id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8643 Graphics crash, macOS 12.5, Intel HD Graphics 615 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x0000000113456600 (most recent call first): File ""/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 235 in swap_buffers File ""/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 497 in swap_buffers File ""/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 191 in draw File ""/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File 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: 240000251 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/SZ3_NTd.pdb Chain information for SZ3_NTd.pdb #1 --- Chain | Description A | No description available > set bgColor white > hide atoms > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Omicron_7wk2_NTD.pdb Omicron_7wk2_NTD.pdb title: Sars-cov-2 ο S-close [more info...] Chain information for Omicron_7wk2_NTD.pdb #2 --- Chain | Description | UniProt A | spike glycoprotein | SPIKE_SARS2 > ui tool show ""Side View"" > ui mousemode right select Drag select of 262 residues, 4 pseudobonds > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-88.011,0,1,0,31.72,0,0,1,-59.275 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.17893,0.6391,-0.74802,164.13,0.88075,-0.44288,-0.16771,110.08,-0.43847,-0.62882,-0.64213,522.2 > view matrix models > #2,0.14547,0.7139,-0.68497,145.07,0.86987,-0.42212,-0.25522,128.41,-0.47134,-0.55871,-0.68241,526.69 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.14547,0.7139,-0.68497,136.99,0.86987,-0.42212,-0.25522,128.2,-0.47134,-0.55871,-0.68241,521.34 > view matrix models > #2,0.14547,0.7139,-0.68497,136.09,0.86987,-0.42212,-0.25522,126.33,-0.47134,-0.55871,-0.68241,518.64 > 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 SZ3_NTd.pdb, chain A (#1) with Omicron_7wk2_NTD.pdb, chain A (#2), sequence alignment score = 3227.6 RMSD between 197 pruned atom pairs is 1.020 angstroms; (across all 254 pairs: 2.394) > select add #2 2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected > select subtract #2 Nothing selected > hide #1 models > show #1 models > select add #1 4346 atoms, 4423 bonds, 294 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium sea green > select subtract #1 Nothing selected > select add #2 2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light salmon > color sel salmon > color sel dark salmon > color sel maroon > color sel coral > color sel light salmon > color sel salmon > color sel peach puff > color sel moccasin > color sel wheat > color sel pale goldenrod > color sel tan > color sel burly wood > color sel tan > select subtract #2 Nothing selected > lighting full > save /Users/bostinalab/Desktop/image1.png supersample 3 > select add #2 2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected > close #2 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/RatG13_NTD.pdb RatG13_NTD.pdb title: Cryo-em structure of bat RATG13 spike glycoprotein [more info...] Chain information for RatG13_NTD.pdb #2 --- Chain | Description A | spike glycoprotein Non-standard residues in RatG13_NTD.pdb #2 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > select add #2 2208 atoms, 2268 bonds, 296 residues, 1 model selected > view matrix models #2,1,0,0,17.045,0,1,0,-29.042,0,0,1,31.335 > view matrix models #2,1,0,0,15.734,0,1,0,-21.689,0,0,1,33.355 > view matrix models #2,1,0,0,-6.2958,0,1,0,58.452,0,0,1,29.721 > hide sel atoms > view matrix models #2,1,0,0,-4.4385,0,1,0,50.95,0,0,1,29.382 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.66957,-0.73116,0.1307,113.51,0.7427,0.65699,-0.12946,26.866,0.0087865,0.18375,0.98293,6.3096 > view matrix models > #2,0.91886,-0.37728,0.11555,39.074,0.18245,0.1466,-0.97222,279.64,0.34986,0.91442,0.20354,-21.553 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #2,0.91886,-0.37728,0.11555,68.734,0.18245,0.1466,-0.97222,291.49,0.34986,0.91442,0.20354,-46.995 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.94227,-0.32695,0.072373,65.348,0.075,-0.0045842,-0.99717,327.82,0.32636,0.94503,0.020202,-22.485 > view matrix models > #2,0.053025,0.98311,-0.17514,31.226,-0.97437,0.012539,-0.22461,341.05,-0.21862,0.18256,0.95858,11.37 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.053025,0.98311,-0.17514,30.448,-0.97437,0.012539,-0.22461,353.9,-0.21862,0.18256,0.95858,21.573 > 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 SZ3_NTd.pdb, chain A (#1) with RatG13_NTD.pdb, chain A (#2), sequence alignment score = 3364.1 RMSD between 208 pruned atom pairs is 0.835 angstroms; (across all 273 pairs: 2.911) > ui tool show ""Color Actions"" > color sel tan > select subtract #2 Nothing selected > save /Users/bostinalab/Desktop/image2.png supersample 3 > close #2 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/pCoV-GX_NTD.pdb pCoV-GX_NTD.pdb title: Structure of coronavirus spike from smuggled guangdong pangolin [more info...] Chain information for pCoV-GX_NTD.pdb #2 --- Chain | Description A | surface glycoprotein Non-standard residues in pCoV-GX_NTD.pdb #2 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > ui mousemode right select Drag select of 145 atoms, 249 residues, 4 pseudobonds, 140 bonds > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-28.344,0,1,0,-2.6339,0,0,1,-101.95 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.73959,0.44457,-0.50533,56.112,-0.44722,0.8857,0.12466,108.83,0.50299,0.13379,0.85387,-227.05 > view matrix models > #2,-0.99928,-0.010959,0.036423,477.74,-0.0016656,0.96928,0.24595,-53.366,-0.038,0.24571,-0.9686,322.11 > show sel cartoons > hide sel atoms > 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 SZ3_NTd.pdb, chain A (#1) with pCoV-GX_NTD.pdb, chain A (#2), sequence alignment score = 3332.9 RMSD between 230 pruned atom pairs is 0.748 angstroms; (across all 243 pairs: 1.525) > ui tool show ""Color Actions"" > color sel tan > select add #2 2081 atoms, 2140 bonds, 4 pseudobonds, 255 residues, 2 models selected > select subtract #2 Nothing selected > save /Users/bostinalab/Desktop/image3.png supersample 3 > close #2 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/MERS_8h15_NTD.pdb MERS_8h15_NTD.pdb title: Structure of sars-cov-1 spike protein (S/native) At pH 5.5, closed conformation [more info...] Chain information for MERS_8h15_NTD.pdb #2 --- Chain | Description | UniProt A | spike glycoprotein | SPIKE_SARS Non-standard residues in MERS_8h15_NTD.pdb #2 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > select add #2 1638 atoms, 1680 bonds, 6 pseudobonds, 202 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-12.307,0,1,0,22.159,0,0,1,-20.132 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.75167,0.25014,-0.61027,91.758,0.61867,-0.58807,0.52098,122.23,-0.22856,-0.76916,-0.59679,447.82 > view matrix models > #2,0.43594,-0.88488,-0.16414,245.87,-0.74728,-0.45755,0.48189,281.73,-0.50152,-0.087417,-0.86072,413.76 > view matrix models > #2,0.20459,-0.95149,-0.22979,299.61,-0.85821,-0.28726,0.42538,276.93,-0.47076,0.11018,-0.87536,378.08 > view matrix models > #2,0.35485,-0.92051,-0.16352,262.35,-0.79548,-0.38917,0.46451,279.26,-0.49122,-0.034753,-0.87034,405.07 > view matrix models > #2,0.3263,-0.93196,0.15806,206.81,-0.84453,-0.21231,0.49162,249.48,-0.42461,-0.2939,-0.85635,439.15 > view matrix models > #2,0.81914,-0.57065,0.058148,99.618,-0.40378,-0.50165,0.76506,191.58,-0.4074,-0.65016,-0.64133,458.28 > view matrix models > #2,-0.065096,-0.99623,-0.057345,309.12,-0.9294,0.039608,0.36693,239.79,-0.36328,0.077182,-0.92848,379.92 > view matrix models > #2,0.47974,-0.85826,-0.18232,239.06,-0.76483,-0.51089,0.39245,310.3,-0.42998,-0.048828,-0.90152,405.26 