,0.7809,0.59119,-0.20173,142.49,-0.16342,0.50505,0.84748,138.16 > view matrix models > #6,0.67074,-0.56184,0.4842,83.095,0.70182,0.69195,-0.16929,141.86,-0.23993,0.45337,0.85842,138.4 > view matrix models > #6,0.67074,-0.56184,0.4842,82.518,0.70182,0.69195,-0.16929,143.36,-0.23993,0.45337,0.85842,135.38 > view matrix models > #6,0.72918,-0.54151,0.4184,82.657,0.60842,0.79288,-0.034166,142.34,-0.31324,0.27948,0.90762,136.1 > view matrix models > #6,0.47466,-0.8553,-0.20777,86.738,0.17134,-0.14175,0.97496,143.34,-0.86333,-0.49837,0.079262,143.41 > view matrix models > #6,0.83645,-0.13468,-0.53123,84.206,-0.27534,-0.94139,-0.19488,152.06,-0.47385,0.30927,-0.82451,142.66 > view matrix models > #6,0.93659,0.08024,-0.3411,82.345,-0.095442,-0.87821,-0.46865,152.76,-0.33717,0.47149,-0.81487,141.77 > view matrix models > #6,0.93659,0.08024,-0.3411,66.503,-0.095442,-0.87821,-0.46865,155.11,-0.33717,0.47149,-0.81487,138.47 > view matrix models > #6,0.86089,0.46458,-0.20744,64.017,0.45924,-0.53402,0.70988,148.68,0.21902,-0.70639,-0.67308,143.9 > view matrix models > #6,0.88491,0.42446,-0.19175,69.061,0.43032,-0.58758,0.68525,154.53,0.17819,-0.6889,-0.70261,130.66 > view matrix models > #6,0.92048,-0.35326,-0.16712,72.973,-0.015904,0.39343,-0.91922,155.74,0.39047,0.84878,0.35653,118.6 > view matrix models > #6,0.56846,-0.7688,0.29293,73.402,0.82054,0.50391,-0.26982,152.51,0.059824,0.39374,0.91727,118.84 > view matrix models > #6,0.76205,-0.64243,0.081015,73.534,0.5794,0.73239,0.35762,148.96,-0.28908,-0.22558,0.93035,122.04 > view matrix models > #6,0.75694,-0.64793,0.085032,64.362,0.58855,0.73247,0.34219,147.02,-0.284,-0.20897,0.93578,134.53 > view matrix models > #6,0.75382,-0.49991,0.42642,62.281,0.4997,0.85756,0.122,147.24,-0.42667,0.12112,0.89626,133 > show #!1 models > mmaker #2/B to #1/C 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 MERGE_real_space_refined_002.pdb, chain C (#1) with merged_251009_real_space_refined_006_real_space_refined_002_best.pdb, chain B (#2), sequence alignment score = 2068.4 RMSD between 407 pruned atom pairs is 0.777 angstroms; (across all 420 pairs: 1.511) > hide #!2 models > hide #!1 models > show #!2 models > view matrix models > #6,0.75382,-0.49991,0.42642,70.007,0.4997,0.85756,0.122,146.43,-0.42667,0.12112,0.89626,149.94 > view matrix models > #6,0.81222,-0.46967,0.346,70.151,0.49163,0.87038,0.027392,146.73,-0.31402,0.14786,0.93783,149.63 > view matrix models > #6,0.81222,-0.46967,0.346,71.494,0.49163,0.87038,0.027392,146.17,-0.31402,0.14786,0.93783,140.45 > view matrix models > #6,0.81222,-0.46967,0.346,70.143,0.49163,0.87038,0.027392,144.86,-0.31402,0.14786,0.93783,140.15 > view matrix models > #6,0.56712,-0.71377,-0.41098,74.368,-0.71055,-0.17164,-0.6824,153.18,0.41653,0.67902,-0.60451,143.23 > view matrix models > #6,0.34983,-0.24352,-0.90461,73.885,-0.57126,-0.82077,3.5879e-05,153.87,-0.74249,0.51675,-0.42624,143.58 > view matrix models > #6,0.6724,-0.30554,-0.67418,73.259,-0.3274,-0.93965,0.099324,154.06,-0.66384,0.15394,-0.73186,146.62 > view matrix models > #6,0.93981,-0.33326,-0.075472,71.044,-0.32802,-0.94178,0.073847,154.17,-0.095688,-0.044646,-0.99441,148.56 > view matrix models > #6,0.13327,-0.77522,0.61747,70.79,-0.31512,-0.62384,-0.71521,155.57,0.93965,-0.099264,-0.32743,146.09 > view matrix models > #6,0.82051,0.25556,0.51132,65.761,-0.56834,0.26895,0.77759,145.25,0.061203,-0.92863,0.36592,147.84 > view matrix models > #6,0.46354,-0.86301,0.20089,72.793,0.7668,0.27708,-0.579,150.21,0.44402,0.42243,0.79019,139.17 > view matrix models > #6,-0.45193,0.33091,-0.82841,70.767,-0.070576,0.91248,0.40299,143.29,0.88926,0.24059,-0.38902,144.58 > view matrix models > #6,0.96367,0.25724,-0.071949,67.98,-0.17658,0.41138,-0.8942,150.9,-0.20042,0.87441,0.44186,138.29 > view matrix models > #6,0.54629,0.31144,-0.77754,70.497,-0.39034,-0.72668,-0.56531,155.54,-0.74109,0.61232,-0.27541,142.51 > view matrix models > #6,0.49884,0.10563,-0.86023,71.886,-0.31361,-0.90329,-0.29278,155.39,-0.80796,0.41583,-0.41747,144.08 > view matrix models > #6,0.38235,-0.22342,-0.8966,73.745,-0.54723,-0.83662,-0.024887,154.05,-0.74455,0.50016,-0.44214,143.73 > view matrix models > #6,0.38235,-0.22342,-0.8966,64.208,-0.54723,-0.83662,-0.024887,157.41,-0.74455,0.50016,-0.44214,163.44 > view matrix models > #6,0.38235,-0.22342,-0.8966,64.035,-0.54723,-0.83662,-0.024887,152.71,-0.74455,0.50016,-0.44214,164.06 > color sel byhetero > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for stand.pdb_A SES surface #6.1: minimum, -19.03, mean -1.01, maximum 14.42 To also show corresponding color key, enter the above coulombic command and add key true > show sel surfaces > select add #2 41483 atoms, 42584 bonds, 12 pseudobonds, 5225 residues, 4 models selected > show sel surfaces > coulombic sel Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_A SES surface #2.2: minimum, -22.89, mean -2.13, maximum 12.44 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_B SES surface #2.3: minimum, -19.22, mean -1.57, maximum 17.26 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_C SES surface #2.4: minimum, -17.81, mean -1.38, maximum 17.52 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_D SES surface #2.5: minimum, -19.84, mean -1.44, maximum 17.37 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_E SES surface #2.6: minimum, -25.54, mean -1.07, maximum 15.87 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_F SES surface #2.7: minimum, -30.85, mean -1.04, maximum 16.78 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_G SES surface #2.8: minimum, -12.95, mean 1.67, maximum 12.27 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_H SES surface #2.9: minimum, -11.77, mean 2.20, maximum 12.43 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_I SES surface #2.10: minimum, -16.36, mean -0.43, maximum 13.84 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_J SES surface #2.11: minimum, -18.88, mean -1.15, maximum 12.85 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_K SES surface #2.12: minimum, -13.74, mean 2.48, maximum 15.14 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_L SES surface #2.13: minimum, -15.05, mean -7.76, maximum -0.49 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_M SES surface #2.14: minimum, -22.56, mean -10.24, maximum -1.10 Coulombic values for merged_251009_real_space_refined_006_real_space_refined_002_best.pdb_N SES surface #2.15: minimum, -23.46, mean -11.85, maximum -2.57 Coulombic values for stand.pdb_A SES surface #6.1: minimum, -19.03, mean -1.01, maximum 14.42 To also show corresponding color key, enter the above coulombic command and add key true > hide #2.13 models > hide #2.14 models > hide #2.15 models > hide #2.12 models > hide #2.11 models > show #2.11 models > hide #2.10 models > show #2.10 models > hide #2.9 models > hide #2.8 models > hide #2.7 models > hide #2.6 models > hide #2.5 models > hide #2.4 models > hide #2.3 models > hide #2.2 models > close #2.2-9 > close #2.12-15 > hide #!6 models > select subtract #6 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 5 models selected > hide #!2 models > show #!3 models > show #3.4 models > coulombic #!3 Coulombic values for 6c66_A SES surface #3.4: minimum, -19.83, mean -1.72, maximum 13.57 Coulombic values for 6c66_B SES surface #3.5: minimum, -22.52, mean -2.41, maximum 13.13 Coulombic values for 6c66_C SES surface #3.6: minimum, -15.96, mean -1.16, maximum 15.98 Coulombic values for 6c66_D SES surface #3.7: minimum, -16.61, mean -0.99, maximum 15.30 Coulombic values for 6c66_E SES surface #3.8: minimum, -15.78, mean -0.82, maximum 16.29 Coulombic values for 6c66_F SES surface #3.9: minimum, -15.28, mean -1.13, maximum 15.29 Coulombic values for 6c66_G SES surface #3.10: minimum, -21.54, mean -2.52, maximum 15.14 Coulombic values for 6c66_H SES surface #3.11: minimum, -15.59, mean -0.67, maximum 14.48 Coulombic values for 6c66_I SES surface #3.12: minimum, -19.93, mean 1.56, maximum 15.48 Coulombic values for 6c66_J SES surface #3.13: minimum, -22.95, mean -11.34, maximum -2.12 Coulombic values for 6c66_K SES surface #3.14: minimum, -14.43, mean 1.67, maximum 15.87 Coulombic values for 6c66_L SES surface #3.15: minimum, -21.32, mean -10.47, maximum -1.18 Coulombic values for 6c66_M SES surface #3.16: minimum, -14.78, mean 0.86, maximum 15.12 Coulombic values for 6c66_N SES surface #3.17: minimum, -20.28, mean -9.24, maximum -1.60 Coulombic values for 6c66_O SES surface #3.18: minimum, -16.26, mean 1.89, maximum 18.57 To also show corresponding color key, enter the above coulombic command and add key true > hide #3.1 models > hide #3.2 models > hide #3.4 models > hide #3.5 models > hide #3.17 models > hide #3.18 models > hide #3.16 models > hide #3.15 models > select subtract #2 2 models selected > hide #3.6 models > hide #3.7 models > hide #3.8 models > show #3.6 models > hide #3.6 models > show #3.5 models > hide #3.5 models > show #3.4 models > hide #3.9 models > hide #3.10 models > show #3.10 models > hide #3.11 models > hide #3.12 models > hide #3.13 models > hide #3.14 models > close #3.5-9 > close #3.11-18 > hide #3.10 models > hide #3.4 models > hide #!3 models > show #!2 models > show #!6 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.57442,0.015474,-0.81842,62.944,-0.64036,-0.6143,-0.46106,153.32,-0.50988,0.78892,-0.34295,162.73 > view matrix models > #6,0.57442,0.015474,-0.81842,56.419,-0.64036,-0.6143,-0.46106,152.91,-0.50988,0.78892,-0.34295,154.36 > view matrix models > #6,0.96612,0.25507,-0.039404,52.954,-0.13227,0.35824,-0.92421,151.08,-0.22162,0.89811,0.37984,151.55 > view matrix models > #6,0.96423,0.26397,-0.024263,52.862,-0.22179,0.75322,-0.61925,148.32,-0.14519,0.60248,0.78482,151.33 > view matrix models > #6,0.96423,0.26397,-0.024263,67.266,-0.22179,0.75322,-0.61925,151.27,-0.14519,0.60248,0.78482,147.73 > hide sel surfaces > view matrix models > #6,0.9767,0.21422,-0.012579,60.403,-0.19603,0.86683,-0.45845,153.23,-0.087306,0.45023,0.88863,132.4 > show sel atoms > view matrix models > #6,0.9767,0.21422,-0.012579,55.487,-0.19603,0.86683,-0.45845,162.41,-0.087306,0.45023,0.88863,124.96 > view matrix models > #6,0.94014,-0.26833,0.21006,56.502,0.28168,0.95884,-0.035849,161.08,-0.1918,0.092874,0.97703,125.9 > view matrix models > #6,0.94014,-0.26833,0.21006,77.687,0.28168,0.95884,-0.035849,146.4,-0.1918,0.092874,0.97703,136.3 > view matrix models > #6,0.94014,-0.26833,0.21006,70.782,0.28168,0.95884,-0.035849,146.82,-0.1918,0.092874,0.97703,129.77 > show sel surfaces > view matrix models > #6,0.32968,-0.76572,0.55225,71.07,0.91641,0.40017,0.0077951,149.4,-0.22697,0.50352,0.83364,128.61 > hide sel atoms > view matrix models > #6,-0.62373,-0.73904,0.2545,71.296,0.63747,-0.66939,-0.3815,154.88,0.45231,-0.075718,0.88864,131.26 > view matrix models > #6,-0.8434,-0.44486,0.3013,69.776,0.28161,-0.84358,-0.45724,155.57,0.45758,-0.30079,0.83675,132.36 > view matrix models > #6,0.21409,-0.45235,0.86576,68.593,0.28759,0.87622,0.3867,145.63,-0.93352,0.16619,0.31768,131.27 > view matrix models > #6,0.056183,-0.97216,0.22748,72.857,0.88584,-0.056564,-0.46053,152.89,0.46057,0.22738,0.858,130.16 > view matrix models > #6,0.34918,-0.90426,0.24574,72.746,0.92355,0.28774,-0.25351,150.8,0.15854,0.31547,0.9356,129.3 > view matrix models > #6,0.93382,-0.3343,0.12736,71.34,0.30469,0.9298,0.20649,146.08,-0.18744,-0.15402,0.97013,130.79 > view matrix models > #6,0.95819,0.0024637,-0.28612,71.499,-0.15473,0.84562,-0.51088,148.65,0.24069,0.53379,0.81064,128.93 > view matrix models > #6,0.95819,0.0024637,-0.28612,71.484,-0.15473,0.84562,-0.51088,162.06,0.24069,0.53379,0.81064,117.71 > view matrix models > #6,0.98271,0.17425,0.062508,69.557,-0.1204,0.85808,-0.4992,162,-0.14062,0.48304,0.86423,117.43 > view matrix models > #6,0.94593,0.32397,0.01593,69.096,-0.30762,0.9116,-0.27268,160.82,-0.10286,0.25304,0.96197,118.03 > view matrix models > #6,0.94593,0.32397,0.01593,71.564,-0.30762,0.9116,-0.27268,163.36,-0.10286,0.25304,0.96197,120.99 > view matrix models > #6,0.88813,0.45958,0.0017482,71.026,-0.45678,0.88312,-0.10699,162.76,-0.050717,0.094227,0.99426,121.55 > view matrix models > #6,0.88813,0.45958,0.0017482,73.699,-0.45678,0.88312,-0.10699,164.35,-0.050717,0.094227,0.99426,125.79 > view matrix models > #6,0.88813,0.45958,0.0017482,70.411,-0.45678,0.88312,-0.10699,166.57,-0.050717,0.094227,0.99426,125.71 > view matrix models > #6,0.87734,0.47986,0.0045889,70.311,-0.47988,0.87727,0.011059,166.15,0.0012811,-0.011905,0.99993,126.16 > view matrix models > #6,0.87734,0.47986,0.0045889,71.41,-0.47988,0.87727,0.011059,165.45,0.0012811,-0.011905,0.99993,127.63 > view matrix models > #6,0.87734,0.47986,0.0045889,68.645,-0.47988,0.87727,0.011059,165.64,0.0012811,-0.011905,0.99993,121.36 > view matrix models > #6,0.87734,0.47986,0.0045889,66.649,-0.47988,0.87727,0.011059,168.93,0.0012811,-0.011905,0.99993,116.99 > view matrix models > #6,0.86203,0.073145,0.50155,66.477,-0.1421,0.98473,0.10062,168.44,-0.48653,-0.158,0.85926,117.7 > view matrix models > #6,0.92985,-0.11358,0.34996,67.826,0.059603,0.9851,0.16135,168.38,-0.36307,-0.12917,0.92277,117.45 > view matrix models > #6,0.92985,-0.11358,0.34996,71.048,0.059603,0.9851,0.16135,167.85,-0.36307,-0.12917,0.92277,117.01 > view matrix models > #6,0.92985,-0.11358,0.34996,73.542,0.059603,0.9851,0.16135,160.6,-0.36307,-0.12917,0.92277,114.69 > view matrix models > #6,0.92985,-0.11358,0.34996,74.632,0.059603,0.9851,0.16135,148.41,-0.36307,-0.12917,0.92277,123.02 > view matrix models > #6,0.95545,-0.023361,0.29424,74.491,-0.039913,0.97748,0.20721,148.2,-0.29246,-0.20972,0.933,123.36 > view matrix models > #6,0.95545,-0.023361,0.29424,77.438,-0.039913,0.97748,0.20721,141.73,-0.29246,-0.20972,0.933,124.55 > view matrix models > #6,0.95545,-0.023361,0.29424,73.297,-0.039913,0.97748,0.20721,142.4,-0.29246,-0.20972,0.933,134.85 > view matrix models > #6,0.95545,-0.023361,0.29424,69.761,-0.039913,0.97748,0.20721,148.26,-0.29246,-0.20972,0.933,139.77 > view matrix models > #6,0.95545,-0.023361,0.29424,70.015,-0.039913,0.97748,0.20721,148.74,-0.29246,-0.20972,0.933,140.54 > view matrix models > #6,0.96605,0.026025,0.25704,69.959,-0.058716,0.99099,0.12034,148.99,-0.25159,-0.13135,0.95888,140.17 > view matrix models > #6,0.96605,0.026025,0.25704,70.41,-0.058716,0.99099,0.12034,151.82,-0.25159,-0.13135,0.95888,136.56 > view matrix models > #6,0.96605,0.026025,0.25704,68.498,-0.058716,0.99099,0.12034,153.54,-0.25159,-0.13135,0.95888,133.41 > view matrix models > #6,0.96605,0.026025,0.25704,66.736,-0.058716,0.99099,0.12034,156.66,-0.25159,-0.13135,0.95888,129.25 > view matrix models > #6,0.96605,0.026025,0.25704,69.162,-0.058716,0.99099,0.12034,158.59,-0.25159,-0.13135,0.95888,131.49 > view matrix models > #6,0.94285,0.20736,0.26084,68.463,-0.18503,0.97681,-0.10771,159.36,-0.27712,0.053293,0.95936,130.85 > view matrix models > #6,0.94285,0.20736,0.26084,67.542,-0.18503,0.97681,-0.10771,158.96,-0.27712,0.053293,0.95936,135.86 > view matrix models > #6,0.94285,0.20736,0.26084,68.692,-0.18503,0.97681,-0.10771,158.52,-0.27712,0.053293,0.95936,134.84 > view matrix models > #6,0.94285,0.20736,0.26084,68.326,-0.18503,0.97681,-0.10771,161.71,-0.27712,0.053293,0.95936,136.57 > view matrix models > #6,0.9708,0.19624,0.13801,68.835,-0.18497,0.97858,-0.090359,161.64,-0.15278,0.062193,0.9863,136.53 > view matrix models > #6,0.9708,0.19624,0.13801,68.54,-0.18497,0.97858,-0.090359,161.61,-0.15278,0.062193,0.9863,134.34 > hide sel surfaces > view matrix models > #6,0.9708,0.19624,0.13801,69.938,-0.18497,0.97858,-0.090359,162.16,-0.15278,0.062193,0.9863,132.31 > view matrix models > #6,0.9708,0.19624,0.13801,67.83,-0.18497,0.97858,-0.090359,159.41,-0.15278,0.062193,0.9863,129.55 > undo > select subtract #6 1 model selected > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.9708,0.19624,0.13801,72.699,-0.18497,0.97858,-0.090359,163.77,-0.15278,0.062193,0.9863,133.15 > show sel surfaces > hide sel surfaces > view matrix models > #6,0.9708,0.19624,0.13801,71.606,-0.18497,0.97858,-0.090359,164.3,-0.15278,0.062193,0.9863,133.21 > view matrix models > #6,0.96864,0.20177,0.14497,71.551,-0.19104,0.97793,-0.084586,164.28,-0.15884,0.054238,0.98581,133.26 > view matrix models > #6,0.96727,0.18827,0.17013,71.524,-0.15958,0.97261,-0.16902,164.63,-0.19729,0.13634,0.97082,132.9 > view matrix models > #6,0.96012,0.2182,0.17481,71.353,-0.2005,0.97311,-0.11342,164.42,-0.19485,0.073848,0.97805,133.19 > view matrix models > #6,0.96012,0.2182,0.17481,70.501,-0.2005,0.97311,-0.11342,164.84,-0.19485,0.073848,0.97805,132.93 > show sel surfaces > view matrix models > #6,0.97419,0.18126,0.13452,70.805,-0.16443,0.97815,-0.12724,164.9,-0.15464,0.10184,0.98271,132.83 > view matrix models > #6,0.97419,0.18126,0.13452,70.442,-0.16443,0.97815,-0.12724,165.11,-0.15464,0.10184,0.98271,133.05 > hide sel surfaces > hide #!6 models > hide #!2 models > show #!3 models > select subtract #6 1 model selected > show #!3 surfaces > hide #!3 models > show #!3 models > hide #!3 surfaces > hide #!3 models > show #!2 models > show #!6 models > show #!2,6 surfaces > hide #!2 models > show #!2 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > hide sel surfaces > view matrix models > #6,0.94908,0.24495,0.1981,69.872,-0.20791,0.95946,-0.19028,165.46,-0.23668,0.13941,0.96153,132.95 > view matrix models > #6,0.94908,0.24495,0.1981,68.474,-0.20791,0.95946,-0.19028,164.69,-0.23668,0.13941,0.96153,133.87 > view matrix models > #6,0.93675,0.21308,0.27768,68.333,-0.17303,0.97154,-0.1618,164.51,-0.30425,0.10352,0.94695,134.12 > view matrix models > #6,0.93675,0.21308,0.27768,67.946,-0.17303,0.97154,-0.1618,163.65,-0.30425,0.10352,0.94695,135.47 > select subtract #6 1 model selected > hide #!6 models > hide #!2 models > show #!3 models > hide #3.4 models > show #3.4 models > show #!3 surfaces > hide #3.5 models > hide #3.6 models > hide #3.7 models > hide #3.8 models > hide #3.9 models > hide #3.11 models > hide #3.12 models > hide #3.13 models > hide #3.14 models > hide #3.15 models > hide #3.16 models > hide #3.17 models > hide #3.18 models > hide #3.10 models > hide #3.4 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > show #3.4 models > hide #3.4 models > show #!2 models > hide #!3 models > show #!6 models > hide #6.1 models > show #6.1 models > show #!2,6 surfaces > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.97124,-0.037384,0.23516,69.131,0.10994,0.94644,-0.3036,164.48,-0.21121,0.32072,0.92332,134.76 > view matrix models > #6,0.97124,-0.037384,0.23516,67.197,0.10994,0.94644,-0.3036,157.63,-0.21121,0.32072,0.92332,133.31 > view matrix models > #6,0.97124,-0.037384,0.23516,68.398,0.10994,0.94644,-0.3036,159.47,-0.21121,0.32072,0.92332,133.8 > view matrix models > #6,0.97124,-0.037384,0.23516,67.175,0.10994,0.94644,-0.3036,158.84,-0.21121,0.32072,0.92332,136.37 > view matrix models > #6,0.97124,-0.037384,0.23516,67.581,0.10994,0.94644,-0.3036,159.12,-0.21121,0.32072,0.92332,136.66 > view matrix models > #6,0.97124,-0.037384,0.23516,55.921,0.10994,0.94644,-0.3036,159.28,-0.21121,0.32072,0.92332,144.42 > view matrix models > #6,0.99631,0.013523,0.084742,56.279,0.034964,0.83785,-0.54478,160.52,-0.078369,0.54573,0.83429,143.95 > view matrix models > #6,0.99631,0.013523,0.084742,51.208,0.034964,0.83785,-0.54478,164.33,-0.078369,0.54573,0.83429,138.52 > view matrix models > #6,0.95561,-0.26261,0.13362,52.108,0.091859,-0.16535,-0.98195,169.97,0.27996,0.95063,-0.13389,140.66 > hide #6.1 models > select subtract #6.1 1 model selected > show #6.1 models > hide #6.1 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.95561,-0.26261,0.13362,58.424,0.091859,-0.16535,-0.98195,181.51,0.27996,0.95063,-0.13389,143.77 > view matrix models > #6,0.97893,-0.19278,0.067382,58.316,0.10677,0.20189,-0.97357,179.58,0.17408,0.96025,0.21822,142.38 > view matrix models > #6,0.94512,-0.28131,0.16618,58.397,0.25601,0.3216,-0.91161,178.7,0.20301,0.90412,0.37597,142.06 > view matrix models > #6,0.58136,-0.76966,0.26391,60.603,0.2423,-0.14588,-0.95917,181.3,0.77673,0.62157,0.10168,144.47 > view matrix models > #6,0.83862,-0.52324,0.15147,59.721,0.25181,0.1258,-0.95956,179.9,0.48302,0.84285,0.23726,142.86 > view matrix models > #6,0.83862,-0.52324,0.15147,65.323,0.25181,0.1258,-0.95956,180.96,0.48302,0.84285,0.23726,142.89 > view matrix models > #6,0.95786,-0.28621,0.024104,64.571,0.12152,0.32779,-0.9369,179.86,0.26025,0.90036,0.34875,142.2 > view matrix models > #6,0.95786,-0.28621,0.024104,69.081,0.12152,0.32779,-0.9369,179.6,0.26025,0.90036,0.34875,145.25 > view matrix models > #6,0.99166,-0.12718,0.020762,68.268,0.078066,0.46469,-0.88202,178.69,0.10253,0.87629,0.47075,144.93 > view matrix models > #6,0.99166,-0.12718,0.020762,71.296,0.078066,0.46469,-0.88202,178.16,0.10253,0.87629,0.47075,142.07 > view matrix models > #6,0.99681,-0.079703,-0.0035541,71.144,0.03998,0.53757,-0.84227,177.64,0.069042,0.83944,0.53904,142 > view matrix models > #6,0.99716,-0.074257,-0.012303,71.15,0.031711,0.56269,-0.82606,177.45,0.068264,0.82332,0.56345,141.99 > view matrix models > #6,0.99716,-0.074257,-0.012303,73.013,0.031711,0.56269,-0.82606,179.07,0.068264,0.82332,0.56345,139.72 > view matrix models > #6,0.99137,-0.10112,0.083463,72.783,0.12388,0.5138,-0.84892,179.4,0.042957,0.85193,0.52189,139.74 > view matrix models > #6,0.97472,-0.16585,0.14971,72.864,0.21862,0.56975,-0.79221,178.87,0.046091,0.80491,0.5916,139.71 > view matrix models > #6,0.97472,-0.16585,0.14971,66.388,0.21862,0.56975,-0.79221,177,0.046091,0.80491,0.5916,139.85 > view matrix models > #6,0.97472,-0.16585,0.14971,65.891,0.21862,0.56975,-0.79221,170.48,0.046091,0.80491,0.5916,140.2 > view matrix models > #6,0.96533,-0.18599,0.18318,65.867,0.261,0.70116,-0.66352,169.3,-0.0050305,0.68832,0.72539,140.29 > view matrix models > #6,0.96533,-0.18599,0.18318,66.511,0.261,0.70116,-0.66352,168.3,-0.0050305,0.68832,0.72539,143.24 > show #6.1 models > select subtract #6.1 1 model selected > hide #6.1 models > show #6.1 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.94443,-0.2328,0.23207,66.506,0.32652,0.74573,-0.58075,167.87,-0.03786,0.62426,0.7803,143.27 > view matrix models > #6,0.95088,-0.20342,0.23333,66.389,0.30346,0.76132,-0.57298,167.76,-0.061086,0.61564,0.78566,143.27 > view matrix models > #6,0.95088,-0.20342,0.23333,66.524,0.30346,0.76132,-0.57298,165.1,-0.061086,0.61564,0.78566,141.46 > view matrix models > #6,0.95088,-0.20342,0.23333,65.026,0.30346,0.76132,-0.57298,165.15,-0.061086,0.61564,0.78566,142.44 > hide #!6 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260302 update/STAND-Cas3.cxs"" > select subtract #6 1 model selected > show #!6 models > hide #6.1 models > hide #!6 models > hide #!2 models > show #!3 models > show #3.4 models > lighting simple > lighting soft > hide #!3 models > show #!4 models > show #4.4 models > hide #!4 models > show #!2 models > select add #2.2 3188 atoms, 417 residues, 1 model selected > select add #2.3 6402 atoms, 837 residues, 2 models selected > select add #2.4 9638 atoms, 1260 residues, 3 models selected > select add #2.5 12874 atoms, 1683 residues, 4 models selected > select add #2.6 16040 atoms, 2097 residues, 5 models selected > select add #2.7 19049 atoms, 2489 residues, 6 models selected > select add #2.8 20341 atoms, 2649 residues, 7 models selected > select add #2.9 21610 atoms, 2806 residues, 8 models selected > select add #2.12 23365 atoms, 3034 residues, 9 models selected > select add #2.13 23531 atoms, 3042 residues, 10 models selected > select add #2.14 24329 atoms, 3081 residues, 11 models selected > select add #2.15 25638 atoms, 3142 residues, 12 models selected > hide sel surfaces > hide #2.10 models > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 14 models selected > select subtract #2 14 models selected > show #!6 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > show #6.1 models > view matrix models > #6,0.93837,0.10489,0.32933,63.433,-0.053,0.98524,-0.16277,162.49,-0.34154,0.13528,0.93008,143.63 > view matrix models > #6,0.93837,0.10489,0.32933,64.697,-0.053,0.98524,-0.16277,156.83,-0.34154,0.13528,0.93008,145.33 > view matrix models > #6,0.93837,0.10489,0.32933,64.315,-0.053,0.98524,-0.16277,155.51,-0.34154,0.13528,0.93008,143.28 > view matrix models > #6,0.95344,-0.00022601,0.30157,64.849,0.075634,0.96822,-0.2384,155.95,-0.29193,0.25011,0.92316,142.89 > select subtract #6 1 model selected > ui tool show ""Side View"" > save /Users/xuchengtao/Desktop/image478.png supersample 3 > hide #!6.1 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > show sel atoms > select subtract #6.1 1 model selected > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > select subtract #6 1 model selected > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.95344,-0.00022601,0.30157,67.428,0.075634,0.96822,-0.2384,156.45,-0.29193,0.25011,0.92316,143.3 > select subtract #6.1 1 model selected > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.95344,-0.00022601,0.30157,67.843,0.075634,0.96822,-0.2384,155.19,-0.29193,0.25011,0.92316,142.75 > view matrix models > #6,0.95344,-0.00022601,0.30157,69.787,0.075634,0.96822,-0.2384,154.99,-0.29193,0.25011,0.92316,135.85 > view matrix models > #6,0.95344,-0.00022601,0.30157,71.259,0.075634,0.96822,-0.2384,153.51,-0.29193,0.25011,0.92316,134.75 > select subtract #6.1 1 model selected > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > select subtract #6 1 model selected > save /Users/xuchengtao/Desktop/image479.png supersample 3 > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > combine #6 > hide #!6 models > select add #7 19210 atoms, 19586 bonds, 2564 residues, 3 models selected > select subtract #6 9605 atoms, 9793 bonds, 1282 residues, 2 models selected > rainbow sel > hide sel atoms > select subtract #7 Nothing selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260302 update/STAND-Cas3.cxs"" ——— End of log from Mon Mar 2 20:22:33 2026 ——— > view name session-start opened ChimeraX session > hide #7 models > show #7 models > show #7#!2 surfaces > hide #!2,7 surfaces > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 3 models selected > select subtract #2 14 models selected > open ""/Users/xuchengtao/Documents/Building models undergoing/20250505 I-E > apo/all_251219.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Building models undergoing/20250505 I-E apo/all_251219.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 LYS A 33 ALA A 43 1 11 Start residue of secondary structure not found: HELIX 2 2 PRO A 92 THR A 97 1 6 Start residue of secondary structure not found: HELIX 3 3 HIS A 99 ASP A 110 1 12 Start residue of secondary structure not found: HELIX 4 4 GLY A 114 SER A 116 1 3 Start residue of secondary structure not found: HELIX 5 5 ARG A 172 GLU A 183 1 12 165 messages similar to the above omitted End residue of secondary structure not found: SHEET 2 2 1 LEU A 65 ARG A 69 0 Start residue of secondary structure not found: SHEET 3 3 1 LYS A 75 VAL A 83 0 Start residue of secondary structure not found: SHEET 4 4 1 ARG A 87 PRO A 89 0 Start residue of secondary structure not found: SHEET 5 5 1 GLU A 121 GLU A 123 0 Start residue of secondary structure not found: SHEET 6 6 1 ILE A 132 THR A 134 0 Start residue of secondary structure not found: SHEET 7 7 1 LEU A 141 SER A 143 0 1 messages similar to the above omitted End residue of secondary structure not found: SHEET 9 9 1 ALA A 161 GLY A 169 0 Start residue of secondary structure not found: SHEET 10 10 1 THR A 203 PRO A 208 0 Start residue of secondary structure not found: SHEET 11 11 1 TRP A 237 SER A 242 0 Start residue of secondary structure not found: SHEET 12 12 1 ALA A 250 VAL A 252 0 Start residue of secondary structure not found: SHEET 13 13 1 GLN A 255 HIS A 258 0 Start residue of secondary structure not found: SHEET 14 14 1 ARG A 265 ALA A 267 0 47 messages similar to the above omitted Chain information for all_251219.pdb --- Chain | Description 8.1/A | No description available 8.2/A | No description available 8.4/A 8.5/A 8.6/A | No description available 8.7/A | No description available 8.8/A | No description available 8.9/A | No description available 8.10/A | No description available 8.11/A | No description available 8.3/B | No description available Computing secondary structure > select add #8 29422 atoms, 30140 bonds, 5 pseudobonds, 3739 residues, 17 models selected > select subtract #8 Nothing selected > hide #8.1 models > hide #!8.2 models > show #!8.2 models > show #8.1 models > select add #8 29422 atoms, 30140 bonds, 5 pseudobonds, 3739 residues, 17 models selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,23.052,0,1,0,12.255,0,0,1,-0.27371 > view matrix models #8,1,0,0,8.1073,0,1,0,12.43,0,0,1,-16.335 > view matrix models > #8,-0.47605,0.87485,-0.089455,106.89,-0.87815,-0.47837,-0.0051047,331.22,-0.047258,0.076124,0.99598,-15.867 > view matrix models > #8,-0.47605,0.87485,-0.089455,129.25,-0.87815,-0.47837,-0.0051047,303.52,-0.047258,0.076124,0.99598,63.539 > view matrix models > #8,-0.80337,0.58959,-0.083512,209.75,-0.48883,-0.57289,0.65791,180.23,0.34005,0.56937,0.74845,-21.854 > view matrix models > #8,-0.59688,0.14575,0.78898,135.66,0.72291,0.52428,0.45004,-101.53,-0.34805,0.83898,-0.41829,175.06 > view matrix models > #8,-0.59688,0.14575,0.78898,128.53,0.72291,0.52428,0.45004,-123.18,-0.34805,0.83898,-0.41829,211.29 > view matrix models > #8,-0.066312,0.18,0.98143,34.641,0.98738,-0.12991,0.090542,-29.962,0.1438,0.97505,-0.16912,95.673 > cartoon style (#8.1,3,8-11#!8.2,4-7 & sel) modeHelix tube sides 20 > view matrix models > #8,-0.066312,0.18,0.98143,40.77,0.98738,-0.12991,0.090542,5.5925,0.1438,0.97505,-0.16912,30.345 > view matrix models > #8,-0.23998,0.23931,0.94082,61.663,0.90516,-0.29511,0.30594,10.047,0.35086,0.92501,-0.14579,5.9962 > view matrix models > #8,-0.23998,0.23931,0.94082,66.105,0.90516,-0.29511,0.30594,15.166,0.35086,0.92501,-0.14579,0.33371 > mmaker #8 to #2 No matrix compatible with both reference structure and all match structures > view matrix models > #8,-0.43793,-0.0067132,0.89898,127.53,0.86148,-0.28905,0.4175,7.4158,0.25705,0.95729,0.13237,-25.092 > view matrix models > #8,-0.43793,-0.0067132,0.89898,125.18,0.86148,-0.28905,0.4175,-34.179,0.25705,0.95729,0.13237,9.6447 > view matrix models > #8,-0.43793,-0.0067132,0.89898,132.26,0.86148,-0.28905,0.4175,-57.743,0.25705,0.95729,0.13237,27.339 > view matrix models > #8,-0.45675,-0.01941,0.88939,136.85,0.85392,-0.28986,0.43221,-58.038,0.2494,0.95687,0.14896,25.218 > view matrix models > #8,-0.45675,-0.01941,0.88939,100.92,0.85392,-0.28986,0.43221,-10.074,0.2494,0.95687,0.14896,-26.039 > view matrix models > #8,-0.29121,-0.094845,0.95195,80.996,0.89174,-0.38722,0.23421,20.811,0.3464,0.9171,0.19734,-39.663 > view matrix models > #8,-0.29121,-0.094845,0.95195,93.761,0.89174,-0.38722,0.23421,43.303,0.3464,0.9171,0.19734,-31.919 > view matrix models > #8,-0.40751,0.038729,0.91238,96.708,0.85418,-0.33719,0.39583,22.801,0.32298,0.94064,0.10433,-20.861 > view matrix models > #8,-0.48413,-0.0021604,0.87499,116.74,0.79672,-0.4145,0.4398,35.362,0.36174,0.91005,0.20239,-33.7 > view matrix models > #8,-0.53206,-0.02434,0.84635,129.9,0.75617,-0.46337,0.46205,45.693,0.38093,0.88583,0.26495,-39.851 > view matrix models > #8,-0.61881,-0.0091684,0.78548,146.92,0.73106,-0.37261,0.57159,24.058,0.28744,0.92794,0.23728,-29.436 > view matrix models > #8,-0.61881,-0.0091684,0.78548,150.07,0.73106,-0.37261,0.57159,31.339,0.28744,0.92794,0.23728,-25.629 > hide #!2 models > hide #!7 models > show #!7 models > hide #!7 models > show #!6 models > combine #6 > hide #!6 models > select subtract #8 Nothing selected > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > select subtract #9 Nothing selected > select add #8 29422 atoms, 30140 bonds, 5 pseudobonds, 3739 residues, 17 models selected > hide #9 models > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: all_251219.pdb #8.3/B A -14 all_251219.pdb #8.3/B U -13 all_251219.pdb #8.3/B G -12 all_251219.pdb #8.3/B G -11 all_251219.pdb #8.3/B A -10 all_251219.pdb #8.3/B C -9 all_251219.pdb #8.3/B C -8 all_251219.pdb #8.3/B C -7 all_251219.pdb #8.3/B G -6 all_251219.pdb #8.3/B A -5 all_251219.pdb #8.3/B G -4 all_251219.pdb #8.3/B G -3 all_251219.pdb #8.3/B U -2 all_251219.pdb #8.3/B G -1 all_251219.pdb #8.3/B G 0 all_251219.pdb #8.3/B U 1 all_251219.pdb #8.3/B G 2 all_251219.pdb #8.3/B A 3 all_251219.pdb #8.3/B C 4 all_251219.pdb #8.3/B G 5 all_251219.pdb #8.3/B C 6 all_251219.pdb #8.3/B C 7 all_251219.pdb #8.3/B C 8 all_251219.pdb #8.3/B A 9 all_251219.pdb #8.3/B U 10 all_251219.pdb #8.3/B G 11 all_251219.pdb #8.3/B U 12 all_251219.pdb #8.3/B C 13 all_251219.pdb #8.3/B C 14 all_251219.pdb #8.3/B C 15 all_251219.pdb #8.3/B G 16 all_251219.pdb #8.3/B C 17 all_251219.pdb #8.3/B A 18 all_251219.pdb #8.3/B G 19 all_251219.pdb #8.3/B C 20 all_251219.pdb #8.3/B C 21 all_251219.pdb #8.3/B C 22 all_251219.pdb #8.3/B G 23 all_251219.pdb #8.3/B U 24 all_251219.pdb #8.3/B G 25 all_251219.pdb #8.3/B G 26 Using Amber 20 recommended default charges and atom types for standard residues copy of all_251219.pdb #/B G -1 RG Nonstandard name for heavy atom copy of all_251219.pdb #/B G -1 . > close #8 > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20250505 I-E apo/MERGE.pdb"" Chain information for MERGE.pdb #8 --- Chain | Description A | No description available B | No description available C D E F G I | No description available H | No description available J K | No description available L | No description available > show #9 models > hide #9 models > show #8 cartoons Computing secondary structure > hide #8 atoms > cartoon style #8 modeHelix tube sides 20 > show #9 models > hide #9 models > show #!2 models > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 2 models selected > select subtract #2 14 models selected > select add #8 31370 atoms, 32136 bonds, 4001 residues, 1 model selected > view matrix models > #8,0.30539,0.33129,-0.89274,159.57,0.33816,-0.91415,-0.22356,240.34,-0.89016,-0.23362,-0.3912,323.91 > view matrix models > #8,0.50653,0.10085,-0.8563,158.97,0.51094,-0.83509,0.20389,153.46,-0.69452,-0.5408,-0.47452,349.22 > view matrix models > #8,-0.6648,0.46756,0.58261,90.129,0.56636,-0.19309,0.80122,-14.542,0.48711,0.86261,-0.13644,-41.952 > view matrix models > #8,-0.6648,0.46756,0.58261,99.514,0.56636,-0.19309,0.80122,14.345,0.48711,0.86261,-0.13644,-19.221 > view matrix models > #8,-0.6648,0.46756,0.58261,97.246,0.56636,-0.19309,0.80122,4.512,0.48711,0.86261,-0.13644,21.285 > view matrix models > #8,-0.59547,-0.045852,0.80207,130.07,0.78442,0.18241,0.5928,-49.941,-0.17348,0.98215,-0.072652,86.644 > mmaker #8 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 merged_251009_real_space_refined_006_real_space_refined_002_best.pdb, chain J (#2) with MERGE.pdb, chain H (#8), sequence alignment score = 2455.9 RMSD between 333 pruned atom pairs is 0.626 angstroms; (across all 500 pairs: 4.873) > view matrix models > #8,-0.66416,0.035737,0.74674,149.66,0.68973,-0.35603,0.63049,29.715,0.28839,0.93379,0.21181,-25.855 > view matrix models > #8,-0.70719,0.10291,0.69949,152.25,0.64475,-0.31215,0.69776,21.563,0.29015,0.94444,0.1544,-20.436 > view matrix models > #8,-0.7067,0.10212,0.70011,152.22,0.6453,-0.31271,0.69699,21.658,0.29011,0.94434,0.15509,-20.502 > view matrix models > #8,-0.7067,0.10212,0.70011,153.64,0.6453,-0.31271,0.69699,22.859,0.29011,0.94434,0.15509,-20.413 > select subtract #8 Nothing selected > show #9 models > hide #!2 models > hide #9 models > select add #8 31370 atoms, 32136 bonds, 4001 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for MERGE.pdb_A SES surface #8.1: minimum, -13.81, mean -0.31, maximum 14.85 Coulombic values for MERGE.pdb_B SES surface #8.2: minimum, -23.35, mean -10.48, maximum 0.21 Coulombic values for MERGE.pdb_C SES surface #8.3: minimum, -18.43, mean -1.83, maximum 18.68 Coulombic values for MERGE.pdb_D SES surface #8.4: minimum, -20.41, mean -1.83, maximum 14.33 Coulombic values for MERGE.pdb_E SES surface #8.5: minimum, -17.99, mean -1.80, maximum 17.14 Coulombic values for MERGE.pdb_F SES surface #8.6: minimum, -22.79, mean -1.78, maximum 14.19 Coulombic values for MERGE.pdb_G SES surface #8.7: minimum, -18.83, mean -1.85, maximum 15.64 Coulombic values for MERGE.pdb_H SES surface #8.8: minimum, -16.09, mean -1.63, maximum 15.67 Coulombic values for MERGE.pdb_I SES surface #8.9: minimum, -16.90, mean -1.63, maximum 14.58 Coulombic values for MERGE.pdb_J SES surface #8.10: minimum, -20.15, mean 0.48, maximum 14.12 Coulombic values for MERGE.pdb_K SES surface #8.11: minimum, -18.70, mean 0.45, maximum 12.95 Coulombic values for MERGE.pdb_L SES surface #8.12: minimum, -14.01, mean 2.11, maximum 13.45 To also show corresponding color key, enter the above coulombic command and add key true > select subtract #8 12 models selected > show #9 models > color #9#!8 byhetero > undo > hide #!8 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > coulombic sel Coulombic values for copy of stand.pdb_A SES surface #9.1: minimum, -19.03, mean -1.01, maximum 14.42 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > show sel surfaces > hide sel surfaces > show #!8 models > view matrix models > #9,0.95344,-0.00022601,0.30157,69.816,0.075634,0.96822,-0.2384,156.85,-0.29193,0.25011,0.92316,144.84 > view matrix models > #9,0.87756,0.092192,0.47052,68.806,-0.030617,0.99011,-0.1369,156.3,-0.47848,0.10573,0.87171,145.38 > select subtract #9 1 model selected > select add #8 31370 atoms, 32136 bonds, 4001 residues, 1 model selected > view matrix models > #8,-0.7067,0.10212,0.70011,153.6,0.6453,-0.31271,0.69699,22.905,0.29011,0.94434,0.15509,-20.308 > select subtract #8 12 models selected > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,0.87756,0.092192,0.47052,68.519,-0.030617,0.99011,-0.1369,156.28,-0.47848,0.10573,0.87171,148.36 > view matrix models > #9,0.87756,0.092192,0.47052,66.454,-0.030617,0.99011,-0.1369,156.6,-0.47848,0.10573,0.87171,147.67 > show sel surfaces > view matrix models > #9,0.87756,0.092192,0.47052,58.514,-0.030617,0.99011,-0.1369,122.51,-0.47848,0.10573,0.87171,124.69 > hide sel surfaces > select subtract #9 1 model selected > select add #8 31370 atoms, 32136 bonds, 4001 residues, 3 models selected > hide sel surfaces > hide #!8 models > select subtract #8 12 models selected > show #!9 surfaces > hide #!9 surfaces > rainbow #!9 > color #!9 byhetero > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260302 update/STAND-Cas3.cxs"" > open 8D9F Summary of feedback from opening 8D9F fetched from pdb --- note | Fetching compressed mmCIF 8d9f from http://files.rcsb.org/download/8d9f.cif 8d9f title: gRAMP-TPR-CHAT (Craspase) [more info...] Chain information for 8d9f #10 --- Chain | Description | UniProt A | CHAT domain protein | A0A0B0EKL4_9BACT 15-716 B | RAMP superfamily protein | A0A0B0EGF3_9BACT 1-1019 1391-1688 C | RNA (33-MER) | Non-standard residues in 8d9f #10 --- ZN — zinc ion > hide #!9 models > select #10/A 5436 atoms, 5553 bonds, 670 residues, 1 model selected > cartoon sel > cartoon style sel modeHelix tube sides 20 > ui tool show ""Side View"" > color sel orange > select add #10 16163 atoms, 16597 bonds, 17 pseudobonds, 1949 residues, 3 models selected > select subtract #10 Nothing selected > open 8D9E Summary of feedback from opening 8D9E fetched from pdb --- note | Fetching compressed mmCIF 8d9e from http://files.rcsb.org/download/8d9e.cif 8d9e title: gRAMP-match PFS target [more info...] Chain information for 8d9e #11 --- Chain | Description | UniProt B | RAMP superfamily protein | A0A0B0EGF3_9BACT 1-1031 1388-1693 C | RNA (36-MER) | D | RNA (5'-R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*GP*UP*A)-3') | Non-standard residues in 8d9e #11 --- ZN — zinc ion > mmaker #11 to #10 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 8d9f, chain B (#10) with 8d9e, chain B (#11), sequence alignment score = 5521.8 RMSD between 955 pruned atom pairs is 1.156 angstroms; (across all 1198 pairs: 3.625) > open 8D8N Summary of feedback from opening 8D8N fetched from pdb --- note | Fetching compressed mmCIF 8d8n from http://files.rcsb.org/download/8d8n.cif 8d8n title: gRAMP non-match PFS target RNA [more info...] Chain information for 8d8n #12 --- Chain | Description | UniProt B | RAMP superfamily protein | A0A0B0EGF3_9BACT 1-1722 C | RNA (35-MER) | D | RNA (5'-R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*A)-3') | Non-standard residues in 8d8n #12 --- ZN — zinc ion > mmaker #12 to #10 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 8d9f, chain B (#10) with 8d8n, chain B (#12), sequence alignment score = 5558.1 RMSD between 942 pruned atom pairs is 1.203 angstroms; (across all 1198 pairs: 2.641) > select add #10 16163 atoms, 16597 bonds, 17 pseudobonds, 1949 residues, 3 models selected > select add #11 27464 atoms, 28268 bonds, 69 pseudobonds, 3266 residues, 6 models selected > select add #12 38739 atoms, 39905 bonds, 112 pseudobonds, 4582 residues, 11 models selected > cartoon style (#!10-12 & sel) modeHelix tube sides 20 > select subtract #10 22576 atoms, 23308 bonds, 95 pseudobonds, 2633 residues, 8 models selected > select subtract #11 11275 atoms, 11637 bonds, 43 pseudobonds, 1316 residues, 5 models selected > select subtract #12 Nothing selected > hide #!12 models > hide #!11 models > open 8D97 Summary of feedback from opening 8D97 fetched from pdb --- note | Fetching compressed mmCIF 8d97 from http://files.rcsb.org/download/8d97.cif 8d97 title: Apo gRAMP [more info...] Chain information for 8d97 #13 --- Chain | Description | UniProt A | RAMP superfamily protein | A0A0B0EGF3_9BACT 1-1688 C | RNA (42-MER) | Non-standard residues in 8d97 #13 --- ZN — zinc ion > mmaker #13 to #10 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 8d9f, chain B (#10) with 8d97, chain A (#13), sequence alignment score = 5898.6 RMSD between 1183 pruned atom pairs is 1.137 angstroms; (across all 1242 pairs: 1.369) > rename #13 8d97-apo > hide #!13 models > show #!12 models > rename #12 ""8d8n-gRAMP non-match PFS target RNA"" > rename #13 ""8d97-apo gRAMP"" > rename #10 ""8d9f-gRAMP-TPR-CHAT (Craspase) apo"" > rename #11 ""8d9e-gRAMP-match PFS target"" > open 8D9G Summary of feedback from opening 8D9G fetched from pdb --- note | Fetching compressed mmCIF 8d9g from http://files.rcsb.org/download/8d9g.cif 8d9g title: gRAMP-TPR-CHAT Non match PFS target RNA(Craspase) [more info...] Chain information for 8d9g #14 --- Chain | Description | UniProt A | CHAT domain protein | A0A0B0EKL4_9BACT 14-716 B | RAMP superfamily protein | A0A0B0EGF3_9BACT 1-1025 1386-1688 C | RNA (36-MER) | D | RNA (5'-R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*GP*AP*U)-3') | Non-standard residues in 8d9g #14 --- ZN — zinc ion > hide #!12 models > mmaker #14 to #10 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain B (#10) with 8d9g, chain B (#14), sequence alignment score = 6185.1 RMSD between 1076 pruned atom pairs is 0.847 angstroms; (across all 1240 pairs: 2.104) > cartoon style #10,14 modeHelix tube sides 20 > rename #14 ""8d9g-gRAMP-TPR-CHAT Non match PFS target RNA(Craspase)"" > open 8D9H Summary of feedback from opening 8D9H fetched from pdb --- note | Fetching compressed mmCIF 8d9h from http://files.rcsb.org/download/8d9h.cif 8d9h title: gRAMP-TPR-CHAT match PFS target RNA(Craspase) [more info...] Chain information for 8d9h #15 --- Chain | Description | UniProt B | RAMP superfamily protein | A0A0B0EGF3_9BACT 1-1025 1386-1688 C | RNA (36-MER) | D | RNA (5'-R(P*UP*CP*CP*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*GP*U)-3') | E | CHAT domain protein | A0A0B0EKL4_9BACT 15-716 Non-standard residues in 8d9h #15 --- PO4 — phosphate ion ZN — zinc ion > mmaker #15 to #10 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain B (#10) with 8d9h, chain B (#15), sequence alignment score = 6076.1 RMSD between 994 pruned atom pairs is 1.214 angstroms; (across all 1224 pairs: 2.244) > cartoon style #10,14-15 modeHelix tube sides 20 > rename #15 ""8d9hgRAMP-TPR-CHAT match PFS target RNA(Craspase)"" > hide #!14 models > hide #!15 models > show #!15 models > hide #!15 models > show #!14 models > hide #!10 models > show #!15 models > hide #!14 models > hide #!15 models > show #!14 models > show #!15 models > hide #!15 models > show #!10 models > hide #!14 models > hide #!10 models > show #!8 models > show #!9 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > hide #!8 models > mlp sel Map values for surface ""copy of stand.pdb_A SES surface"": minimum -27.81, mean -5.549, maximum 23.54 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select subtract #9 1 model selected > show #!15 models > show #!14 models > hide #!9 models > hide #!14 models > show #!10 models > hide #!15 models > show #!9 models > hide #!9 models > show #!7 models > select add #7 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #7,0.47,0.69693,0.54165,66.802,-0.83228,0.55428,0.0089929,154.86,-0.29396,-0.45503,0.84056,138.72 > view matrix models > #7,0.47,0.69693,0.54165,107.67,-0.83228,0.55428,0.0089929,177.92,-0.29396,-0.45503,0.84056,131.07 > view matrix models > #7,-0.48795,0.6251,0.60923,107.95,-0.20929,-0.76138,0.61359,182.3,0.84741,0.17189,0.50234,128.92 > view matrix models > #7,-0.48795,0.6251,0.60923,120,-0.20929,-0.76138,0.61359,210.97,0.84741,0.17189,0.50234,95.604 > view matrix models > #7,-0.58883,0.70066,0.40293,120.42,-0.528,-0.71089,0.46459,211.34,0.61196,0.060814,0.78855,95.115 > view matrix models > #7,-0.58883,0.70066,0.40293,138.45,-0.528,-0.71089,0.46459,199.43,0.61196,0.060814,0.78855,110.6 > view matrix models > #7,-0.59303,0.74636,0.30211,138.61,-0.51933,-0.64128,0.56485,198.68,0.61532,0.17808,0.7679,110.07 > view matrix models > #7,-0.59254,0.7516,0.28982,148.53,-0.53226,-0.63536,0.55948,187.49,0.60464,0.17726,0.77652,123.58 > view matrix models > #7,-0.54823,0.78231,0.29569,148.34,-0.3104,-0.51864,0.79666,185.93,0.77659,0.34497,0.52717,123.65 > view matrix models > #7,-0.5237,0.81724,0.24055,139.8,-0.35285,-0.46509,0.81191,174.63,0.7754,0.34032,0.53192,121.09 > view matrix models > #7,-0.36184,0.83602,0.41248,139.01,-0.38214,-0.5366,0.75235,175.23,0.85032,0.11461,0.51364,122.32 > view matrix models > #7,-0.36975,0.86533,0.33837,134.61,-0.40083,-0.4771,0.78212,162.17,0.83823,0.15356,0.52325,115.47 > view matrix models > #7,-0.36975,0.86533,0.33837,151.03,-0.40083,-0.4771,0.78212,207.42,0.83823,0.15356,0.52325,54.849 > view matrix models > #7,-0.31793,0.88058,0.35143,150.89,-0.23354,-0.43197,0.87113,206.81,0.9189,0.19489,0.34299,55.317 > view matrix models > #7,-0.31793,0.88058,0.35143,117.36,-0.23354,-0.43197,0.87113,180.95,0.9189,0.19489,0.34299,98.274 > view matrix models > #7,-0.39239,0.86929,0.3006,117.63,-0.0010642,-0.32724,0.94494,180.08,0.9198,0.37047,0.12933,98.189 > view matrix models > #7,-0.39239,0.86929,0.3006,108.74,-0.0010642,-0.32724,0.94494,155.7,0.9198,0.37047,0.12933,97.506 > view matrix models > #7,-0.39239,0.86929,0.3006,110.82,-0.0010642,-0.32724,0.94494,159.89,0.9198,0.37047,0.12933,87.621 > view matrix models > #7,-0.28755,0.71221,0.64037,110.3,-0.35126,-0.70044,0.62129,163.13,0.89103,-0.04628,0.45158,88.542 > view matrix models > #7,-0.28755,0.71221,0.64037,104.68,-0.35126,-0.70044,0.62129,167.96,0.89103,-0.04628,0.45158,87.251 > view matrix models > #7,-0.25682,0.96342,0.076624,105.55,0.088929,-0.05539,0.9945,163.1,0.96236,0.26222,-0.07145,87.66 > view matrix models > #7,-0.25682,0.96342,0.076624,101.25,0.088929,-0.05539,0.9945,163.09,0.96236,0.26222,-0.07145,92.327 > view matrix models > #7,-0.25682,0.96342,0.076624,109.07,0.088929,-0.05539,0.9945,156.85,0.96236,0.26222,-0.07145,95.319 > view matrix models > #7,-0.12452,0.95197,0.27973,108.32,0.38794,-0.21278,0.89679,157.99,0.91323,0.22019,-0.34282,96.594 > view matrix models > #7,-0.12452,0.95197,0.27973,100.71,0.38794,-0.21278,0.89679,150.87,0.91323,0.22019,-0.34282,81.341 > view matrix models > #7,0.0027682,0.93744,0.34813,100.5,0.27561,-0.33536,0.90087,151.51,0.96126,0.093455,-0.2593,81.666 > view matrix models > #7,-0.0036892,0.86415,0.50322,100.28,0.31767,-0.47615,0.81998,152.55,0.94819,0.16289,-0.27276,81.361 > view matrix models > #7,-0.0036892,0.86415,0.50322,103.78,0.31767,-0.47615,0.81998,153.25,0.94819,0.16289,-0.27276,80.166 > view matrix models > #7,-0.26787,0.9583,0.099551,104.9,-0.10688,-0.13225,0.98544,150.9,0.95751,0.25333,0.13785,78.11 > view matrix models > #7,-0.26787,0.9583,0.099551,105.1,-0.10688,-0.13225,0.98544,151.03,0.95751,0.25333,0.13785,88.453 > select subtract #7 1 model selected > hide #!10 models > show #!8 models > hide #!7 models > show #!9 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,0.1054,-0.56853,0.81588,59.041,0.34668,0.78999,0.5057,121.42,-0.93204,0.22955,0.28036,125.82 > view matrix models > #9,-0.059313,-0.24439,-0.96786,63.826,-0.7351,-0.64526,0.20798,126.79,-0.67535,0.72382,-0.14138,125.67 > view matrix models > #9,-0.65587,-0.3711,0.65735,58.082,-0.048086,-0.84851,-0.52699,130.79,0.75334,-0.37725,0.53867,128.9 > view matrix models > #9,-0.28135,0.83487,-0.4731,57.816,0.94548,0.1569,-0.28539,127.15,-0.16404,-0.52761,-0.8335,133.3 > view matrix models > #9,0.20045,0.97808,0.05638,55.925,0.79465,-0.12866,-0.59328,129.14,-0.57302,0.16372,-0.80302,130.17 > hide #!8 models > mlp sel Map values for surface ""copy of stand.pdb_A SES surface"": minimum -27.84, mean -5.548, maximum 23.52 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for copy of stand.pdb_A SES surface #9.1: minimum, -19.03, mean -1.01, maximum 14.42 To also show corresponding color key, enter the above coulombic command and add key true > select subtract #9 1 model selected > mlp #!9 Map values for surface ""copy of stand.pdb_A SES surface"": minimum -27.84, mean -5.548, maximum 23.52 To also show corresponding color key, enter the above mlp command and add key true > hide #!9 surfaces > show #!7 models > hide #!7 models > show #!8 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260302 update/STAND-Cas3.cxs"" > hide #!9 models > show #!9 models > hide #!9 models > hide #!8 models > show #!9 models > show #!10 models > hide #!10 models > show #!10 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,-0.76555,0.61901,0.17535,55.902,-0.22015,-0.50815,0.83266,124.62,0.60453,0.59884,0.52529,125.11 > mmaker #9 to #10/A 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain A (#10) with copy of stand.pdb, chain A (#9), sequence alignment score = 232 RMSD between 