id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17795 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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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======= ======= \nTOTAL 9.3G 6441 \nTOTAL, minus reserved VM space 9.0G 6441 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""076d9c98801b994954e144cef8621baeea1587ce"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000012 }, { ""rolloutId"" : ""6761d0c9df60af01adb250fb"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250521-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"" Chain information for 20250521-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb #1 --- Chain | Description A B C | No description available > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1098 atoms, 1125 bonds, 81 residues, 1 model selected > delete sel > show cartoons > hide atoms > save ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"" > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C Alignment identifier is 1 Could not find virtual screen for QCocoaScreen(0x6000026e46e0, ""HDMI (2)"", QRect(0,0 1920x1080), dpr=1, displayId=6, ) with displayId 6 > select #1/A-C:736-775 867 atoms, 885 bonds, 120 residues, 1 model selected > select #1/A-C:736-770 765 atoms, 780 bonds, 105 residues, 1 model selected > hide sel > hide sel cartoons > select #1/A-C:771-1242 10518 atoms, 10686 bonds, 3 pseudobonds, 1380 residues, 2 models selected > show sel surfaces > lighting soft > set bgColor white > select #1/A:791-793 28 atoms, 28 bonds, 3 residues, 1 model selected > transparency #1 50 surfaces > transparency #1 80 surfaces > show sel atoms > select #1/A:747,749,762,763,764,765 42 atoms, 40 bonds, 6 residues, 1 model selected > show sel > hide sel atoms > select #1/A:773,775,776,1165,1166,1167 39 atoms, 37 bonds, 6 residues, 1 model selected > show sel atoms > select #1/A-C:736-770 765 atoms, 780 bonds, 105 residues, 1 model selected > delete sel > show cartoons > save ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250522-pdb6U7K-PEDV-CoV-S2-res771-1242.pdb"" > open 6VC0 Summary of feedback from opening 6VC0 fetched from pdb --- note | Fetching compressed mmCIF 6vc0 from http://files.rcsb.org/download/6vc0.cif 6vc0 title: Crystal structure of the horse MLKL pseudokinase domain [more info...] Chain information for 6vc0 #2 --- Chain | Description | UniProt A B C | Mixed lineage kinase domain like pseudokinase | F6S337_HORSE 189-475 Non-standard residues in 6vc0 #2 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 6vc0 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly > hide #!1 models > close #2 > open 6CV0 Summary of feedback from opening 6CV0 fetched from pdb --- note | Fetching compressed mmCIF 6cv0 from http://files.rcsb.org/download/6cv0.cif 6cv0 title: Cryo-electron microscopy structure of infectious bronchitis coronavirus spike protein [more info...] Chain information for 6cv0 #2 --- Chain | Description | UniProt A B C | Spike glycoprotein | F4MIW6_9GAMC 19-1090 Non-standard residues in 6cv0 #2 --- 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) > select > #1/A-C:804-811,813-821,825-849,852-860,871-876,892-904,913-919,925-933,943-960,970-981,991-1011,1014-1024,1027-1055,1063-1070,1072-1120,1234-1239 5526 atoms, 5547 bonds, 720 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B #2/C Alignment identifier is 1 Could not find virtual screen for QCocoaScreen(0x6000026e46e0, ""HDMI (2)"", QRect(0,0 1920x1080), dpr=1, displayId=6, ) with displayId 6 > select #2/A:856-875 152 atoms, 151 bonds, 20 residues, 1 model selected > select #2/A-C:1-701 15858 atoms, 16272 bonds, 2043 residues, 1 model selected > select #2/A-C:1-600 13488 atoms, 13851 bonds, 1740 residues, 1 model selected > select #2/A-C:1-500 11133 atoms, 11451 bonds, 1440 residues, 1 model selected > select #2/A-C:1-414 9120 atoms, 9390 bonds, 1182 residues, 1 model selected > hide sel cartoons > hide sel atoms > select ::name=""NAG"" 1218 atoms, 1245 bonds, 87 residues, 1 model selected > delete sel > hide #!2 atoms > select #2/A-C:415-500 2013 atoms, 2058 bonds, 258 residues, 1 model selected > select #2/A-C:415-538 2919 atoms, 2973 bonds, 372 residues, 1 model selected > hide sel cartoons > select #2/A-C:1-537 12021 atoms, 12348 bonds, 1551 residues, 1 model selected > delete sel > save ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/IBV- > CoV/20250522-PDB-6CV0-res578-1022.pdb"" models #2 > hide #!2 models > show #!1 models > hide #!1 models > open 6U7K 6u7k title: Prefusion structure of PEDV spike [more info...] Chain information for 6u7k #3 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_PEDV7 1-1319 Non-standard residues in 6u7k #3 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 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) > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1098 atoms, 1125 bonds, 81 residues, 1 model selected > delete sel > hide #!3 atoms > hide pseudobonds > graphics silhouettes true > select #3/A-C:1-755 13569 atoms, 13926 bonds, 15 pseudobonds, 1767 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > ~select Nothing selected > ui tool show ""Show Sequence Viewer"" > select #3/A-C:1-755 13569 atoms, 13926 bonds, 15 pseudobonds, 1767 residues, 2 models selected > select #3/A-C:892-910 423 atoms, 423 bonds, 57 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #3/A #3/B #3/C Alignment identifier is 1 Could not find virtual screen for QCocoaScreen(0x6000026b2f70, ""HDMI (2)"", QRect(0,0 1920x1080), dpr=1, displayId=9, ) with displayId 9 > close #1 > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #3/B #3/C Alignment identifier is 1 Could not find virtual screen for QCocoaScreen(0x6000026b2f70, ""HDMI (2)"", QRect(0,0 1920x1080), dpr=1, displayId=9, ) with displayId 9 > select > #3/A-C:230-235,242-246,322-326,463-473,572-577,804-811,813-821,825-849,852-860,871-876,892-904,913-919,925-933,943-960,970-981,991-1011,1014-1024,1027-1055,1063-1070,1072-1120,1234-1239 6249 atoms, 6264 bonds, 819 residues, 1 model selected > select #3/A-C:892 18 atoms, 15 bonds, 3 residues, 1 model selected > select #3/A-C:892-907 369 atoms, 369 bonds, 48 residues, 1 model selected > select > #3/A-C:230-235,242-246,322-326,463-473,572-577,804-811,813-821,825-849,852-860,871-876,892-904,913-919,925-933,943-960,970-981,991-1011,1014-1024,1027-1055,1063-1070,1072-1120,1234-1239 6249 atoms, 6264 bonds, 819 residues, 1 model selected > ~select Nothing selected > select #3/A-C:1-755 13569 atoms, 13926 bonds, 15 pseudobonds, 1767 residues, 2 models selected > hide sel cartoons > select #3/A-C:756-770 330 atoms, 336 bonds, 45 residues, 1 model selected > select #3/A-C:756-765 207 atoms, 210 bonds, 30 residues, 1 model selected > ~select Nothing selected > color dim gray > select #1/A Nothing selected > select #3/A 8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected > color sel gray > select #3/B 8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected > color sel light gray > ~select Nothing selected > select #3/A 8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected > color sel gray > ui tool show ""Color Actions"" > color sel gainsboro > color sel silver > ~select Nothing selected > select #3/A 8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected > color sel dim gray > color sel dark gray > ~select Nothing selected > color dim gray > ui tool show ""Side View"" > save /Users/adonisrubio/Desktop/image34.png supersample 3 > save /Users/adonisrubio/Desktop/image35.png supersample 3 > select #3/A:1069-1089 162 atoms, 161 bonds, 21 residues, 1 model selected > show sel atoms > hide sel atoms > ~select Nothing selected > select #3/A-C:756-770 330 atoms, 336 bonds, 45 residues, 1 model selected > select #3/A-C:756-760 84 atoms, 81 bonds, 15 residues, 1 model selected > select #3/A-C:756-765 207 atoms, 210 bonds, 30 residues, 1 model selected > delete sel > ui tool show Contacts > 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. chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.6 which is incompatible. nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you have numpy 2.2.6 which is incompatible. \--- pip standard output: \--- \--- > kvfinder #3 153 cavities found for 6u7k #3 6u7k Cavities --- ID | | Volume | Area | Points 3.2.13 | | 18339.3 | 13561.8 | 84904 3.2.48 | | 2401.06 | 2036.74 | 11116 3.2.4 | | 1766.45 | 1396.08 | 8178 3.2.100 | | 1766.02 | 1418.94 | 8176 3.2.77 | | 1594.3 | 1364.02 | 7381 3.2.52 | | 841.75 | 669.43 | 3897 3.2.31 | | 840.67 | 682.51 | 3892 3.2.122 | | 839.38 | 650.22 | 3886 3.2.72 | | 581.26 | 579.22 | 2691 3.2.40 | | 527.69 | 496.57 | 2443 3.2.9 | | 475.2 | 509.15 | 2200 3.2.105 | | 440.42 | 403.09 | 2039 3.2.50 | | 416.88 | 384.47 | 1930 3.2.8 | | 382.54 | 357.89 | 1771 3.2.82 | | 367.63 | 337.31 | 1702 3.2.132 | | 325.08 | 317.33 | 1505 3.2.61 | | 287.28 | 278.92 | 