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.47974,-0.85826,-0.18232,238.31,-0.76483,-0.51089,0.39245,312.03,-0.42998,-0.048828,-0.90152,404.41 > 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 SZ3_NTd.pdb, chain A (#1) with MERS_8h15_NTD.pdb, chain A (#2), sequence alignment score = 4096.2 RMSD between 200 pruned atom pairs is 0.627 angstroms; (across all 200 pairs: 0.627) > ui tool show ""Color Actions"" > color sel tan > show sel cartoons > hide sel atoms > select subtract #2 Nothing selected > save /Users/bostinalab/Desktop/image4.png supersample 3 > close #2 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Delta_7e7b_NTD.pdb Delta_7e7b_NTD.pdb title: Cryo-em structure of the sars-cov-2 furin site mutant S-trimer from A subunit vaccine candidate [more info...] Chain information for Delta_7e7b_NTD.pdb #2 --- Chain | Description | UniProt A | spike glycoprotein,collagen α-1(I) chain | CO1A1_HUMAN Non-standard residues in Delta_7e7b_NTD.pdb #2 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) VCG — 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-α-L- xylo-hexofuranoside (polysorbate 80) > ui mousemode right select > select add #2 2391 atoms, 2452 bonds, 1 pseudobond, 299 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-27.694,0,1,0,60.065,0,0,1,-34.737 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.71067,0.50688,-0.48787,53.084,0.50537,-0.85025,-0.14722,193.95,-0.48944,-0.14193,-0.86041,386.72 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.71067,0.50688,-0.48787,46.065,0.50537,-0.85025,-0.14722,237.96,-0.48944,-0.14193,-0.86041,407.73 > 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 SZ3_NTd.pdb, chain A (#1) with Delta_7e7b_NTD.pdb, chain A (#2), sequence alignment score = 3406.6 RMSD between 249 pruned atom pairs is 0.745 angstroms; (across all 273 pairs: 1.875) > show sel cartoons > hide sel atoms > ui tool show ""Color Actions"" > color sel tan > select subtract #2 Nothing selected > save /Users/bostinalab/Desktop/image1.png supersample 3 > select add #2 2391 atoms, 2452 bonds, 1 pseudobond, 299 residues, 2 models selected > close #2 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/007_NTD.pdb Chain information for 007_NTD.pdb #2 --- Chain | Description A | No description available > select add #2 4369 atoms, 4447 bonds, 293 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.003,0,1,0,23.715,0,0,1,-41.963 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.090444,-0.75393,0.6507,228.03,0.99558,-0.085068,0.039816,5.6637,0.025336,0.65143,0.75829,-121.75 > view matrix models > #2,-0.0683,-0.98884,0.13242,364.14,-0.064925,0.13685,0.98846,10.006,-0.99555,0.058914,-0.073547,359.23 > view matrix models > #2,-0.32415,0.941,-0.097203,103.9,0.89793,0.33839,0.28146,-98.614,0.29775,0.0039552,-0.95464,261.59 > view matrix models > #2,-0.67218,0.72759,-0.13707,224.33,0.6864,0.6818,0.253,-111.58,0.27754,0.075979,-0.95771,252.94 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.67218,0.72759,-0.13707,218.07,0.6864,0.6818,0.253,-93.373,0.27754,0.075979,-0.95771,249.85 > 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 SZ3_NTd.pdb, chain A (#1) with 007_NTD.pdb, chain A (#2), sequence alignment score = 4343.5 RMSD between 272 pruned atom pairs is 0.384 angstroms; (across all 274 pairs: 0.435) > show sel cartoons > hide sel atoms > ui tool show ""Color Actions"" > color sel royal blue > select subtract #2 Nothing selected > save /Users/bostinalab/Desktop/image2.png supersample 3 > close #1 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Omicron_7wk2_NTD.pdb Omicron_7wk2_NTD.pdb title: Sars-cov-2 ο S-close [more info...] Chain information for Omicron_7wk2_NTD.pdb #1 --- Chain | Description | UniProt A | spike glycoprotein | SPIKE_SARS2 > select add #1 