12 pruned atom pairs is 1.230 angstroms; (across all 263 pairs: 23.258) > select subtract #9 1 model selected > hide #!9 models > select #10/A 5436 atoms, 5553 bonds, 670 residues, 1 model selected > rainbow sel > select add #10 16163 atoms, 16597 bonds, 17 pseudobonds, 1949 residues, 3 models selected > select subtract #10 Nothing selected > show #!9 models > hide #!10 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > hide sel atoms > select subtract #9 1 model selected > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,-0.76485,0.53809,-0.35422,138.86,0.28367,0.77498,0.56475,167.09,0.5784,0.33146,-0.74538,96.873 > view matrix models > #9,-0.76485,0.53809,-0.35422,134.06,0.28367,0.77498,0.56475,165.82,0.5784,0.33146,-0.74538,116.5 > view matrix models > #9,-0.51327,0.2362,0.82508,132.08,-0.08772,-0.97078,0.22335,176.48,0.85373,0.042261,0.51899,108.97 > hide #!9 models > show #!9 models > show #!10 models > select subtract #9 1 model selected > select #10/A 5436 atoms, 5553 bonds, 670 residues, 1 model selected > color sel orange > select add #10 16163 atoms, 16597 bonds, 17 pseudobonds, 1949 residues, 3 models selected > select subtract #10 Nothing selected > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > select add #9 9605 atoms, 9793 bonds, 1282 residues, 2 models selected > view matrix models > #9,-0.16029,0.43317,0.88694,130.75,-0.37252,-0.85866,0.35204,175.46,0.91408,-0.27398,0.299,111.45 > view matrix models > #9,-0.25838,0.80303,0.53701,130.21,-0.51726,-0.58449,0.62515,173,0.81589,-0.11625,0.5664,109.61 > view matrix models > #9,-0.25838,0.80303,0.53701,125.12,-0.51726,-0.58449,0.62515,179.85,0.81589,-0.11625,0.5664,105.2 > view matrix models > #9,-0.25263,0.85768,0.44783,125.18,-0.53738,-0.50928,0.67221,179.29,0.80461,-0.070835,0.58956,104.87 > view matrix models > #9,-0.24545,0.93054,0.27174,125.48,-0.54771,-0.3644,0.75314,178.23,0.79986,0.036026,0.59911,104.28 > view matrix models > #9,-0.21669,0.53776,0.81477,125.42,-0.65066,0.54265,-0.5312,178.5,-0.7278,-0.64524,0.23231,109.5 > view matrix models > #9,-0.79266,0.59188,-0.14617,128.95,0.56994,0.80453,0.16706,174.23,0.21648,0.049119,-0.97505,110.4 > view matrix models > #9,-0.41287,0.82785,-0.37973,128.56,0.40433,0.54019,0.73805,173.43,0.81612,0.15118,-0.55776,108.15 > view matrix models > #9,0.025769,0.92453,0.38023,125.05,0.019143,-0.38074,0.92448,177.55,0.99948,-0.016545,-0.02751,106.94 > view matrix models > #9,-0.06083,0.99811,-0.0081377,99.499,0.12861,0.015922,0.99157,154.18,0.98983,0.059271,-0.12934,89.886 > view matrix models > #9,0.012462,0.79634,0.60472,98.165,0.15891,-0.59866,0.78508,158.16,0.98721,0.086313,-0.13401,89.764 > view matrix models > #9,0.005849,0.80738,0.59,97.171,0.1679,-0.58243,0.79536,157.48,0.98579,0.094406,-0.13896,87.586 > view matrix models > #9,0.005849,0.80738,0.59,63.028,0.1679,-0.58243,0.79536,189.16,0.98579,0.094406,-0.13896,40.217 > view matrix models > #9,0.005849,0.80738,0.59,75.646,0.1679,-0.58243,0.79536,172.76,0.98579,0.094406,-0.13896,67.074 > view matrix models > #9,0.005849,0.80738,0.59,76.905,0.1679,-0.58243,0.79536,171.07,0.98579,0.094406,-0.13896,65.023 > view matrix models > #9,-0.15758,0.85213,0.49905,77.053,0.28644,-0.44419,0.84891,170.12,0.94505,0.27672,-0.17409,64.22 > view matrix models > #9,-0.395,0.81844,0.41729,77.585,0.057244,-0.43142,0.90033,169.9,0.9169,0.37952,0.12356,62.543 > view matrix models > #9,-0.395,0.81844,0.41729,84.987,0.057244,-0.43142,0.90033,175.56,0.9169,0.37952,0.12356,57.738 > view matrix models > #9,-0.395,0.81844,0.41729,85.659,0.057244,-0.43142,0.90033,174.89,0.9169,0.37952,0.12356,57.788 > view matrix models > #9,-0.395,0.81844,0.41729,86.444,0.057244,-0.43142,0.90033,174.31,0.9169,0.37952,0.12356,58.723 > view matrix models > #9,-0.395,0.81844,0.41729,116.25,0.057244,-0.43142,0.90033,159.65,0.9169,0.37952,0.12356,81.871 > view matrix models > #9,-0.39647,0.74226,0.54025,116.17,0.081124,-0.55785,0.82597,160.58,0.91446,0.3713,0.16095,81.77 > view matrix models > #9,-0.39647,0.74226,0.54025,116.97,0.081124,-0.55785,0.82597,159.57,0.91446,0.3713,0.16095,80.035 > view matrix models > #9,-0.39647,0.74226,0.54025,122.15,0.081124,-0.55785,0.82597,157.77,0.91446,0.3713,0.16095,79.016 > view matrix models > #9,-0.39861,0.75169,0.52544,122.16,-0.025417,-0.58175,0.81297,157.97,0.91677,0.3107,0.251,78.982 > view matrix models > #9,-0.39861,0.75169,0.52544,111.93,-0.025417,-0.58175,0.81297,149.71,0.91677,0.3107,0.251,87.831 > view matrix models > #9,-0.39861,0.75169,0.52544,111.9,-0.025417,-0.58175,0.81297,149.96,0.91677,0.3107,0.251,86.823 > view matrix models > #9,-0.38072,0.75934,0.52769,111.85,-0.069571,-0.59257,0.80251,150.07,0.92207,0.26882,0.27843,86.934 > view matrix models > #9,-0.37534,0.84121,0.38922,111.96,0.013048,-0.41509,0.90969,148.72,0.9268,0.34652,0.14482,87.046 > view matrix models > #9,-0.39077,0.91711,0.078841,112.76,-0.027385,-0.097196,0.99489,146.75,0.92008,0.38661,0.063096,87.155 > view matrix models > #9,-0.50676,0.80562,0.30686,113.73,-0.068361,-0.39239,0.91726,147.01,0.85937,0.44385,0.25392,87.553 > view matrix models > #9,-0.50676,0.80562,0.30686,113.79,-0.068361,-0.39239,0.91726,149.07,0.85937,0.44385,0.25392,79.336 > view matrix models > #9,-0.50676,0.80562,0.30686,117.39,-0.068361,-0.39239,0.91726,158.52,0.85937,0.44385,0.25392,79.339 > view matrix models > #9,-0.20547,0.75622,0.62122,116.38,0.35466,-0.53407,0.76745,159.75,0.91214,0.37801,-0.15846,81.264 > view matrix models > #9,-0.2083,0.75199,0.6254,121.82,0.34872,-0.5403,0.76581,155.1,0.91378,0.37761,-0.14969,90.486 > cartoon style (#!9 & sel) xsection oval modeHelix default > mmaker #9 to #10/A 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain A (#10) with copy of stand.pdb, chain A (#9), sequence alignment score = 232 RMSD between 12 pruned atom pairs is 1.230 angstroms; (across all 263 pairs: 23.258) > open 4KSF Summary of feedback from opening 4KSF fetched from pdb --- note | Fetching compressed mmCIF 4ksf from http://files.rcsb.org/download/4ksf.cif 4ksf title: Crystal Structure of Malonyl-CoA decarboxylase from Agrobacterium vitis, Northeast Structural Genomics Consortium Target RiR35 [more info...] Chain information for 4ksf #16 --- Chain | Description | UniProt A | Malonyl-CoA decarboxylase | B9K0V9_AGRVS 1-449 Non-standard residues in 4ksf #16 --- CL — chloride ion NI — nickel (II) ion 4ksf mmCIF Assemblies --- 1| author_and_software_defined_assembly > select subtract #9 1 model selected > mmaker #16 to #10/A 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain A (#10) with 4ksf, chain A (#16), sequence alignment score = 76.9 RMSD between 18 pruned atom pairs is 1.115 angstroms; (across all 322 pairs: 24.170) > hide #!10 models > show #!10 models > hide #!9 models > select add #16 3257 atoms, 3299 bonds, 2 pseudobonds, 433 residues, 4 models selected > cartoon style (#!16 & sel) modeHelix tube sides 20 > view matrix models > #16,-0.66043,-0.44207,0.60696,137.47,0.70825,-0.098253,0.69909,191.95,-0.24941,0.89158,0.37799,154.57 > view matrix models > #16,-0.70534,-0.66519,0.24499,125.81,0.60964,-0.74557,-0.26918,159.31,0.36172,-0.040507,0.93141,135.46 > view matrix models > #16,-0.70534,-0.66519,0.24499,121.39,0.60964,-0.74557,-0.26918,138.91,0.36172,-0.040507,0.93141,125.87 > view matrix models > #16,-0.52049,-0.44858,0.72654,133.48,0.21153,-0.8921,-0.39926,137.69,0.82725,-0.054128,0.55922,112.95 > view matrix models > #16,-0.049254,0.75476,0.65415,155.28,0.00076187,0.65497,-0.75565,170.46,-0.99879,-0.03672,-0.032835,123.93 > view matrix models > #16,-0.049254,0.75476,0.65415,139.99,0.00076187,0.65497,-0.75565,172.88,-0.99879,-0.03672,-0.032835,138.73 > view matrix models > #16,0.48938,-0.078554,0.86853,117.7,0.2894,0.95413,-0.076765,189.45,-0.82266,0.28891,0.48966,154.31 > view matrix models > #16,0.88964,0.10645,-0.44409,92.498,0.28311,0.63447,0.71924,196.95,0.35832,-0.76559,0.53431,115.85 > view matrix models > #16,0.30956,-0.62015,-0.72082,76.794,0.041336,0.76612,-0.64137,177.22,0.94998,0.16875,0.2628,126 > view matrix models > #16,0.30956,-0.62015,-0.72082,85.205,0.041336,0.76612,-0.64137,158.19,0.94998,0.16875,0.2628,106.59 > select subtract #16 Nothing selected > show #!9 models > hide #!16 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,-0.76485,0.53809,-0.35422,134.66,0.28367,0.77498,0.56475,194.57,0.5784,0.33146,-0.74538,106.03 > view matrix models > #9,-0.76485,0.53809,-0.35422,141.43,0.28367,0.77498,0.56475,199.16,0.5784,0.33146,-0.74538,96.602 > cartoon style (#!9 & sel) modeHelix tube sides 20 > view matrix models > #9,-0.76485,0.53809,-0.35422,135.19,0.28367,0.77498,0.56475,187.96,0.5784,0.33146,-0.74538,87.138 > view matrix models > #9,-0.85705,0.51487,-0.019165,134.03,0.42934,0.73424,0.52589,188.29,0.28484,0.44249,-0.85034,87.022 > view matrix models > #9,-0.55805,0.53487,0.63443,131.35,0.38343,-0.51183,0.76878,193.79,0.73591,0.67227,0.08054,82.163 > hide #!10 models > show #!15 models > select #15/A Nothing selected > select #15/E 5415 atoms, 5530 bonds, 668 residues, 1 model selected > color sel orange > select add #15 16858 atoms, 17352 bonds, 35 pseudobonds, 1999 residues, 3 models selected > show #!14 models > hide #!15 models > select subtract #15 Nothing selected > select #14/A 5516 atoms, 5635 bonds, 679 residues, 1 model selected > color sel orange > select add #14 17148 atoms, 17656 bonds, 54 pseudobonds, 2028 residues, 3 models selected > select subtract #14 Nothing selected > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,-0.55805,0.53487,0.63443,137.36,0.38343,-0.51183,0.76878,163.14,0.73591,0.67227,0.08054,92.715 > view matrix models > #9,-0.45091,0.64298,0.61908,136.84,0.35444,-0.50757,0.78533,163.06,0.81918,0.57354,0.00096944,93.517 > view matrix models > #9,-0.45091,0.64298,0.61908,129.78,0.35444,-0.50757,0.78533,154.16,0.81918,0.57354,0.00096944,83.328 > view matrix models > #9,-0.72639,0.64895,0.22634,131.31,-0.086013,-0.41257,0.90686,153.28,0.68188,0.63926,0.3555,81.644 > view matrix models > #9,-0.53041,0.79599,0.29168,130.26,0.32814,-0.12447,0.93639,151.61,0.78166,0.59238,-0.19518,83.994 > view matrix models > #9,-0.53041,0.79599,0.29168,124.91,0.32814,-0.12447,0.93639,151.04,0.78166,0.59238,-0.19518,89.58 > view matrix models > #9,-0.53041,0.79599,0.29168,112.1,0.32814,-0.12447,0.93639,140.68,0.78166,0.59238,-0.19518,87.31 > view matrix models > #9,-0.54623,0.81955,0.17311,112.44,0.2345,-0.048778,0.97089,140.17,0.80414,0.57092,-0.16554,87.303 > view matrix models > #9,-0.54623,0.81955,0.17311,112.18,0.2345,-0.048778,0.97089,135.9,0.80414,0.57092,-0.16554,86.788 > view matrix models > #9,-0.55186,0.83253,0.048425,112.59,0.36632,0.18984,0.91092,134.88,0.74917,0.52044,-0.40974,88.001 > view matrix models > #9,-0.61797,0.77201,0.14871,112.53,0.4958,0.23587,0.83579,134.91,0.61016,0.59023,-0.52852,88.124 > view matrix models > #9,-0.61797,0.77201,0.14871,112.69,0.4958,0.23587,0.83579,132.25,0.61016,0.59023,-0.52852,93.506 > view matrix models > #9,-0.61797,0.77201,0.14871,111.73,0.4958,0.23587,0.83579,132.27,0.61016,0.59023,-0.52852,95.279 > hide #!14 models > view matrix models > #9,-0.61797,0.77201,0.14871,110.37,0.4958,0.23587,0.83579,132.44,0.61016,0.59023,-0.52852,95.703 > show #!10 models > select subtract #9 1 model selected > hide #!9 models > show #!9 models > select add #9 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #9,-0.61797,0.77201,0.14871,130.14,0.4958,0.23587,0.83579,151.14,0.61016,0.59023,-0.52852,74.157 > view matrix models > #9,-0.61797,0.77201,0.14871,138.09,0.4958,0.23587,0.83579,159.37,0.61016,0.59023,-0.52852,81.888 > view matrix models > #9,-0.058813,-0.094725,0.99376,139.21,0.89546,-0.44502,0.010575,166,0.44125,0.8905,0.111,77.899 > view matrix models > #9,0.042887,0.17443,0.98374,137.84,0.98461,-0.17436,-0.012009,164.68,0.16943,0.96911,-0.17922,78.662 > view matrix models > #9,0.05007,0.21016,0.97638,137.68,0.99008,-0.13894,-0.020866,164.53,0.13127,0.96774,-0.21503,78.814 > mmaker #9 to #10/A 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain A (#10) with copy of stand.pdb, chain A (#9), sequence alignment score = 232 RMSD between 12 pruned atom pairs is 1.230 angstroms; (across all 263 pairs: 23.258) > hide #!10 models > select subtract #9 1 model selected > hide #!9 models > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and blast/Sca_TPR > part_Cas8_AF/fold_tpr_cas8_sca_model_0.cif"" Chain information for fold_tpr_cas8_sca_model_0.cif #17 --- Chain | Description A | . B | . Computing secondary structure > show #!7 models > hide #!7 models > show #!8 models > mmaker #17 to #10/A 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 8d9f-gRAMP-TPR-CHAT (Craspase) apo, chain A (#10) with fold_tpr_cas8_sca_model_0.cif, chain A (#17), sequence alignment score = 228.4 RMSD between 4 pruned atom pairs is 0.849 angstroms; (across all 263 pairs: 19.537) > select add #17 6736 atoms, 6905 bonds, 882 residues, 1 model selected > mmaker #17 to #8/H 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 MERGE.pdb, chain H (#8) with fold_tpr_cas8_sca_model_0.cif, chain B (#17), sequence alignment score = 2553.6 RMSD between 384 pruned atom pairs is 0.829 angstroms; (across all 505 pairs: 2.593) > select subtract #17 Nothing selected > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and blast/Sca_TPR > part_Cas8_AF/fold_tpr_cas8_sca_model_1.cif"" Chain information for fold_tpr_cas8_sca_model_1.cif #18 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and blast/Sca_TPR > part_Cas8_AF/fold_tpr_cas8_sca_model_2.cif"" Chain information for fold_tpr_cas8_sca_model_2.cif #19 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and blast/Sca_TPR > part_Cas8_AF/fold_tpr_cas8_sca_model_3.cif"" Chain information for fold_tpr_cas8_sca_model_3.cif #20 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and blast/Sca_TPR > part_Cas8_AF/fold_tpr_cas8_sca_model_4.cif"" Chain information for fold_tpr_cas8_sca_model_4.cif #21 --- Chain | Description A | . B | . Computing secondary structure > mmaker #18 to #8/H 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 MERGE.pdb, chain H (#8) with fold_tpr_cas8_sca_model_1.cif, chain B (#18), sequence alignment score = 2535 RMSD between 384 pruned atom pairs is 0.788 angstroms; (across all 505 pairs: 2.636) > mmaker #19 to #8/H 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 MERGE.pdb, chain H (#8) with fold_tpr_cas8_sca_model_2.cif, chain B (#19), sequence alignment score = 2566.2 RMSD between 398 pruned atom pairs is 0.860 angstroms; (across all 505 pairs: 2.292) > mmaker #20 to #8/H 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 MERGE.pdb, chain H (#8) with fold_tpr_cas8_sca_model_3.cif, chain B (#20), sequence alignment score = 2562.6 RMSD between 383 pruned atom pairs is 0.811 angstroms; (across all 505 pairs: 2.606) > mmaker #21 to #8/H 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 MERGE.pdb, chain H (#8) with fold_tpr_cas8_sca_model_4.cif, chain B (#21), sequence alignment score = 2566.2 RMSD between 393 pruned atom pairs is 0.860 angstroms; (across all 505 pairs: 2.515) > hide #!8 models > show #!1 models > hide #!1 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!1 models > hide #!8 models > hide #17 models > hide #18 models > hide #19 models > hide #20 models > hide #21 models > show #!8 models > hide #!1 models > show #!2 models > hide #!8 models > select #2/J 4025 atoms, 4132 bonds, 1 pseudobond, 513 residues, 2 models selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_Cas8_Rloop.cxs"" > show #17 models > hide #!2 models > select add #2 31878 atoms, 32791 bonds, 12 pseudobonds, 3943 residues, 3 models selected > select subtract #2 14 models selected > mlp #17 Map values for surface ""fold_tpr_cas8_sca_model_0.cif_A SES surface"": minimum -28.83, mean -4.915, maximum 22.26 Map values for surface ""fold_tpr_cas8_sca_model_0.cif_B SES surface"": minimum -27.82, mean -4.942, maximum 25.35 To also show corresponding color key, enter the above mlp command and add key true > mlp #!17 Map values for surface ""fold_tpr_cas8_sca_model_0.cif_A SES surface"": minimum -28.83, mean -4.915, maximum 22.26 Map values for surface ""fold_tpr_cas8_sca_model_0.cif_B SES surface"": minimum -27.82, mean -4.942, maximum 25.35 To also show corresponding color key, enter the above mlp command and add key true > hide #!17 surfaces > coulombic #!17 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_tpr_cas8_sca_model_0.cif_A SES surface #17.1: minimum, -13.00, mean -1.44, maximum 11.32 Coulombic values for fold_tpr_cas8_sca_model_0.cif_B SES surface #17.2: minimum, -16.98, mean -1.39, maximum 13.39 To also show corresponding color key, enter the above coulombic command and add key true > hide #!17 models > show #!8 models > show #!6 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > view matrix models > #6,0.95344,-0.00022601,0.30157,62.394,0.075634,0.96822,-0.2384,161.55,-0.29193,0.25011,0.92316,162.87 > view matrix models > #6,0.33373,-0.82838,-0.4499,67.501,-0.25202,-0.5383,0.80419,163.3,-0.90835,-0.155,-0.38842,168.33 > view matrix models > #6,0.86953,0.22259,-0.44088,51.71,0.064147,-0.93602,-0.34605,172.7,-0.4897,0.27262,-0.82817,180.16 > view matrix models > #6,-0.27746,0.95875,0.061671,46.043,0.65093,0.14039,0.74604,165.44,0.70661,0.24714,-0.66304,180.89 > view matrix models > #6,-0.30729,0.94926,0.066856,46.031,0.34996,0.047397,0.93556,164.84,0.88493,0.31089,-0.34677,179.73 > view matrix models > #6,-0.30729,0.94926,0.066856,110.12,0.34996,0.047397,0.93556,171.46,0.88493,0.31089,-0.34677,123.53 > view matrix models > #6,0.96512,0.26089,-0.021906,114.3,0.25339,-0.90976,0.32882,177.07,0.065857,-0.3229,-0.94414,127.17 > view matrix models > #6,0.96512,0.26089,-0.021906,89.601,0.25339,-0.90976,0.32882,183.69,0.065857,-0.3229,-0.94414,98.398 > view matrix models > #6,-0.47551,-0.40138,-0.78281,93.293,-0.86077,0.39593,0.31986,177.67,0.18155,0.82592,-0.53376,92.756 > view matrix models > #6,-0.47551,-0.40138,-0.78281,98.402,-0.86077,0.39593,0.31986,201.54,0.18155,0.82592,-0.53376,123.43 > view matrix models > #6,-0.83112,0.24639,-0.49853,94.617,-0.35777,0.44939,0.81857,200.11,0.42572,0.85869,-0.28535,122.69 > select subtract #6 1 model selected > hide #!8 models > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > coulombic sel Coulombic values for stand.pdb_A SES surface #6.1: minimum, -19.03, mean -1.01, maximum 14.42 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > show #!8 models > view matrix models > #6,-0.62856,-0.62211,-0.4668,97.989,-0.74135,0.66072,0.11771,201.36,0.23519,0.42005,-0.8765,126.2 > view matrix models > #6,0.05685,-0.93549,-0.34875,99.449,-0.26847,-0.35078,0.89715,202.95,-0.96161,0.042628,-0.2711,124.33 > view matrix models > #6,-0.14437,-0.74719,-0.64874,99.575,-0.30318,-0.59067,0.74778,204.34,-0.94193,0.30464,-0.14126,122.91 > view matrix models > #6,-0.11626,-0.7572,-0.64275,99.621,-0.64762,-0.43286,0.62708,203.82,-0.75304,0.48916,-0.44005,123.44 > view matrix models > #6,-0.11626,-0.7572,-0.64275,74.337,-0.64762,-0.43286,0.62708,181.21,-0.75304,0.48916,-0.44005,161.59 > view matrix models > #6,0.099893,-0.52118,-0.84758,74.371,-0.84283,-0.49707,0.20632,182.71,-0.52884,0.69375,-0.48892,161.21 > view matrix models > #6,0.099893,-0.52118,-0.84758,79.395,-0.84283,-0.49707,0.20632,171.46,-0.52884,0.69375,-0.48892,167.24 > view matrix models > #6,-0.11737,-0.40947,-0.90474,78.953,-0.78063,-0.52512,0.33892,171.17,-0.61388,0.74604,-0.25801,166.16 > view matrix models > #6,-0.23793,-0.34649,-0.90738,78.604,-0.73442,-0.54717,0.40153,171.08,-0.63562,0.76194,-0.12428,165.61 > view matrix models > #6,-0.23793,-0.34649,-0.90738,97.978,-0.73442,-0.54717,0.40153,161.79,-0.63562,0.76194,-0.12428,164.51 > view matrix models > #6,-0.23793,-0.34649,-0.90738,90.182,-0.73442,-0.54717,0.40153,163.68,-0.63562,0.76194,-0.12428,158.73 > view matrix models > #6,-0.23793,-0.34649,-0.90738,85.028,-0.73442,-0.54717,0.40153,164.45,-0.63562,0.76194,-0.12428,165.62 > view matrix models > #6,-0.23793,-0.34649,-0.90738,84.064,-0.73442,-0.54717,0.40153,169.12,-0.63562,0.76194,-0.12428,166.63 > view matrix models > #6,-0.23793,-0.34649,-0.90738,82.73,-0.73442,-0.54717,0.40153,172.33,-0.63562,0.76194,-0.12428,176.8 > view matrix models > #6,-0.085414,-0.36522,-0.92699,83.021,-0.71289,-0.62758,0.31294,172.96,-0.69606,0.68757,-0.20676,177.31 > view matrix models > #6,-0.37309,-0.44666,-0.8132,82.647,-0.56358,-0.58715,0.58106,172.03,-0.73701,0.67509,-0.032674,176.71 > view matrix models > #6,-0.37309,-0.44666,-0.8132,81.893,-0.56358,-0.58715,0.58106,172.31,-0.73701,0.67509,-0.032674,177.38 > view matrix models > #6,-0.47347,-0.48311,-0.7365,81.665,-0.40811,-0.62067,0.66949,172.28,-0.78056,0.61756,0.096705,177.11 > view matrix models > #6,-0.50069,-0.3426,-0.79494,81.309,-0.4118,-0.71349,0.56687,172.99,-0.7614,0.61119,0.21616,176.74 > view matrix models > #6,-0.22869,-0.254,-0.93978,81.748,-0.71126,-0.61554,0.33945,173.1,-0.66469,0.74606,-0.039889,177.21 > view matrix models > #6,-0.22869,-0.254,-0.93978,82.64,-0.71126,-0.61554,0.33945,168.73,-0.66469,0.74606,-0.039889,177.79 > view matrix models > #6,-0.23309,-0.27216,-0.9336,82.683,-0.70289,-0.61629,0.35515,168.68,-0.67202,0.739,-0.047646,177.84 > view matrix models > #6,-0.23309,-0.27216,-0.9336,80.995,-0.70289,-0.61629,0.35515,169.02,-0.67202,0.739,-0.047646,176.91 > view matrix models > #6,-0.19567,-0.30227,-0.93292,81.144,-0.70743,-0.61532,0.34774,169.04,-0.67916,0.72802,-0.093437,177.11 > select subtract #6 1 model selected > select add #8 31370 atoms, 32136 bonds, 4001 residues, 1 model selected > show sel surfaces > select subtract #8 12 models selected > select add #6 9605 atoms, 9793 bonds, 1282 residues, 1 model selected > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260302 update/STAND-Cas3.cxs"" > hide #!8 models > select subtract #6 1 model selected > hide #!6 models > show #!17 models > hide #!17 models > show #!8 models > hide #!8 surfaces > show #!17 models > hide #!8,17 surfaces > close #18-21#17 > select add #8 31370 atoms, 32136 bonds, 4001 residues, 1 model selected > hide #!8 models > select subtract #8 12 models selected > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_7XSTAND_NoTPR/fold_stand_7x_model_0.cif"" Chain information for fold_stand_7x_model_0.cif #17 --- Chain | Description A B C D E F G | . > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_4XSTAND_NoTPR/fold_stand4x_notpr_model_0.cif"" Chain information for fold_stand4x_notpr_model_0.cif #18 --- Chain | Description A B C D | . Computing secondary structure > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_3XSTAND_FL/fold_stand_fl_3x_model_0.cif"" Chain information for fold_stand_fl_3x_model_0.cif #19 --- Chain | Description A B C | . Computing secondary structure > show #!9 models > mmaker #17 to #9 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker copy of stand.pdb, chain A (#9) with fold_stand_7x_model_0.cif, chain A (#17), sequence alignment score = 3604.6 RMSD between 205 pruned atom pairs is 0.409 angstroms; (across all 709 pairs: 20.832) > hide #18 models > hide #19 models > select add #17 37247 atoms, 37947 bonds, 4963 residues, 1 model selected > hide sel atoms > show sel cartoons > cartoon style sel modeHelix tube sides 20 > view matrix models > #17,0.39888,0.91648,-0.031005,193.43,0.43687,-0.16019,0.88515,148.96,0.80625,-0.36661,-0.46428,48.764 > undo > select subtract #17 Nothing selected > mmaker #18 to #9 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 copy of stand.pdb, chain A (#9) with fold_stand4x_notpr_model_0.cif, chain A (#18), sequence alignment score = 4616.2 RMSD between 144 pruned atom pairs is 0.636 angstroms; (across all 919 pairs: 25.063) > mmaker #19 to #9 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 copy of stand.pdb, chain A (#9) with fold_stand_fl_3x_model_0.cif, chain A (#19), sequence alignment score = 6466 RMSD between 733 pruned atom pairs is 1.023 angstroms; (across all 1282 pairs: 10.066) > hide #17 models > show #19 models > select add #19 28815 atoms, 29379 bonds, 3846 residues, 1 model selected > show #18 models > select add #18 56559 atoms, 57619 bonds, 7522 residues, 2 models selected > cartoon style sel modeHelix tube sides 20 > select subtract #18 28815 atoms, 29379 bonds, 3846 residues, 1 model selected > select subtract #19 Nothing selected > hide #18 models > hide #19 models > show #18 models > hide #18 models > show #17 models > hide #17 models > show #17 models > hide #17 models > show #18 models > hide #18 models > show #17 models > hide #17 models > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_7XSTAND_NoTPR/fold_stand_7x_model_1.cif"" Chain information for fold_stand_7x_model_1.cif #20 --- Chain | Description A B C D E F G | . > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_7XSTAND_NoTPR/fold_stand_7x_model_2.cif"" Chain information for fold_stand_7x_model_2.cif #21 --- Chain | Description A B C D E F G | . > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_7XSTAND_NoTPR/fold_stand_7x_model_3.cif"" Chain information for fold_stand_7x_model_3.cif #22 --- Chain | Description A B C D E F G | . > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Stan > Brouns_Type I-E/20260326 IE STAND loci CRISPR comparison and > blast/Sca_7XSTAND_NoTPR/fold_stand_7x_model_4.cif"" Chain information for fold_stand_7x_model_4.cif #23 --- Chain | Description A B C D E F G | . > hide #20 models > show #17 models > hide #!9 models > hide #21 models > hide #22 models > hide #23 models > show #!14 models > hide #!14 models > show #!9 models > mmaker #20 to #19 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_stand_fl_3x_model_0.cif, chain A (#19) with fold_stand_7x_model_1.cif, chain A (#20), sequence alignment score = 3554.2 RMSD between 196 pruned atom pairs is 0.418 angstroms; (across all 709 pairs: 20.172) > mmaker #21 to #19 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_stand_fl_3x_model_0.cif, chain A (#19) with fold_stand_7x_model_2.cif, chain F (#21), sequence alignment score = 3541.6 RMSD between 214 pruned atom pairs is 0.563 angstroms; (across all 709 pairs: 21.909) > mmaker #22 to #19 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_stand_fl_3x_model_0.cif, chain A (#19) with fold_stand_7x_model_3.cif, chain A (#22), sequence alignment score = 3556.6 RMSD between 197 pruned atom pairs is 0.518 angstroms; (across all 709 pairs: 20.263) > mmaker #23 to #19 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_stand_fl_3x_model_0.cif, chain B (#19) with fold_stand_7x_model_4.cif, chain E (#23), sequence alignment score = 3562 RMSD between 206 pruned atom pairs is 0.475 angstroms; (across all 709 pairs: 20.407) > hide #17 models > show #20 models > show #20#!9 cartoons > hide #20#!9 atoms > cartoon style #9,20 modeHelix tube sides 20 > select add #21 37247 atoms, 37947 bonds, 4963 residues, 1 model selected > select add #22 74494 atoms, 75894 bonds, 9926 residues, 2 models selected > select add #23 111741 atoms, 113841 bonds, 14889 residues, 3 models selected > hide #20#!9 atoms > show #20#!9 cartoons > cartoon style #9,20 modeHelix tube sides 20 > select subtract #21 74494 atoms, 75894 bonds, 9926 residues, 2 models selected > select subtract #22 37247 atoms, 37947 bonds, 4963 residues, 1 model selected > select subtract #23 Nothing selected > hide #20 models > show #21 models > hide #21#!9 atoms > show #21#!9 cartoons > cartoon style #9,21 modeHelix tube sides 20 > hide #21 models > show #22 models > show #23 models > hide #22-23#!9 atoms > show #22-23#!9 cartoons > cartoon style #9,22-23 modeHelix tube sides 20 > hide #23 models > hide #22 models > show #20 models > mmaker #23 to #9 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_4.cif, chain G (#23), sequence alignment score = 3596.8 RMSD between 204 pruned atom pairs is 0.495 angstroms; (across all 709 pairs: 21.694) > mmaker #22 to #9 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_3.cif, chain A (#22), sequence alignment score = 3593.2 RMSD between 187 pruned atom pairs is 0.494 angstroms; (across all 709 pairs: 20.170) > mmaker #21 to #9 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_2.cif, chain F (#21), sequence alignment score = 3591.4 RMSD between 209 pruned atom pairs is 0.468 angstroms; (across all 709 pairs: 22.647) > mmaker #20 to #9 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_1.cif, chain A (#20), sequence alignment score = 3597.4 RMSD between 145 pruned atom pairs is 0.743 angstroms; (across all 709 pairs: 18.820) > hide #20 models > mmaker #20 to #9:100-319 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_1.cif, chain A (#20), sequence alignment score = 1107.7 RMSD between 203 pruned atom pairs is 0.384 angstroms; (across all 220 pairs: 2.953) > show #20 models > mmaker #21 to #9:100-319 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_2.cif, chain A (#21), sequence alignment score = 1107.7 RMSD between 207 pruned atom pairs is 0.451 angstroms; (across all 220 pairs: 1.499) > mmaker #22 to #9:100-319 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_3.cif, chain A (#22), sequence alignment score = 1111.3 RMSD between 203 pruned atom pairs is 0.556 angstroms; (across all 220 pairs: 2.610) > mmaker #23 to #9:100-319 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 copy of stand.pdb, chain A (#9) with fold_stand_7x_model_4.cif, chain A (#23), sequence alignment score = 1118.5 RMSD between 207 pruned atom pairs is 0.473 angstroms; (across all 220 pairs: 1.682) > select add #20 37247 atoms, 37947 bonds, 4963 residues, 1 model selected > select subtract #20 Nothing selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: Z1FF000ENLL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 48 GB System Firmware Version: 13822.1.2 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.1 (24G231) Kernel Version: Darwin 24.6.0 Time since boot: 29 days, 20 hours, 58 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LS27D70xE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 2.16.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 2.4.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 plotly: 6.5.2 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tomlkit: 0.14.0 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX