id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18674 Crash on Mac waking from sleep nuren.tasneem@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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: [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/BIO- > SAXS_data/AvrStb6_dimer_refine_027.pdb format pdb Chain information for AvrStb6_dimer_refine_027.pdb #1 --- Chain | Description A B | No description available Computing secondary structure > lighting soft > graphics silhouettes true > select clear > hide atoms > select ::name=""CYS"" 240 atoms, 230 bonds, 24 residues, 1 model selected > show sel atoms > select clear > hide #1 models > open 4fz0 Summary of feedback from opening 4fz0 fetched from pdb --- notes | Fetching compressed mmCIF 4fz0 from http://files.rcsb.org/download/4fz0.cif Fetching CCD GOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif 4fz0 title: Crystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at low pH [more info...] Chain information for 4fz0 #2 --- Chain | Description | UniProt A B C | Acid-sensing ion channel 1 | ASIC1_CHICK 14-463 M N O | Pi-theraphotoxin-Pc1a | TXP1_PSACA 1-40 Non-standard residues in 4fz0 #2 --- CL — chloride ion GOL — glycerol (glycerin; propane-1,2,3-triol) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > sequence chain #2/A#2/B#2/C Alignment identifier is 1 > select #2/M 299 atoms, 304 bonds, 43 residues, 1 model selected > select ~sel 12081 atoms, 12180 bonds, 1632 residues, 2 models selected > hide sel & #2 cartoons > hide sel & #2 atoms > select clear > show #2 cartoons > hide #2 atoms > select #2/M 299 atoms, 304 bonds, 43 residues, 1 model selected > select ~sel 12081 atoms, 12180 bonds, 1632 residues, 2 models selected > hide sel & #2 cartoons > select clear > graphics silhouettes width 1 > lighting soft > select clear > select #2/M:2-38 293 atoms, 304 bonds, 37 residues, 1 model selected Alignment identifier is 2/M > select clear > select #2/M:3 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/M:3 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/M:10 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/M:10 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/M:3,10 12 atoms, 10 bonds, 2 residues, 1 model selected > select #2/M:3,10,17-18 24 atoms, 22 bonds, 4 residues, 1 model selected > select #2/M:3,10,17-18,23 30 atoms, 28 bonds, 5 residues, 1 model selected > select #2/M:3,10,17-18,23,33 36 atoms, 34 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 36 atom styles > color sel byhetero > select clear > color #2 #76d6ffff > color #2 #ebebebff > color #2 #d6d6d6ff > color #2 #ebebebff > color #2 #d6d6d6ff > color #2 #ebebebff > color #2 #d6d6d6ff > select #2/M:3 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/M:3 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/M:3,10 12 atoms, 10 bonds, 2 residues, 1 model selected > select #2/M:3,10,17-18 24 atoms, 22 bonds, 4 residues, 1 model selected > select #2/M:3,10,17-18,23 30 atoms, 28 bonds, 5 residues, 1 model selected > select #2/M:3,10,17-18,23,33 36 atoms, 34 bonds, 6 residues, 1 model selected > color sel byhetero > select clear > save /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/4fz0.png > width 867 height 739 supersample 4 transparentBackground true > select add #2 10557 atoms, 10686 bonds, 1486 residues, 1 model selected > close #2 > show #1 models > view clip false > open 8f2f Summary of feedback from opening 8f2f fetched from pdb --- note | Fetching compressed mmCIF 8f2f from http://files.rcsb.org/download/8f2f.cif 8f2f title: NMR solution structure of lambda-MeuKTx-1 [more info...] Chain information for 8f2f --- Chain | Description | UniProt 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | Neurotoxin lambda-MeuTx | CLML_MESEU 1-37 > close #2 Alignment identifier is 1 > select /B 880 atoms, 896 bonds, 66 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select /A:42 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:42-71 399 atoms, 407 bonds, 30 residues, 1 model selected > select ~sel & ##selected 544 atoms, 495 bonds, 93 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > save /Users/u6290062/Documents/Figures/AvrStb6-CT.pdb displayedOnly true > relModel #1 > open 2r33 Summary of feedback from opening 2r33 fetched from pdb --- note | Fetching compressed mmCIF 2r33 from http://files.rcsb.org/download/2r33.cif 2r33 title: Crystal structure of a Bowman-Birk inhibitor from Vigna unguiculata seeds [more info...] Chain information for 2r33 #2 --- Chain | Description A B | Bowman-Birk type seed trypsin and chymotrypsin inhibitor > ui tool show Matchmaker > matchmaker #!2 to #1 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 AvrStb6_dimer_refine_027.pdb, chain A (#1) with 2r33, chain B (#2), sequence alignment score = 55.3 RMSD between 10 pruned atom pairs is 0.426 angstroms; (across all 28 pairs: 6.582) > select ::name=""CYS"" 228 atoms, 213 bonds, 34 residues, 2 models selected > show sel atoms > select clear > open /Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/BIO- > SAXS_data/AvrStb6_dimer_refine_027.pdb Chain information for AvrStb6_dimer_refine_027.pdb #3 --- Chain | Description A B | No description available Computing secondary structure > select clear > hide atoms > ui tool show Matchmaker > matchmaker #3 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 2r33, chain A (#2) with AvrStb6_dimer_refine_027.pdb, chain A (#3), sequence alignment score = 68.5 RMSD between 9 pruned atom pairs is 0.998 angstroms; (across all 45 pairs: 9.832) > hide #1 models > ui tool show Matchmaker > matchmaker #3 & sel to #2 & sel No 'to' model specified > matchmaker #3 & sel to #2 & sel No 'to' model specified > matchmaker #3 to #2 & sel No 'to' model specified > matchmaker #3 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 2r33, chain A (#2) with AvrStb6_dimer_refine_027.pdb, chain A (#3), sequence alignment score = 68.5 RMSD between 9 pruned atom pairs is 0.998 angstroms; (across all 45 pairs: 9.832) > select clear > hide #3 models > show #1 models > close > open /Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/BIO- > SAXS_data/EPN_24196/reduced_data/standard_mode_reduction/1E4_12mgml_2565fa7c_E12k4_D750/DENSS/A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_average.mrc > format mrc Opened A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_average.mrc as #1, grid size 32,32,32, pixel 5.16, shown at level 0.0147, step 1, values float32 > select clear > volume #1 style mesh > volume #1 style surface > select clear > graphics silhouettes width 1 > open /Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/BIO- > SAXS_data/AvrStb6_dimer_refine_027.pdb Chain information for AvrStb6_dimer_refine_027.pdb #2 --- Chain | Description A B | No description available Computing secondary structure > select clear > select add #1 2 models selected > transparency #1.1 30 > select clear > select add #2 1823 atoms, 1798 bonds, 189 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,8.275,0,1,0,-23.095,0,0,1,-10.542 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.91544,0.27667,0.29228,-10.872,0.35654,-0.22063,-0.90785,39.061,-0.18669,0.93529,-0.30062,54.939 > view matrix models > #2,0.65175,-0.71381,0.2563,21.516,0.42835,0.067567,-0.90108,29.831,0.62589,0.69707,0.3498,-14.075 > view matrix models > #2,0.65203,-0.59289,0.47259,6.5335,0.46846,-0.17507,-0.86596,31.084,0.59616,0.78603,0.16359,-4.0796 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.65203,-0.59289,0.47259,-40.333,0.46846,-0.17507,-0.86596,19.815,0.59616,0.78603,0.16359,-42.216 > view matrix models > #2,0.65203,-0.59289,0.47259,-40.253,0.46846,-0.17507,-0.86596,19.671,0.59616,0.78603,0.16359,-42.971 > view matrix models > #2,0.65203,-0.59289,0.47259,-39.94,0.46846,-0.17507,-0.86596,32.422,0.59616,0.78603,0.16359,-43.949 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.25826,0.823,0.50593,-53.486,0.0097598,-0.5259,0.85049,-41.229,0.96603,-0.21471,-0.14385,-20.567 > volume #1 level 0.1022 > view matrix models > #2,-0.045261,-0.84852,-0.52722,54.4,-0.32686,-0.48613,0.81045,-25.452,-0.94399,0.20901,-0.25534,58.534 > volume #1 style image > volume #1 style mesh > graphics silhouettes false > view matrix models > #2,0.53251,-0.7834,-0.32049,16.321,0.26483,-0.20542,0.94216,-64.006,-0.80393,-0.58658,0.098078,48.378 > volume #1 change image level -8.272e-05,0 level 0.01465,0.8 level 1.097,1 > volume #1 level 0.0347 > view matrix models > #2,-0.74986,-0.57393,-0.32913,66.936,-0.061018,-0.43536,0.89819,-43.018,-0.65878,0.69359,0.29144,4.7179 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.74986,-0.57393,-0.32913,56.842,-0.061018,-0.43536,0.89819,-42.718,-0.65878,0.69359,0.29144,-0.19789 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.41694,-0.54058,-0.73071,65.785,-0.49801,-0.53665,0.68118,-9.252,-0.76036,0.64791,-0.045462,24.983 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.41694,-0.54058,-0.73071,71.941,-0.49801,-0.53665,0.68118,-7.1044,-0.76036,0.64791,-0.045462,29.42 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.49422,-0.39972,-0.77199,74.833,-0.53954,-0.55526,0.63292,-2.0958,-0.68164,0.72932,0.058754,18.237 > view matrix models > #2,-0.43699,-0.46544,-0.76968,73.597,-0.47677,-0.60574,0.637,-3.9779,-0.76271,0.64532,0.042795,24.312 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.5266,-0.48532,-0.69796,73.517,-0.39084,-0.59089,0.70575,-12.011,-0.75494,0.64445,0.12148,19.312 > view matrix models > #2,-0.55273,-0.42683,-0.71575,74.504,-0.43485,-0.58495,0.68464,-9.0102,-0.71091,0.68967,0.13771,15.57 > view matrix models > #2,-0.80412,0.19628,-0.56113,63.574,-0.59443,-0.27608,0.75527,-12.705,-0.0066742,0.94088,0.33867,-31.169 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.80412,0.19628,-0.56113,65.259,-0.59443,-0.27608,0.75527,-14.404,-0.0066742,0.94088,0.33867,-32.835 > volume #1 level 0.1083 > volume #1 level 0.02475 > view matrix models > #2,-0.80412,0.19628,-0.56113,65.065,-0.59443,-0.27608,0.75527,-12.498,-0.0066742,0.94088,0.33867,-32.665 > view matrix models > #2,-0.80412,0.19628,-0.56113,65.708,-0.59443,-0.27608,0.75527,-13.938,-0.0066742,0.94088,0.33867,-33.398 > volume #1 level 0.1202 > view matrix models > #2,-0.80412,0.19628,-0.56113,65.2,-0.59443,-0.27608,0.75527,-14.163,-0.0066742,0.94088,0.33867,-32.963 > volume #1 level 0.02674 > view matrix models > #2,-0.80412,0.19628,-0.56113,65.522,-0.59443,-0.27608,0.75527,-13.434,-0.0066742,0.94088,0.33867,-32.971 > volume #1 level 0.07249 > view matrix models > #2,-0.80412,0.19628,-0.56113,64.605,-0.59443,-0.27608,0.75527,-14.717,-0.0066742,0.94088,0.33867,-32.792 > hide sel atoms > select clear > volume #1 level 0.1361 > select add #2 1823 atoms, 1798 bonds, 189 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.80586,0.35903,0.47084,-68.308,-0.47643,-0.078982,0.87566,-30.857,0.35157,-0.92998,0.1074,3.5351 > view matrix models > #2,-0.36173,0.93143,0.039928,-4.7517,-0.71726,-0.30541,0.62631,-1.242,0.59555,0.19791,0.77855,-69.517 > view matrix models > #2,-0.40095,0.91439,0.055934,-3.7021,-0.59714,-0.30717,0.74099,-13.125,0.69474,0.2637,0.66918,-68.523 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.40095,0.91439,0.055934,-3.2019,-0.59714,-0.30717,0.74099,-13.575,0.69474,0.2637,0.66918,-70.244 > view matrix models > #2,-0.40095,0.91439,0.055934,-4.1602,-0.59714,-0.30717,0.74099,-12.568,0.69474,0.2637,0.66918,-69.67 > view matrix models > #2,-0.40095,0.91439,0.055934,-3.9173,-0.59714,-0.30717,0.74099,-12.615,0.69474,0.2637,0.66918,-69.748 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.32818,0.93867,-0.10587,2.1551,-0.68898,-0.16118,0.70663,-9.6222,0.64623,0.30484,0.69962,-70.338 > select clear > ui mousemode right ""translate selected models"" > select add #2 1823 atoms, 1798 bonds, 189 residues, 1 model selected > view matrix models > #2,-0.32818,0.93867,-0.10587,2.2718,-0.68898,-0.16118,0.70663,-10.671,0.64623,0.30484,0.69962,-70.789 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.34632,0.93305,-0.09739,2.6475,-0.63103,-0.15488,0.76014,-16.439,0.69417,0.32471,0.64242,-69.81 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.34632,0.93305,-0.09739,2.3845,-0.63103,-0.15488,0.76014,-15.042,0.69417,0.32471,0.64242,-69.686 > volume #1 level 0.1421 > volume #1 step 2 > volume #1 step 16 > volume #1 step 1 > volume #1 level 0.1003 > view matrix models > #2,-0.34632,0.93305,-0.09739,1.6883,-0.63103,-0.15488,0.76014,-16.975,0.69417,0.32471,0.64242,-69.296 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.32921,0.93498,-0.13205,2.9911,-0.6778,-0.13662,0.72244,-13.117,0.65743,0.32734,0.6787,-69.956 > view matrix models > #2,-0.3479,0.91047,-0.22364,9.7334,-0.6593,-0.067994,0.7488,-16.854,0.66655,0.40795,0.62392,-68.703 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.3479,0.91047,-0.22364,9.5561,-0.6593,-0.067994,0.7488,-15.297,0.66655,0.40795,0.62392,-69.256 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.33533,0.91917,-0.20661,7.8338,-0.6611,-0.073337,0.74671,-14.989,0.6712,0.38698,0.63225,-69.526 > view matrix models > #2,-0.35254,0.9171,-0.18612,7.3828,-0.633,-0.08722,0.76922,-17.239,0.68922,0.38899,0.61128,-69.08 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.35254,0.9171,-0.18612,7.6222,-0.633,-0.08722,0.76922,-18.172,0.68922,0.38899,0.61128,-69.335 > view matrix models > #2,-0.35254,0.9171,-0.18612,7.2261,-0.633,-0.08722,0.76922,-16.95,0.68922,0.38899,0.61128,-69.075 > view matrix models > #2,-0.35254,0.9171,-0.18612,7.243,-0.633,-0.08722,0.76922,-17.697,0.68922,0.38899,0.61128,-69.196 > view matrix models > #2,-0.35254,0.9171,-0.18612,7.9445,-0.633,-0.08722,0.76922,-17.754,0.68922,0.38899,0.61128,-67.947 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.4043,0.79509,0.45208,-59.657,0.59904,0.14332,-0.78779,18.237,-0.69115,0.58931,-0.41835,47.792 > view matrix models > #2,0.31151,0.75436,0.57784,-62.403,0.60044,0.31505,-0.73499,11.57,-0.7365,0.57592,-0.3548,46.194 > view matrix models > #2,0.27978,0.73403,0.61881,-63.092,0.59662,0.37205,-0.71107,9.1576,-0.75218,0.56814,-0.33385,45.766 > view matrix models > #2,0.10746,0.74992,0.65275,-58.141,0.74551,0.3736,-0.55194,-6.6572,-0.65778,0.54594,-0.51892,53.246 > view matrix models > #2,0.1502,0.79191,0.59188,-57.17,0.77832,0.27444,-0.56471,-5.2869,-0.60963,0.54549,-0.57514,54.568 > view matrix models > #2,0.61813,0.77599,0.12551,-48.862,-0.27407,0.063106,0.95964,-47.321,0.73675,-0.62758,0.25169,-28.041 > view matrix models > #2,0.63368,0.76643,0.10507,-48.11,-0.30966,0.12684,0.94235,-46.069,0.70892,-0.62968,0.31771,-30.755 > view matrix models > #2,0.62536,0.77137,0.11795,-48.625,-0.30637,0.10369,0.94625,-45.975,0.71768,-0.62788,0.30116,-30.176 > view matrix models > #2,0.69795,0.6897,0.19284,-54.513,-0.33758,0.079379,0.93794,-43.669,0.63159,-0.71973,0.28823,-23.911 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.69795,0.6897,0.19284,-52.595,-0.33758,0.079379,0.93794,-43.879,0.63159,-0.71973,0.28823,-26.114 > view matrix models > #2,0.69795,0.6897,0.19284,-54.492,-0.33758,0.079379,0.93794,-44.103,0.63159,-0.71973,0.28823,-27.327 > view matrix models > #2,0.69795,0.6897,0.19284,-54.72,-0.33758,0.079379,0.93794,-44.655,0.63159,-0.71973,0.28823,-29.207 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.7283,0.68181,0.068635,-48.444,-0.34583,0.27924,0.89578,-45.822,0.59159,-0.67613,0.43917,-37.387 > view matrix models > #2,0.90889,-0.41419,0.04853,-32.799,-0.27509,-0.50802,0.81624,-28.208,-0.31343,-0.75522,-0.57568,62.983 > view matrix models > #2,0.78283,-0.59619,-0.17816,-10.287,-0.046101,-0.34111,0.93889,-48.573,-0.62053,-0.72678,-0.29451,58.653 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.78283,-0.59619,-0.17816,-11.12,-0.046101,-0.34111,0.93889,-47.976,-0.62053,-0.72678,-0.29451,59.985 > view matrix models > #2,0.78283,-0.59619,-0.17816,-11.216,-0.046101,-0.34111,0.93889,-46.866,-0.62053,-0.72678,-0.29451,59.771 > view matrix models > #2,0.78283,-0.59619,-0.17816,-11.265,-0.046101,-0.34111,0.93889,-47.579,-0.62053,-0.72678,-0.29451,60.072 > view matrix models > #2,0.78283,-0.59619,-0.17816,-8.5839,-0.046101,-0.34111,0.93889,-47.073,-0.62053,-0.72678,-0.29451,63.483 > view matrix models > #2,0.78283,-0.59619,-0.17816,-9.336,-0.046101,-0.34111,0.93889,-46.047,-0.62053,-0.72678,-0.29451,63.222 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.77851,-0.62046,-0.094627,-13.642,-0.083062,-0.25129,0.96434,-47.81,-0.62211,-0.74289,-0.24717,60.792 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.77851,-0.62046,-0.094627,-13.99,-0.083062,-0.25129,0.96434,-46.279,-0.62211,-0.74289,-0.24717,60.555 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.75154,-0.65945,-0.017724,-16.645,-0.24914,-0.3086,0.91798,-35.333,-0.61083,-0.68548,-0.39622,67.803 > view matrix models > #2,0.71362,-0.69047,0.11835,-22.524,-0.3037,-0.15268,0.94046,-37.506,-0.63128,-0.70707,-0.31865,64.481 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.71362,-0.69047,0.11835,-21.642,-0.3037,-0.15268,0.94046,-39.631,-0.63128,-0.70707,-0.31865,62.563 > volume #1 level 0.1739 > volume #1 level 0.02475 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.74211,0.55337,0.37823,-63.404,-0.58008,0.2475,0.77605,-26.203,0.33583,-0.79532,0.50467,-25.65 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.74211,0.55337,0.37823,-66.792,-0.58008,0.2475,0.77605,-22.082,0.33583,-0.79532,0.50467,-25.549 > view matrix models > #2,0.74211,0.55337,0.37823,-63.831,-0.58008,0.2475,0.77605,-26.038,0.33583,-0.79532,0.50467,-25.745 > select clear Alignment identifier is 1 > select /A-B:7 30 atoms, 28 bonds, 2 residues, 1 model selected > select /A-B:7-10 86 atoms, 84 bonds, 8 residues, 1 model selected > select /A-B:7 30 atoms, 28 bonds, 2 residues, 1 model selected > select /A-B:7-8 52 atoms, 50 bonds, 4 residues, 1 model selected > select /A-B:7 30 atoms, 28 bonds, 2 residues, 1 model selected > select /A-B:7-9 72 atoms, 70 bonds, 6 residues, 1 model selected > select /A-B:7 30 atoms, 28 bonds, 2 residues, 1 model selected > select /A-B:7-8 52 atoms, 50 bonds, 4 residues, 1 model selected > hide sel cartoons > select /A-B:71 28 atoms, 28 bonds, 2 residues, 1 model selected > select /A-B:69-71 62 atoms, 62 bonds, 6 residues, 1 model selected > select /A-B:70 20 atoms, 18 bonds, 2 residues, 1 model selected > select /A-B:70-71 48 atoms, 48 bonds, 4 residues, 1 model selected > hide sel cartoons > select clear > select add #2 1823 atoms, 1798 bonds, 189 residues, 1 model selected > view matrix models > #2,0.74211,0.55337,0.37823,-65.446,-0.58008,0.2475,0.77605,-28.801,0.33583,-0.79532,0.50467,-23.527 > view matrix models > #2,0.74211,0.55337,0.37823,-65.26,-0.58008,0.2475,0.77605,-28.585,0.33583,-0.79532,0.50467,-23.825 > view matrix models > #2,0.74211,0.55337,0.37823,-62.861,-0.58008,0.2475,0.77605,-28.611,0.33583,-0.79532,0.50467,-23.36 > view matrix models > #2,0.74211,0.55337,0.37823,-64.378,-0.58008,0.2475,0.77605,-28.606,0.33583,-0.79532,0.50467,-21.847 > view matrix models > #2,0.74211,0.55337,0.37823,-65.692,-0.58008,0.2475,0.77605,-28.195,0.33583,-0.79532,0.50467,-22.858 > view matrix models > #2,0.74211,0.55337,0.37823,-65.548,-0.58008,0.2475,0.77605,-29.362,0.33583,-0.79532,0.50467,-23.863 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.87419,0.43634,0.21308,-58.816,-0.35897,0.28519,0.88871,-46.035,0.32701,-0.85339,0.40594,-16.431 > view matrix models > #2,0.84001,0.13513,0.52547,-69.877,-0.54255,0.20147,0.8155,-32.336,0.0043287,-0.97013,0.24255,9.0988 > view matrix models > #2,0.49276,0.83329,0.25063,-53.276,-0.61867,0.13295,0.77432,-25.322,0.61191,-0.53661,0.58105,-45.16 > view matrix models > #2,0.81289,0.53929,0.21996,-58.773,-0.4223,0.28567,0.86026,-41.717,0.4011,-0.79218,0.45996,-23.976 > view matrix models > #2,-0.70647,0.70775,0.00096513,14.019,0.53598,0.5359,-0.65233,3.479,-0.4622,-0.46033,-0.75793,77.735 > view matrix models > #2,-0.96137,-0.13888,-0.23767,56.074,0.16022,0.41977,-0.89338,35.83,0.22384,-0.89694,-0.3813,35.657 > view matrix models > #2,-0.79388,-0.45934,-0.39844,65.215,0.14966,0.48749,-0.86021,32.914,0.58936,-0.74254,-0.31826,13.559 > view matrix models > #2,0.64559,-0.74911,-0.14852,-3.6279,0.46978,0.54288,-0.69613,8.6992,0.6021,0.37964,0.70239,-70.638 > volume #1 level 0.1341 > view matrix models > #2,-0.75337,-0.62483,-0.20498,55.372,0.14015,0.15198,-0.9784,47.183,0.64249,-0.76582,-0.026923,-5.5365 > view matrix models > #2,-0.22882,-0.97245,0.044522,25.772,-0.20425,0.0032445,-0.97891,64.562,0.9518,-0.23309,-0.19937,-18.967 > view matrix models > #2,-0.15812,-0.98603,0.052388,22.64,-0.19868,-0.020201,-0.97986,64.864,0.96723,-0.16534,-0.19271,-21.385 > view matrix models > #2,-0.94786,-0.17688,-0.26508,57.92,0.05406,0.73052,-0.68075,21.247,0.31406,-0.65959,-0.68287,45.043 > view matrix models > #2,-0.16798,-0.98031,-0.10379,32.24,0.1886,0.071381,-0.97946,46.873,0.96758,-0.1841,0.17289,-42.804 > view matrix models > #2,-0.16614,-0.98602,-0.012549,26.843,0.33529,-0.044517,-0.94106,40.846,0.92735,-0.16056,0.338,-51.449 > volume #1 level 0.006849 > volume #1 level 0.09437 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.16614,-0.98602,-0.012549,27.014,0.33529,-0.044517,-0.94106,43.332,0.92735,-0.16056,0.338,-52.255 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.21049,-0.87015,-0.44558,52.303,-0.006166,0.45696,-0.88947,44.244,0.97758,-0.18448,-0.10155,-27.664 > view matrix models > #2,-0.34314,-0.80454,-0.48473,58.816,0.027719,0.50717,-0.8614,40.141,0.93887,-0.30902,-0.15173,-20.529 > view matrix models > #2,-0.060577,-0.91133,-0.4072,44.621,-0.0201,0.40898,-0.91232,47.162,0.99796,-0.047081,-0.043093,-34.792 > view matrix models > #2,-0.19828,-0.97283,-0.11956,34.458,0.19017,0.081479,-0.97836,49.023,0.96152,-0.21672,0.16885,-42.452 > view matrix models > #2,-0.29686,-0.93294,-0.2037,42.759,0.29276,0.11412,-0.94935,42.364,0.90894,-0.34146,0.23925,-41.921 > view matrix models > #2,-0.3796,-0.90335,-0.19966,45.356,0.23343,0.11531,-0.96551,45.77,0.89522,-0.41311,0.16709,-35.593 > view matrix models > #2,-0.39343,-0.9053,-0.16011,43.614,0.23883,0.067528,-0.96871,46.709,0.88779,-0.41936,0.18965,-36.5 > view matrix models > #2,-0.37338,-0.89635,-0.23906,47.303,0.24768,0.15202,-0.95684,43.913,0.894,-0.41647,0.16524,-35.363 > view matrix models > #2,-0.54365,-0.81352,-0.20646,50.754,0.14249,0.15296,-0.97791,49.523,0.82713,-0.56106,0.032763,-21.745 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.54365,-0.81352,-0.20646,51.267,0.14249,0.15296,-0.97791,50.14,0.82713,-0.56106,0.032763,-21.03 > ui mousemode right ""rotate selected models"" [deleted to fit within ticket limits] > select add #12/A:67 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #12/A:95 19 atoms, 17 bonds, 2 residues, 1 model selected > select #12/A:67 11 atoms, 10 bonds, 1 residue, 1 model selected > select #12/A:67-95 225 atoms, 226 bonds, 29 residues, 1 model selected > color sel light gray target ac > select clear > select add #12/A:96 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #12/A:180 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #12/A:181 25 atoms, 22 bonds, 3 residues, 1 model selected > select #12/A:96 8 atoms, 7 bonds, 1 residue, 1 model selected > select #12/A:96-181 645 atoms, 661 bonds, 86 residues, 1 model selected > color sel dark khaki target ac > select clear > select add #12/A:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #12/A:6 17 atoms, 15 bonds, 2 residues, 1 model selected > select #12/A:6 9 atoms, 8 bonds, 1 residue, 1 model selected > select #12/A:6-66 475 atoms, 487 bonds, 61 residues, 1 model selected > color sel dark sea green target ac > select clear > select #12/A:6 9 atoms, 8 bonds, 1 residue, 1 model selected > select #12/A:6 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select add #12/A:207 14 atoms, 15 bonds, 1 residue, 1 model selected > select add #12/A:208 20 atoms, 20 bonds, 2 residues, 1 model selected > select subtract #12/A:207 6 atoms, 5 bonds, 1 residue, 1 model selected > select #12/A:208 6 atoms, 5 bonds, 1 residue, 1 model selected > select #12/A:208-312 790 atoms, 809 bonds, 105 residues, 1 model selected > color sel light steel blue target ac > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > color (#12 & sel) byhetero > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/AtWAK1.png"" > width 900 height 739 supersample 4 transparentBackground true > color bfactor palette > 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue 29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191 > select clear > hide #12 atoms > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity > WAKs/AtWAK1-pLDDT.png"" width 900 height 739 supersample 4 > transparentBackground true > select clear > hide #12 models > show #10 models > select clear > color #10 darkgrey > show #!2 models > color #2 #73fa79ff > select clear > ui tool show Matchmaker > matchmaker #!2 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 rfo1_1159a_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A (#10) with stb6.pdb, chain A (#2), sequence alignment score = 73.3 RMSD between 37 pruned atom pairs is 0.894 angstroms; (across all 154 pairs: 13.896) > select clear > select #2/A:25 7 atoms, 6 bonds, 1 residue, 1 model selected Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > select clear > select #10/A:26 4 atoms, 3 bonds, 1 residue, 1 model selected Alignment identifier is 10/A > select clear > select add #10/A:36 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #10/A:34 20 atoms, 19 bonds, 2 residues, 1 model selected > setattr #10:36-39 res ss_type 0 Assigning ss_type attribute to 4 items > select #10/A:63 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:34 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #10/A:35 30 atoms, 29 bonds, 3 residues, 1 model selected > setattr #10:34-36 res ss_type 0 Assigning ss_type attribute to 3 items > select add #10/A:38 37 atoms, 35 bonds, 4 residues, 1 model selected > select subtract #10/A:35 23 atoms, 20 bonds, 3 residues, 1 model selected > select add #10/A:35 37 atoms, 35 bonds, 4 residues, 1 model selected > select subtract #10/A:34 29 atoms, 28 bonds, 3 residues, 1 model selected > setattr #10:34-35 res ss_type 2 Assigning ss_type attribute to 2 items > setattr #10:34-36 res ss_type 2 Assigning ss_type attribute to 3 items > setattr #10:34-37 res ss_type 2 Assigning ss_type attribute to 4 items > setattr #10:34-38 res ss_type 2 Assigning ss_type attribute to 5 items > select add #10/A:34 37 atoms, 35 bonds, 4 residues, 1 model selected > select clear > select add #10/A:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:35 22 atoms, 22 bonds, 2 residues, 1 model selected > setattr #10:34-35 res ss_type 0 Assigning ss_type attribute to 2 items > select clear > select add #10/A:23 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #10/A:25 19 atoms, 18 bonds, 2 residues, 1 model selected > select clear > select add #10/A:23 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #10/A:25 19 atoms, 18 bonds, 2 residues, 1 model selected > setattr #10:23-25 res ss_type 2 Assigning ss_type attribute to 3 items > select clear > select add #10/A:30 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #10/A:29 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #10/A:28 25 atoms, 22 bonds, 3 residues, 1 model selected > setattr #10:28-29 res ss_type 0 Assigning ss_type attribute to 2 items > select clear > hide #!2 models > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > show sel & #10 atoms > color (#10 & sel) byhetero > select clear > select S 288 atoms, 123 bonds, 288 residues, 13 models selected > bond sel Created 0 bonds > select clear > select add #10/A:275 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/A:275 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/A:275-287 94 atoms, 96 bonds, 13 residues, 1 model selected > hide sel cartoons > select clear > select add #10/A:9 6 atoms, 5 bonds, 1 residue, 1 model selected > select #10/A:8 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A:1-8 54 atoms, 55 bonds, 8 residues, 1 model selected > hide sel cartoons > select clear > select add #10/A:138 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #10/A:146 10 atoms, 8 bonds, 2 residues, 1 model selected > setattr #10/A:138-146 res ss_type 1 Assigning ss_type attribute to 9 items > setattr #10/A:138-146 res ss_type 0 Assigning ss_type attribute to 9 items > select clear > select add #10/A:82 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #10/A:112 15 atoms, 13 bonds, 2 residues, 1 model selected > color sel light gray target ac > select #10/A:82 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A:82-112 227 atoms, 232 bonds, 31 residues, 1 model selected > color sel light gray target ac > select clear > select add #10/A:81 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:9 13 atoms, 12 bonds, 2 residues, 1 model selected > select #10/A:9 6 atoms, 5 bonds, 1 residue, 1 model selected > select #10/A:9-81 570 atoms, 585 bonds, 73 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #10/A:182 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #10/A:155 20 atoms, 19 bonds, 2 residues, 1 model selected > select #10/A:155 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/A:155-182 232 atoms, 240 bonds, 28 residues, 1 model selected > color sel forest green target ac > select clear > select add #10/A:113 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #10/A:154 18 atoms, 16 bonds, 2 residues, 1 model selected > select #10/A:113 11 atoms, 10 bonds, 1 residue, 1 model selected > select #10/A:113-154 298 atoms, 300 bonds, 42 residues, 1 model selected > color sel dark khaki target ac > select clear > select add #10/A:183 11 atoms, 11 bonds, 1 residue, 1 model selected > select #10/A:183 11 atoms, 11 bonds, 1 residue, 1 model selected > select #10/A:183-287 778 atoms, 801 bonds, 105 residues, 1 model selected > color sel light steel blue target ac > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > color (#10 & sel) byhetero > select clear > select add #10/A:131 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:130 15 atoms, 13 bonds, 2 residues, 1 model selected > select add #10/A:134 23 atoms, 20 bonds, 3 residues, 1 model selected > setattr #10/A:130-134 res ss_type 2 Assigning ss_type attribute to 5 items > select clear > select add #10/A:123 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:118 12 atoms, 10 bonds, 2 residues, 1 model selected > setattr #10/A:118-123 res ss_type 2 Assigning ss_type attribute to 6 items > select clear > setattr #10/A:118-123 res ss_type 0 Assigning ss_type attribute to 6 items > setattr #10/A:119-123 res ss_type 2 Assigning ss_type attribute to 5 items > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rfo1.png"" width > 900 height 739 supersample 4 transparentBackground true > select clear > color bfactor palette > 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue 29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191 > select clear > hide #10 atoms > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rfo1-pLDDT.png"" > width 900 height 739 supersample 4 transparentBackground true > select clear > hide #10 models > show #8 models > select clear > color #8 white > select clear > show #!2 models > color #2 #797979ff > ui tool show Matchmaker > matchmaker #!2 to #8 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 ghwak7A_70d62_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A (#8) with stb6.pdb, chain A (#2), sequence alignment score = 67.2 RMSD between 48 pruned atom pairs is 0.996 angstroms; (across all 172 pairs: 13.707) > select clear > select add #8/A:37 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #8/A:33 17 atoms, 15 bonds, 2 residues, 1 model selected > setattr #8:33-37 res ss_type 0 Assigning ss_type attribute to 5 items > select clear > select #8/A:35 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #8/A:37 19 atoms, 18 bonds, 2 residues, 1 model selected > setattr #8:35-37 res ss_type 2 Assigning ss_type attribute to 3 items > select clear > select add #8/A:20 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select add #8/A:23 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #8/A:25 18 atoms, 17 bonds, 2 residues, 1 model selected > setattr #8:25-23 res ss_type 2 Assigning ss_type attribute to 0 items > setattr #8:23-25 res ss_type 2 Assigning ss_type attribute to 3 items > select clear > hide #!2 models > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > show sel & #8 atoms > color (#8 & sel) byhetero > select clear > select add #8/A:151@SG 1 atom, 1 residue, 1 model selected > select clear > select #8/A:130@SG 1 atom, 1 residue, 1 model selected > select add #8/A:151@SG 2 atoms, 2 residues, 1 model selected > bond sel Created 0 bonds > select clear > select add #8/A:215 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #8/A:189 20 atoms, 19 bonds, 2 residues, 1 model selected Alignment identifier is 8/A > select #8/A:189 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:189-215 230 atoms, 236 bonds, 27 residues, 1 model selected > color sel forest green target ac > select clear > select add #8/A:188 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #8/A:104 17 atoms, 15 bonds, 2 residues, 1 model selected > select #8/A:104 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:104-188 645 atoms, 660 bonds, 85 residues, 1 model selected > color sel dark khaki target ac > select clear > select add #8/A:72 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/A:72 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/A:1-72 557 atoms, 572 bonds, 72 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #8/A:9 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:1-8 59 atoms, 59 bonds, 8 residues, 1 model selected > hide sel cartoons > select clear > select add #8/A:216 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:216 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:216-318 753 atoms, 769 bonds, 103 residues, 1 model selected > color sel light steel blue target ac > select clear > select add #8/A:311 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:312 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:312-318 42 atoms, 41 bonds, 7 residues, 1 model selected > select #8/A:311 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:311-318 49 atoms, 48 bonds, 8 residues, 1 model selected > hide sel cartoons > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > color (#8 & sel) byhetero > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/GhWAK7A.png"" > width 900 height 739 supersample 4 transparentBackground true > select clear > color bfactor palette > 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue 29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191 > select clear > hide #8 atoms > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity > WAKs/GhWAK7A-pLDDT.png"" width 900 height 739 supersample 4 > transparentBackground true > select clear > hide #8 models > show #9 models > select clear > color #9 white > show #!2 models > color #2 #5e5e5eff > hide #!2 models > select add #9/A:65 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #9/A:66 15 atoms, 14 bonds, 2 residues, 1 model selected > select add #9/A:67 26 atoms, 25 bonds, 3 residues, 1 model selected > setattr #9:65-67 res ss_type 0 Assigning ss_type attribute to 3 items > select clear > select add #9/A:67 11 atoms, 11 bonds, 1 residue, 1 model selected Alignment identifier is 9/A > select #9/A:67 11 atoms, 11 bonds, 1 residue, 1 model selected > select #9/A:67-69 28 atoms, 28 bonds, 3 residues, 1 model selected > setattr #9:67-69 res ss_type 2 Assigning ss_type attribute to 3 items > select clear > setattr #9:66-69 res ss_type 2 Assigning ss_type attribute to 4 items > setattr #9:66-70 res ss_type 2 Assigning ss_type attribute to 5 items > setattr #9:66-70 res ss_type 2 Assigning ss_type attribute to 5 items > select add #9/A:65 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #9/A:66 15 atoms, 14 bonds, 2 residues, 1 model selected > select add #9/A:67 26 atoms, 25 bonds, 3 residues, 1 model selected > setattr #9:65-67 res ss_type 0 Assigning ss_type attribute to 3 items > select clear > select add #9/A:55 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #9/A:57 19 atoms, 18 bonds, 2 residues, 1 model selected > setattr #9:55-57 res ss_type 2 Assigning ss_type attribute to 3 items > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > show sel & #9 atoms > color (#9 & sel) byhetero > select clear > select add #9/A:338 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:338 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:338-352 123 atoms, 128 bonds, 15 residues, 1 model selected > hide sel cartoons > select clear > select add #9/A:42 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select #9/A:41 4 atoms, 3 bonds, 1 residue, 1 model selected > select #9/A:41 4 atoms, 3 bonds, 1 residue, 1 model selected > select #9/A:1-41 282 atoms, 290 bonds, 41 residues, 1 model selected > hide sel cartoons > select clear > select add #9/A:242 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #9/A:211 10 atoms, 8 bonds, 2 residues, 1 model selected > select #9/A:211 5 atoms, 4 bonds, 1 residue, 1 model selected > select #9/A:211-242 260 atoms, 265 bonds, 32 residues, 1 model selected > color sel forest green target ac > select clear > select add #9/A:210 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/A:130 17 atoms, 15 bonds, 2 residues, 1 model selected > select #9/A:130 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:130-210 604 atoms, 620 bonds, 81 residues, 1 model selected > color sel dark khaki target ac > select clear > select add #9/A:96 11 atoms, 11 bonds, 1 residue, 1 model selected > select subtract #9/A:96 Nothing selected > select add #9/A:95 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:95 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:1-95 688 atoms, 708 bonds, 95 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #9/A:243 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:243-244 12 atoms, 11 bonds, 2 residues, 1 model selected > select #9/A:243-352 811 atoms, 832 bonds, 110 residues, 1 model selected > color sel light steel blue target ac > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > color (#9 & sel) byhetero > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/SlWAK1.png"" > width 900 height 739 supersample 4 transparentBackground true > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/SlWAK1.png"" > width 900 height 739 supersample 4 transparentBackground true > select clear > color bfactor palette > 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue 29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191 > select clear > hide #9 atoms > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity > WAKs/SlWAK1-pLDDT.png"" width 900 height 739 supersample 4 > transparentBackground true > select clear > hide #9 models > show #7 models > select clear > select add #7/A:108 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #7/A:109 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/A:62 18 atoms, 16 bonds, 2 residues, 1 model selected Alignment identifier is 7/A > select #7/A:63 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:63-64 16 atoms, 15 bonds, 2 residues, 1 model selected > select clear > setattr #9/A:63-64 res ss_type 0 Assigning ss_type attribute to 2 items > select clear > setattr #9/A:63-64 res ss_type 0 Assigning ss_type attribute to 2 items > setattr #7/A:63-64 res ss_type 0 Assigning ss_type attribute to 2 items > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > show sel & #7 atoms > select clear > select #7/A:32 11 atoms, 11 bonds, 1 residue, 1 model selected > select #7/A:32-39 63 atoms, 65 bonds, 8 residues, 1 model selected > select #7/A:148 6 atoms, 5 bonds, 1 residue, 1 model selected > select #7/A:32-148 916 atoms, 945 bonds, 117 residues, 1 model selected > select clear > select add #7/A:108 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #7/A:139 19 atoms, 18 bonds, 2 residues, 1 model selected > select subtract #7/A:139 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #7/A:138 13 atoms, 11 bonds, 2 residues, 1 model selected > select subtract #7/A:108 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #7/A:109 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/A:109 11 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:109-138 228 atoms, 234 bonds, 30 residues, 1 model selected > color sel light gray target ac > select clear > select add #7/A:108 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:108 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:1-108 828 atoms, 858 bonds, 108 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #7/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:238 14 atoms, 15 bonds, 1 residue, 1 model selected > select add #7/A:209 25 atoms, 25 bonds, 2 residues, 1 model selected > select #7/A:209 11 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:209-239 253 atoms, 257 bonds, 31 residues, 1 model selected > color sel forest green target ac > select clear > select add #7/A:139 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #7/A:207 18 atoms, 17 bonds, 2 residues, 1 model selected > select subtract #7/A:207 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #7/A:211 16 atoms, 15 bonds, 2 residues, 1 model selected > select add #7/A:208 27 atoms, 25 bonds, 3 residues, 1 model selected > select subtract #7/A:211 22 atoms, 21 bonds, 2 residues, 1 model selected > select #7/A:139-140 19 atoms, 19 bonds, 2 residues, 1 model selected > select #7/A:139-208 558 atoms, 577 bonds, 70 residues, 1 model selected > color sel dark khaki target ac > select clear > select add #7/A:240 11 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:240 11 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:240-291 383 atoms, 392 bonds, 52 residues, 1 model selected > color sel light steel blue target ac > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > color (#7 & sel) byhetero > select clear > select add #7/A:48 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #7/A:60 9 atoms, 7 bonds, 2 residues, 1 model selected > select #7/A:48 5 atoms, 4 bonds, 1 residue, 1 model selected > select #7/A:48-60 94 atoms, 96 bonds, 13 residues, 1 model selected > color sel pale green target ac > color sel medium aquamarine target ac > color sel pale green target ac > color sel lawn green target ac > color sel medium sea green target ac > color sel green yellow target ac > color sel pale green target ac > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1.png"" width > 900 height 739 supersample 4 transparentBackground true > color bfactor palette > 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue 29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191 > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-pLDDT.png"" > width 900 height 739 supersample 4 transparentBackground true > select clear > select add #7/A:66 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #7/A:85 15 atoms, 13 bonds, 2 residues, 1 model selected > select #7/A:67 6 atoms, 5 bonds, 1 residue, 1 model selected > select #7/A:67-85 147 atoms, 150 bonds, 19 residues, 1 model selected > color sel medium spring green target ac > color sel chartreuse target ac > color sel pale green target ac > color sel olive drab target ac > select clear > select add #7/A:66 7 atoms, 6 bonds, 1 residue, 1 model selected > select #7/A:66 7 atoms, 6 bonds, 1 residue, 1 model selected > select #7/A:1-66 504 atoms, 526 bonds, 66 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #7/A:86 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #7/A:108 12 atoms, 10 bonds, 2 residues, 1 model selected > select #7/A:86 4 atoms, 3 bonds, 1 residue, 1 model selected > select #7/A:86-108 177 atoms, 179 bonds, 23 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #7/A:66 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel olive drab target ac > select clear > select #7/A:66 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #7/A:85 15 atoms, 13 bonds, 2 residues, 1 model selected > select #7/A:85 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:66-85 154 atoms, 157 bonds, 20 residues, 1 model selected > color sel dark sea green target ac > select clear > select add #7/A:109 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/A:138 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/A:109-110 19 atoms, 18 bonds, 2 residues, 1 model selected > select #7/A:109-138 228 atoms, 234 bonds, 30 residues, 1 model selected > color sel light gray target ac > select clear > select add #7/A:208 11 atoms, 10 bonds, 1 residue, 1 model selected > select subtract #7/A:208 Nothing selected > select add #7/A:211 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #7/A:210 13 atoms, 11 bonds, 2 residues, 1 model selected > select clear > select add #7/A:208 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/A:209 22 atoms, 20 bonds, 2 residues, 1 model selected > select subtract #7/A:208 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/A:237 20 atoms, 18 bonds, 2 residues, 1 model selected > select #7/A:209 11 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:209-238 245 atoms, 249 bonds, 30 residues, 1 model selected > color sel forest green target ac > select clear > select add #7/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:239-240 19 atoms, 18 bonds, 2 residues, 1 model selected > select #7/A:239-291 391 atoms, 400 bonds, 53 residues, 1 model selected > color sel light steel blue target ac > select clear > select add #7/A:208 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/A:139 22 atoms, 21 bonds, 2 residues, 1 model selected > select #7/A:139 11 atoms, 11 bonds, 1 residue, 1 model selected > select #7/A:139-208 558 atoms, 577 bonds, 70 residues, 1 model selected > color sel dark khaki target ac > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > color (#7 & sel) byhetero > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1.png"" width > 900 height 739 supersample 4 transparentBackground true > color bfactor palette > 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue 29737 atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191 > select clear > hide #7 atoms > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-pLDDT.png"" > width 900 height 739 supersample 4 transparentBackground true > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Immunity- > WAKs.cxs"" includeMaps true > select clear > hide #7 models > show #4 models > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > show sel & #4 atoms > color (#4 & sel) byhetero > select clear > show #10 models > hide #4 models > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 252 residues, 13 models selected > show sel & #10 atoms > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Immunity- > WAKs.cxs"" includeMaps true > hide #10 models > open 4b43 Summary of feedback from opening 4b43 fetched from pdb --- notes | Fetching compressed mmCIF 4b43 from http://files.rcsb.org/download/4b43.cif Fetching CCD IOD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IOD/IOD.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 4b43 title: Bacterial translation initiation factor IF2 (1-363), apo form, double mutant K86L H130A [more info...] Chain information for 4b43 #14 --- Chain | Description | UniProt A | TRANSLATION INITIATION FACTOR IF-2 | IF2_THET8 1-363 Non-standard residues in 4b43 #14 --- GOL — glycerol (glycerin; propane-1,2,3-triol) IOD — iodide ion MG — magnesium ion 97 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 4b43 4b43 title: Bacterial translation initiation factor IF2 (1-363), apo form, double mutant K86L H130A [more info...] Chain information for 4b43 #15 --- Chain | Description | UniProt A | TRANSLATION INITIATION FACTOR IF-2 | IF2_THET8 1-363 Non-standard residues in 4b43 #15 --- GOL — glycerol (glycerin; propane-1,2,3-triol) IOD — iodide ion MG — magnesium ion 97 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!15 models > close #14 > close #15 > show #!2 models > color #2 #ebebebff > color #2 #d6d6d6ff > color #2 silver > select clear > mlp #!2 Map values for surface ""stb6.pdb_A SES surface"": minimum -28.96, mean -4.218, maximum 22 To also show corresponding color key, enter the above mlp command and add key true > open kdHydrophobicity.defattr No such file/path: kdHydrophobicity.defattr > open /Users/u6290062/Downloads/kdHydrophobicity.defattr.txt Unrecognized file suffix '.txt' > open kdHydrophobicity.defattr No such file/path: kdHydrophobicity.defattr > open /Users/u6290062/Downloads/kdHydrophobicity.defattr Summary of feedback from opening /Users/u6290062/Downloads/kdHydrophobicity.defattr --- note | Assigned attribute 'kdHydrophobicity' to 3882 residues using match mode: any > hide #!2 surfaces > ui tool show ""Render/Select by Attribute"" > color byattribute r:kdHydrophobicity #1,3-13#!2 target csab palette > -4.5,#ffcc00:0,white:4.5,#33cccc 29737 atoms, 3887 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to 4.5 > color byattribute r:kdHydrophobicity #1,3-13#!2 target csab palette > -4.5,#ffcc00:0,white:4.5,#33cccc 29737 atoms, 3887 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to 4.5 > show #!2 surfaces > mlp #!2 Map values for surface ""stb6.pdb_A SES surface"": minimum -28.96, mean -4.218, maximum 22 To also show corresponding color key, enter the above mlp command and add key true > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Errors may have occurred when running pip: pip standard error: \--- ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you have numpy 2.2.6 which is incompatible. chimerax-bundlebuilder 1.5.1 requires numpy==1.26.4, but you have numpy 2.2.6 which is incompatible. \--- pip standard output: \--- \--- pyKVFinder module installed from PyPi repository. > kvfinder #2 14 cavities found for stb6.pdb #2 stb6.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.2.7 | | 64.58 | 88.55 | 299 | 0 | 0 2.2.3 | | 60.05 | 71.51 | 278 | 4.07 | 1.76 2.2.11 | | 57.24 | 63.53 | 265 | 3 | 0.88 2.2.2 | | 56.16 | 67.78 | 260 | 2.55 | 0.75 2.2.6 | | 48.82 | 55.81 | 226 | 2.55 | 0.84 2.2.1 | | 42.34 | 53.49 | 196 | 2.4 | 0.75 2.2.8 | | 31.32 | 51.28 | 145 | 0 | 0 2.2.12 | | 22.46 | 41.55 | 104 | 1.34 | 0.37 2.2.5 | | 22.03 | 26.54 | 102 | 1.7 | 0.49 2.2.10 | | 17.28 | 26.3 | 80 | 0.85 | 0.19 2.2.14 | | 8.42 | 16.15 | 39 | 1.04 | 0.47 2.2.4 | | 6.48 | 15.25 | 30 | 1.04 | 0.36 2.2.9 | | 5.83 | 11.19 | 27 | 0.6 | 0.18 2.2.13 | | 5.18 | 9.36 | 24 | 0.6 | 0.05 Populating font family aliases took 68 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > view #2.2.7 @ zoom 0.75 moved plane near -20.493345654074655 [ 0.73049246 -0.67271407 -0.11762899] moved plane far -20.493345654074655 [ 0.73049246 -0.67271407 -0.11762899] > surface #2.2.1-14 transparency 50 > ~surface #2.2 > surface #2.2.7 > show #!2/A:82,85,119,121,144,154,177,179,194,198 > view #!2.2.3 @ zoom 0.75 moved plane near -22.564736841553437 [0.80196687 0.54550576 0.2434598 ] moved plane far -22.564736841553437 [0.80196687 0.54550576 0.2434598 ] > ~surface #2.2 > surface #!2.2.3 > show #!2/A:40,53-56,63,105-107,110 > view #!2.2.11 @ zoom 0.75 moved plane near -25.356174459232662 [0.80196687 0.54550576 0.2434598 ] moved plane far -25.356174459232662 [0.80196687 0.54550576 0.2434598 ] > ~surface #2.2 > surface #!2.2.11 > show #!2/A:139-144,154,190-191,194 > view #!2.2.2 @ zoom 0.75 moved plane near -24.73322198826226 [0.80196687 0.54550576 0.2434598 ] moved plane far -24.73322198826226 [0.80196687 0.54550576 0.2434598 ] > ~surface #2.2 > surface #!2.2.2 > show #!2/A:101-103,112,118,160,166,178-180 > view #!2.2.6 @ zoom 0.75 moved plane near -22.928707369992463 [0.03014309 0.96483721 0.26111418] moved plane far -22.928707369992463 [0.03014309 0.96483721 0.26111418] > ~surface #2.2 > surface #!2.2.6 > show #!2/A:99,121-123,147,152,175-177 > view #!2.2.1 @ zoom 0.75 moved plane near -26.063677987837806 [0.03014309 0.96483721 0.26111418] moved plane far -26.063677987837806 [0.03014309 0.96483721 0.26111418] > ~surface #2.2 > surface #!2.2.1 > show #!2/A:120,122,165-167,169-171,176,178 > view #!2.2.8 @ zoom 0.75 moved plane near -22.54676136699045 [0.03014309 0.96483721 0.26111418] moved plane far -22.54676136699045 [0.03014309 0.96483721 0.26111418] > ~surface #2.2 > surface #!2.2.8 > show #!2/A:77-79,179-181,197-198,201-202 > view #!2.2.12 @ zoom 0.75 moved plane near -23.470300999803538 [0.03014309 0.96483721 0.26111418] moved plane far -23.470300999803538 [0.03014309 0.96483721 0.26111418] > ~surface #2.2 > surface #!2.2.12 > show #!2/A:184-187,189,192-193,196 > view #!2.2.5 @ zoom 0.75 moved plane near -22.107261522120314 [0.03014309 0.96483721 0.26111418] moved plane far -22.107261522120314 [0.03014309 0.96483721 0.26111418] > ~surface #2.2 > surface #!2.2.5 > show #!2/A:7-9,20-23,34-35 > view #!2.2.10 @ zoom 0.75 moved plane near -20.85830133915867 [-0.8452746 0.52288355 0.11001686] moved plane far -20.85830133915867 [-0.8452746 0.52288355 0.11001686] > ~surface #2.2 > surface #!2.2.10 > show #!2/A:60-61,81,97-100 > view #!2.2.14 @ zoom 0.75 moved plane near -13.816832238616934 [-0.8452746 0.52288355 0.11001686] moved plane far -13.816832238616934 [-0.8452746 0.52288355 0.11001686] > ~surface #2.2 > surface #!2.2.14 > show #!2/A:84,89,93,145-146 > view #!2.2.4 @ zoom 0.75 moved plane near -16.26052353022109 [-0.8452746 0.52288355 0.11001686] moved plane far -16.26052353022109 [-0.8452746 0.52288355 0.11001686] > ~surface #2.2 > surface #!2.2.4 > show #!2/A:124,128,132,171,174 > view #!2.2.9 @ zoom 0.75 moved plane near -17.252922620453052 [-0.8452746 0.52288355 0.11001686] moved plane far -17.252922620453052 [-0.8452746 0.52288355 0.11001686] > ~surface #2.2 > surface #!2.2.9 > show #!2/A:16-17,67-68 > view #!2.2.13 @ zoom 0.75 moved plane near -9.948138531668237 [-0.8452746 0.52288355 0.11001686] moved plane far -9.948138531668237 [-0.8452746 0.52288355 0.11001686] > ~surface #2.2 > surface #!2.2.13 > show #!2/A:46,50,80,92-93 > ui tool show ""Side View"" > select clear > close #2.2 > hide #!2 surfaces > show #!2 surfaces > hide #!2 surfaces > show #!2 surfaces > select clear > hide #!2 surfaces > select clear > select #2/A:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/A:200 14 atoms, 12 bonds, 2 residues, 2 models selected > select #2/A:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:80-201 946 atoms, 969 bonds, 122 residues, 1 model selected > hide sel cartoons > hide sel atoms > select clear > mlp #!2 Map values for surface ""stb6.pdb_A SES surface"": minimum -28.96, mean -4.218, maximum 22 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 surfaces > select clear > ui tool show ""Render/Select by Attribute"" > color byattribute r:kdHydrophobicity #!2 target csab palette > -4.5,#339999:0,white:4.5,#cc9933 1622 atoms, 206 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to 4.5 > select clear > color #2 byhetero > select clear > select #2/A:9 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:9 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:13 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:13 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:33 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:33 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:45 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:45 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > ui tool show Distances > select #2/A:9@SG 1 atom, 1 residue, 1 model selected > select add #2/A:45@CB 2 atoms, 2 residues, 1 model selected > distance #2/A:9@SG #2/A:45@CB Distance between stb6.pdb #2/A CYS 9 SG and CYS 45 CB: 9.665Å > select clear > select #2/A:206 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #2/A:33@SG 1 atom, 1 residue, 1 model selected > select add #2/A:54@CG 2 atoms, 2 residues, 2 models selected > distance #2/A:33@SG #2/A:54@CG Distance between stb6.pdb #2/A CYS 33 SG and PRO 54 CG: 15.517Å > distance style dashes 10 > distance style dashes 11 > distance style dashes 12 > distance style dashes 13 > distance style dashes 14 > distance style dashes 15 > distance style dashes 16 > distance style dashes 15 > distance style dashes 10 > select clear > show #!2 cartoons > select clear > hide #!2 atoms > select clear > show #7 models > show #5 models > ui tool show Matchmaker > matchmaker #5 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker stb6.pdb, chain A (#2) with snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A (#5), sequence alignment score = 78.7 RMSD between 44 pruned atom pairs is 0.933 angstroms; (across all 166 pairs: 14.577) > ui tool show Matchmaker > matchmaker #7 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 stb6.pdb, chain A (#2) with Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A (#7), sequence alignment score = 103.3 RMSD between 69 pruned atom pairs is 0.971 angstroms; (across all 182 pairs: 9.215) > ui mousemode right ""translate selected models"" > select add #5 2645 atoms, 2735 bonds, 346 residues, 1 model selected > view matrix models > #5,0.19339,-0.91678,-0.34945,97.757,0.8353,-0.032979,0.5488,3.8581,-0.51465,-0.39803,0.75941,49.25 > select subtract #5 Nothing selected > select add #7 2250 atoms, 2323 bonds, 291 residues, 1 model selected > view matrix models > #7,0.29983,0.71847,-0.62762,50.42,-0.28833,-0.55887,-0.77751,-4.0589,-0.90938,0.41408,0.03959,22.758 > select clear > select #7/A:71 9 atoms, 8 bonds, 1 residue, 1 model selected Alignment identifier is 7/A > select #5/A:77 8 atoms, 7 bonds, 1 residue, 1 model selected Alignment identifier is 5/A > select clear > color #2 white > color #5 #ebebebff > color #7 #d6d6d6ff > select clear > select add #2/A:79 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:80-206 996 atoms, 1022 bonds, 127 residues, 1 model selected > hide sel cartoons > select clear > select add #7/A:109 11 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:110 8 atoms, 7 bonds, 1 residue, 1 model selected > select #7/A:110-291 1411 atoms, 1453 bonds, 182 residues, 1 model selected > hide sel cartoons > select add #5/A:72 1419 atoms, 1460 bonds, 183 residues, 2 models selected > select #5/A:73-74 17 atoms, 16 bonds, 2 residues, 1 model selected > select #5/A:73-346 2090 atoms, 2161 bonds, 274 residues, 1 model selected > hide sel cartoons > select clear > select add #7 2250 atoms, 2323 bonds, 291 residues, 1 model selected > select subtract #7 Nothing selected > select add #5 2645 atoms, 2735 bonds, 346 residues, 1 model selected > view matrix models > #5,0.19339,-0.91678,-0.34945,84.461,0.8353,-0.032979,0.5488,1.6976,-0.51465,-0.39803,0.75941,40.18 > view matrix models > #5,0.19339,-0.91678,-0.34945,84.347,0.8353,-0.032979,0.5488,1.4847,-0.51465,-0.39803,0.75941,40.956 > select clear > select add #2 1622 atoms, 1672 bonds, 2 pseudobonds, 206 residues, 4 models selected > view matrix models > #2,0.78113,-0.5443,-0.3059,10.914,0.49691,0.83859,-0.22328,20.936,0.37805,0.022403,0.92551,-19.643,#14,1,0,0,0,0,1,0,0,0,0,1,0 > select subtract #2 1 model selected > select add #7 2250 atoms, 2323 bonds, 291 residues, 1 model selected > select subtract #7 Nothing selected > select add #5 2645 atoms, 2735 bonds, 346 residues, 1 model selected > view matrix models > #5,0.19339,-0.91678,-0.34945,78.158,0.8353,-0.032979,0.5488,0.37693,-0.51465,-0.39803,0.75941,37.181 > select clear > color dark sea green target c > select clear > select ::name=""CYS"" 1512 atoms, 1391 bonds, 1 pseudobond, 252 residues, 14 models selected > show sel & #5,7#!2 atoms > color sel dark sea green target ac > select clear Drag select of 72 atoms, 66 bonds > hide sel atoms Drag select of 12 atoms, 11 bonds > hide sel atoms Drag select of 33 atoms, 32 bonds > hide sel atoms Drag select of 2 atoms, 1 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 72 atoms, 66 bonds, 2 residues > hide sel atoms > select clear > hide #!14 models > hide #14.1 models > select clear > color #2,5,7 byhetero > select clear > select add #7 2250 atoms, 2323 bonds, 291 residues, 1 model selected > select subtract #7 Nothing selected > select add #5 2645 atoms, 2735 bonds, 346 residues, 1 model selected > view matrix models > #5,0.19339,-0.91678,-0.34945,73.849,0.8353,-0.032979,0.5488,0.073448,-0.51465,-0.39803,0.75941,34.078 > select clear > select add #5 2645 atoms, 2735 bonds, 346 residues, 1 model selected > select subtract #5 Nothing selected > select add #5 2645 atoms, 2735 bonds, 346 residues, 1 model selected > select subtract #5 Nothing selected > select add #7 2250 atoms, 2323 bonds, 291 residues, 1 model selected > view matrix models > #7,0.29983,0.71847,-0.62762,51.203,-0.28833,-0.55887,-0.77751,-3.9715,-0.90938,0.41408,0.03959,23.115 > select clear > hide #7 models > show #7 models > hide #7 models > hide #5 models > select clear > lighting soft > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Stb6-GUB-WAK- > side.png"" width 911 height 739 supersample 4 transparentBackground true > hide #!2 models > show #5 models > hide #5 models > show #5 models > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-GUB-WAK- > side.png"" width 911 height 739 supersample 4 transparentBackground true > select clear > hide #5 models > show #7 models > select add #7/A:109 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-GUB-WAK- > side.png"" width 911 height 739 supersample 4 transparentBackground true > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-GUB-WAK- > top.png"" width 911 height 739 supersample 4 transparentBackground true > hide #7 models > show #5 models > select clear > show #5 surfaces > hide #!5 surfaces > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-GUB-WAK- > top.png"" width 911 height 739 supersample 4 transparentBackground true > select clear > show #!2 models > hide #!5 models > select clear > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Stb6-GUB-WAK- > top.png"" width 911 height 739 supersample 4 transparentBackground true > select clear > show #!5 models > show #7 models > ui tool show Matchmaker > matchmaker #!5 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker stb6.pdb, chain A (#2) with snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A (#5), sequence alignment score = 78.7 RMSD between 44 pruned atom pairs is 0.933 angstroms; (across all 166 pairs: 14.577) > ui tool show Matchmaker > matchmaker #7 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 stb6.pdb, chain A (#2) with Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A (#7), sequence alignment score = 103.3 RMSD between 69 pruned atom pairs is 0.971 angstroms; (across all 182 pairs: 9.215) > select clear > color #5 #ebebebff > color #5 #009193ff > color #7 #4f8f00ff > color #7 #929000ff > color #7 #009051ff > color #7 #929000ff > color #7 #8efa00ff > color #7 #fffb00ff > color #7 #73fa79ff > color #7 #929000ff > select clear > color #2 #d4fb79ff > color #2 #73fa79ff > color #2 #73fcd6ff > color #2 #73fa79ff > color #2 #00f900ff > color #2 #73fa79ff > color #2 #00fa92ff > color #2 #00f900ff > color #2 #73fa79ff > select clear > color #2,5,7 byhetero > select clear > select add #2 1622 atoms, 1672 bonds, 2 pseudobonds, 206 residues, 2 models selected > color sel light green target ac > select clear > color #2,5,7 byhetero > select clear > select #2/A:6 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:6-7 12 atoms, 11 bonds, 2 residues, 1 model selected > hide sel cartoons > select #7/A:1 10 atoms, 10 bonds, 1 residue, 1 model selected > select #7/A:1-2 14 atoms, 14 bonds, 2 residues, 1 model selected > select clear > select add #5/A:6 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select add #7/A:28 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #2/A:8 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:8 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select add #2 1622 atoms, 1672 bonds, 2 pseudobonds, 206 residues, 2 models selected > select add #5 4267 atoms, 4407 bonds, 2 pseudobonds, 552 residues, 4 models selected > select add #7 6517 atoms, 6730 bonds, 2 pseudobonds, 843 residues, 6 models selected > color sel dark sea green target ac > select clear > color #2,5,7 byhetero > select clear > hide #!2 models > show #!2 models > hide #!5 models > hide #7 models > select clear > show #!5 models > show #7 models > hide #!5 models > hide #7 models > show #!5 models > show #7 models > hide #!5 models > hide #7 models > select clear > show #!5 models > show #7 models > hide #!5 models > hide #7 models > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Stb6-GUB-WAK- > top.png"" width 911 height 739 supersample 4 transparentBackground true > show #!5 models > hide #!2 models > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-GUB-WAK- > top.png"" width 911 height 739 supersample 4 transparentBackground true > select clear > show #7 models > hide #!5 models > show #!5 models > show #!2 models > hide #!2 models > hide #!5 models > save ""/Users/u6290062/Library/CloudStorage/OneDrive- > AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-GUB-WAK- > top.png"" width 911 height 739 supersample 4 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 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 M2 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: Mac14,9 Model Number: MPHF3X/A Chip: Apple M2 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 9 days, 2 hours, 33 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 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 DELL S2719H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL S2719H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 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: 14.1.18 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-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 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-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: 1.1.2 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: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 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: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 2.2.0 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: 2.2.6 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: 6.0.1 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 pyelftools: 0.32 Pygments: 2.18.0 pyKVFinder: 0.8.1 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: 0.13.2 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 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