2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected > ui mousemode right select > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-32.84,0,1,0,1.5395,0,0,1,-113.37 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.82808,0.53442,0.16932,279.85,0.15038,-0.079214,0.98545,-61.996,0.54006,0.8415,-0.014771,-169.25 > view matrix models > #1,-0.17644,-0.61087,-0.77182,532.42,0.26919,-0.78417,0.55912,128.3,-0.94679,-0.10912,0.3028,290.63 > view matrix models > #1,0.33381,-0.74421,-0.57856,389.11,0.30611,-0.49492,0.81324,11.85,-0.89155,-0.44857,0.062602,390.47 > view matrix models > #1,0.42993,-0.62416,-0.65237,360.79,-0.029238,-0.7318,0.68089,164.69,-0.90239,-0.27366,-0.33287,449.64 > view matrix models > #1,0.68177,0.15386,-0.7152,175.62,0.59552,-0.68455,0.42042,61.947,-0.4249,-0.71255,-0.55833,461.09 > view matrix models > #1,0.33644,0.86183,-0.37955,59.976,0.90797,-0.18996,0.3735,-91.293,0.24979,-0.47028,-0.84643,317.77 > view matrix models > #1,-0.22747,0.97344,0.025795,87.717,0.80395,0.17278,0.56904,-173.5,0.54947,0.15018,-0.82191,129.53 > view matrix models > #1,-0.351,0.92809,-0.12429,159.02,0.69546,0.34727,0.62907,-191.3,0.627,0.13436,-0.76735,101.39 > view matrix models > #1,-0.22126,0.95418,-0.20144,139.91,0.71089,0.29922,0.63648,-188.18,0.66759,-0.0023724,-0.74452,110.68 > view matrix models > #1,-0.33458,0.93629,-0.10688,149.72,0.6709,0.31631,0.6707,-189.05,0.66178,0.1527,-0.73399,82.298 > view matrix models > #1,-0.50751,0.84444,0.17131,146.5,0.63764,0.23436,0.73382,-180.41,0.57952,0.48166,-0.65739,27.099 > view matrix models > #1,-0.74934,0.64824,0.13516,248.1,0.42683,0.31679,0.84703,-168.77,0.50626,0.69241,-0.51408,-24.116 > view matrix models > #1,-0.92644,0.3752,-0.030558,376.22,0.10568,0.33714,0.9355,-113.81,0.3613,0.86346,-0.35199,-55.011 > view matrix models > #1,-0.91865,-0.061635,0.39023,358.57,0.3755,0.17078,0.91095,-144.56,-0.12279,0.98338,-0.13374,-6.7586 > view matrix models > #1,-0.28509,-0.57684,-0.76549,551.43,0.28838,-0.81325,0.50543,140.66,-0.91409,-0.07666,0.3982,255.81 > view matrix models > #1,0.12426,0.01403,-0.99215,397.33,0.61438,-0.78626,0.065828,153.84,-0.77916,-0.61774,-0.10632,430.46 > view matrix models > #1,-0.40577,0.90318,0.14006,118.26,0.88334,0.3482,0.31378,-167.4,0.23464,0.25104,-0.93911,214.21 > view matrix models > #1,-0.38532,0.918,0.093884,120.88,0.89399,0.34614,0.28455,-163.16,0.22872,0.19357,-0.95405,229.13 > view matrix models > #1,-0.58454,0.80005,-0.13505,240.91,0.47891,0.47457,0.73853,-185.37,0.65495,0.36702,-0.66055,29.748 > view matrix models > #1,-0.41084,0.89317,-0.18294,192.75,0.22758,0.29477,0.92807,-134.32,0.88285,0.33965,-0.32437,-95.256 > view matrix models > #1,-0.3,0.93789,-0.17427,155.94,0.044498,0.19624,0.97954,-83.712,0.9529,0.2861,-0.10061,-152.34 > view matrix models > #1,-0.49624,0.74396,-0.44751,298.51,-0.24579,0.37398,0.89427,-25.686,0.83267,0.55377,-0.0027288,-192.15 > view matrix models > #1,-0.5245,0.59026,-0.61359,369.36,-0.41998,0.44753,0.78951,26.857,0.74062,0.6718,0.013169,-194.17 > view matrix models > #1,-0.41355,-0.098647,-0.90512,528.89,-0.89948,0.19835,0.38936,276.22,0.14112,0.97516,-0.17076,-61.325 > view matrix models > #1,-0.51942,-0.7,-0.49011,569.32,-0.22035,-0.44443,0.86829,118.83,-0.82562,0.559,0.0766,192.87 > view matrix models > #1,-0.96273,0.053506,0.26514,376.59,0.2635,0.40673,0.87472,-151.08,-0.061037,0.91198,-0.40567,51.041 > view matrix models > #1,-0.31911,0.90538,0.2801,65.791,0.94024,0.26539,0.21335,-144.35,0.11883,0.33144,-0.93596,227.45 > view matrix models > #1,-0.1197,0.98421,0.13042,36.432,0.9922,0.11399,0.050439,-94.127,0.034776,0.13544,-0.99017,294.62 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.1197,0.98421,0.13042,39.838,0.9922,0.11399,0.050439,-54.151,0.034776,0.13544,-0.99017,326.01 > ui tool show Matchmaker > matchmaker #!1 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 007_NTD.pdb, chain A (#2) with Omicron_7wk2_NTD.pdb, chain A (#1), sequence alignment score = 3234.6 RMSD between 201 pruned atom pairs is 1.032 angstroms; (across all 254 pairs: 2.404) > view matrix models > #1,-0.10665,0.99095,0.081562,-22.046,0.99326,0.10993,-0.036854,-45.216,-0.045486,0.077081,-0.99599,371.45 > undo > select subtract #1 Nothing selected > select add #1 2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected > ui tool show ""Color Actions"" > color sel tan > select subtract #1 Nothing selected > save /Users/bostinalab/Desktop/image1.png supersample 3 > select add #1 2108 atoms, 2164 bonds, 4 pseudobonds, 262 residues, 2 models selected > close #1 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/RatG13_NTD.pdb RatG13_NTD.pdb title: Cryo-em structure of bat RATG13 spike glycoprotein [more info...] Chain information for RatG13_NTD.pdb #1 --- Chain | Description A | spike glycoprotein Non-standard residues in RatG13_NTD.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > select add #1 2208 atoms, 2268 bonds, 296 residues, 1 model selected > view matrix models #1,1,0,0,-7.5996,0,1,0,50.432,0,0,1,22.015 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98776,0.12219,0.096912,-36.031,-0.042506,0.80879,-0.58655,163.43,-0.15006,0.57526,0.80409,-9.1085 > view matrix models > #1,0.98643,0.13039,0.099784,-37.373,-0.042009,0.78794,-0.61431,170.05,-0.15872,0.60178,0.78273,-8.6395 > view matrix models > #1,-0.60328,0.66753,0.43643,31.999,-0.7482,-0.28423,-0.59951,394.13,-0.27614,-0.6882,0.67091,192.53 > view matrix models > #1,0.091113,0.95401,0.28561,-67.067,-0.78866,0.24424,-0.56424,323.68,-0.60804,-0.17384,0.77464,148.82 > view matrix models > #1,0.66664,0.73438,0.12761,-83.752,-0.5514,0.60106,-0.57852,250.16,-0.50155,0.3153,0.80562,66.814 > view matrix models > #1,0.58538,0.80778,0.069472,-75.714,-0.63703,0.51126,-0.57689,272.01,-0.50152,0.29345,0.81386,68.557 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.58538,0.80778,0.069472,-78.682,-0.63703,0.51126,-0.57689,286.7,-0.50152,0.29345,0.81386,69.649 > ui tool show Matchmaker > matchmaker #1 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 007_NTD.pdb, chain A (#2) with RatG13_NTD.pdb, chain A (#1), sequence alignment score = 3358.5 RMSD between 209 pruned atom pairs is 0.808 angstroms; (across all 274 pairs: 2.841) > show sel cartoons > hide sel atoms > ui tool show ""Color Actions"" > color sel tan > select subtract #1 Nothing selected > save /Users/bostinalab/Desktop/image2.png supersample 3 > select add #1 2208 atoms, 2268 bonds, 296 residues, 1 model selected > close #1 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/pCoV-GX_NTD.pdb pCoV-GX_NTD.pdb title: Structure of coronavirus spike from smuggled guangdong pangolin [more info...] Chain information for pCoV-GX_NTD.pdb #1 --- Chain | Description A | surface glycoprotein Non-standard residues in pCoV-GX_NTD.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > select add #1 2081 atoms, 2140 bonds, 4 pseudobonds, 255 residues, 2 models selected > view matrix models #1,1,0,0,-11.465,0,1,0,4.2934,0,0,1,-74.44 > ui tool show Matchmaker > matchmaker #!1 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 007_NTD.pdb, chain A (#2) with pCoV-GX_NTD.pdb, chain A (#1), sequence alignment score = 3334.7 RMSD between 233 pruned atom pairs is 0.737 angstroms; (across all 244 pairs: 1.488) > show sel cartoons > hide sel atoms > ui tool show ""Color Actions"" > color sel tan > select subtract #1 Nothing selected > save /Users/bostinalab/Desktop/image3.png supersample 3 > select add #1 2081 atoms, 2140 bonds, 4 pseudobonds, 255 residues, 2 models selected > close #1 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/MERS_8h15_NTD.pdb MERS_8h15_NTD.pdb title: Structure of sars-cov-1 spike protein (S/native) At pH 5.5, closed conformation [more info...] Chain information for MERS_8h15_NTD.pdb #1 --- Chain | Description | UniProt A | spike glycoprotein | SPIKE_SARS Non-standard residues in MERS_8h15_NTD.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > select add #1 1638 atoms, 1680 bonds, 6 pseudobonds, 202 residues, 2 models selected > view matrix models #1,1,0,0,-10.393,0,1,0,29.188,0,0,1,-29.546 > show sel cartoons > hide sel atoms > ui tool show ""Color Actions"" > color sel tan > ui tool show Matchmaker > matchmaker #!1 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 007_NTD.pdb, chain A (#2) with MERS_8h15_NTD.pdb, chain A (#1), sequence alignment score = 4116.9 RMSD between 200 pruned atom pairs is 0.620 angstroms; (across all 200 pairs: 0.620) > select subtract #1 Nothing selected > save /Users/bostinalab/Desktop/image4.png supersample 3 > select add #1 1638 atoms, 1680 bonds, 6 pseudobonds, 202 residues, 2 models selected > close #1 > open /Users/bostinalab/Documents/PDBs/Mine/NTDs/Delta_7e7b_NTD.pdb Delta_7e7b_NTD.pdb title: Cryo-em structure of the sars-cov-2 furin site mutant S-trimer from A subunit vaccine candidate [more info...] Chain information for Delta_7e7b_NTD.pdb #1 --- Chain | Description | UniProt A | spike glycoprotein,collagen α-1(I) chain | CO1A1_HUMAN Non-standard residues in Delta_7e7b_NTD.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) VCG — 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-α-L- xylo-hexofuranoside (polysorbate 80) > ui tool show Matchmaker > matchmaker #!1 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 007_NTD.pdb, chain A (#2) with Delta_7e7b_NTD.pdb, chain A (#1), sequence alignment score = 3409.6 RMSD between 252 pruned atom pairs is 0.696 angstroms; (across all 274 pairs: 1.747) > show cartoons > hide atoms > save /Users/bostinalab/Desktop/image5.png supersample 3 > select add #1 2391 atoms, 2452 bonds, 1 pseudobond, 299 residues, 2 models selected > select add #2 6760 atoms, 6899 bonds, 1 pseudobond, 592 residues, 3 models selected > close #2 > close #1 > open /Users/bostinalab/Documents/PDBs/Mine/RBDs/SZ3_RBD.pdb Chain information for SZ3_RBD.pdb #1 --- Chain | Description A | No description available > open /Users/bostinalab/Documents/PDBs/Mine/RBDs/Omicron_7wk2_RBD.pdb Omicron_7wk2_RBD.pdb title: Sars-cov-2 ο S-close [more info...] Chain information for Omicron_7wk2_RBD.pdb #2 --- Chain | Description | UniProt A | spike glycoprotein | SPIKE_SARS2 > select add #2 1793 atoms, 1848 bonds, 223 residues, 1 model selected > select add #1 4791 atoms, 4894 bonds, 419 residues, 2 models selected > select subtract #2 2998 atoms, 3046 bonds, 196 residues, 1 model selected > view matrix models #1,1,0,0,30.055,0,1,0,63.687,0,0,1,0 > view matrix models #1,1,0,0,36.716,0,1,0,46.825,0,0,1,107.3 > 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 SZ3_RBD.pdb, chain A (#1) with Omicron_7wk2_RBD.pdb, chain A (#2), sequence alignment score = 3127.6 RMSD between 165 pruned atom pairs is 1.161 angstroms; (across all 194 pairs: 2.162) > view matrix models #1,1,0,0,36.795,0,1,0,46.581,0,0,1,108.68 > close #1 > open /Users/bostinalab/Downloads/Complete_SZ3.pdb Chain information for Complete_SZ3.pdb #1 --- Chain | Description A B C | No description available > select #1/A 16663 atoms, 16899 bonds, 3 pseudobonds, 1132 residues, 2 models selected > select ~sel 35119 atoms, 35646 bonds, 6 pseudobonds, 2487 residues, 3 models selected > select subtract #2 33326 atoms, 33798 bonds, 6 pseudobonds, 2264 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > show cartoons > hide atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A:292 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/A:3-292 4316 atoms, 4381 bonds, 290 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:517 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:517-1106 8284 atoms, 8365 bonds, 3 pseudobonds, 570 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select add #1 4063 atoms, 4146 bonds, 272 residues, 1 model selected > view matrix models #1,1,0,0,3.3905,0,1,0,26.834,0,0,1,35.241 > view matrix models #1,1,0,0,4.0703,0,1,0,54.603,0,0,1,97.953 > 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 Complete_SZ3.pdb, chain A (#1) with Omicron_7wk2_RBD.pdb, chain A (#2), sequence alignment score = 3146.2 RMSD between 193 pruned atom pairs is 1.161 angstroms; (across all 222 pairs: 2.060) > ui tool show ""Color Actions"" > color sel medium sea green > select add #2 5856 atoms, 5994 bonds, 495 residues, 2 models selected > select subtract #1 1793 atoms, 1848 bonds, 223 residues, 1 model selected > ui tool show ""Color Actions"" > color sel tan > select subtract #2 Nothing selected > save /Users/bostinalab/Desktop/image1.png supersample 3 > select add #2 1793 atoms, 1848 bonds, 223 residues, 1 model selected > close #2 > open /Users/bostinalab/Documents/PDBs/Mine/RBDs/007_RBD.pdb Chain information for 007_RBD.pdb #2 --- Chain | Description A | No description available > select add #2 3496 atoms, 3558 bonds, 229 residues, 1 model selected > close #2 > open /Users/bostinalab/Downloads/Complete_007.pdb Chain information for Complete_007.pdb #2 --- Chain | Description A B C | No description available Undo failed, probably because structures have been modified. > select #2/A 16438 atoms, 16677 bonds, 3 pseudobonds, 1116 residues, 2 models selected > select ~sel 36939 atoms, 37500 bonds, 6 pseudobonds, 2504 residues, 3 models selected > select subtract #1 32876 atoms, 33354 bonds, 6 pseudobonds, 2232 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:291-292 34 atoms, 34 bonds, 2 residues, 1 model selected > select #2/A:3-292 4378 atoms, 4445 bonds, 290 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/A:517-519 40 atoms, 39 bonds, 3 residues, 1 model selected > select #2/A:517-1107 8251 atoms, 8335 bonds, 3 pseudobonds, 574 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select add #2 3809 atoms, 3882 bonds, 252 residues, 1 model selected > view matrix models #2,1,0,0,-15.776,0,1,0,-35.006,0,0,1,-7.8099 > ui mousemode right select > select subtract #2 Nothing selected Drag select of 273 atoms, 283 bonds > delete atoms sel > delete bonds sel Drag select of 39 atoms, 41 bonds > delete atoms sel > delete bonds sel > select add #2 3497 atoms, 3558 bonds, 230 residues, 1 model selected > show sel cartoons > hide sel atoms Drag select of 10 residues > select add #2 3497 atoms, 3558 bonds, 230 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,57.536,0,1,0,21.875,0,0,1,22.87 > 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 Complete_SZ3.pdb, chain A (#1) with Complete_007.pdb, chain A (#2), sequence alignment score = 4243.9 RMSD between 224 pruned atom pairs is 0.309 angstroms; (across all 224 pairs: 0.309) > view matrix models > #2,-0.77186,0.63578,0.0036126,194.05,0.63576,0.77187,-0.004394,-11.781,-0.0055821,-0.0010948,-0.99998,436.66 > undo > ui tool show ""Side View"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.4 OpenGL renderer: Intel(R) HD Graphics 615 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Model Identifier: MacBook10,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 451.140.1.0.0 OS Loader Version: 540.120.3~19 SMC Version (system): 2.42f13 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 94 days 4:05 Graphics/Displays: Intel HD Graphics 615: Chipset Model: Intel HD Graphics 615 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591e Revision ID: 0x0002 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2304 x 1440 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX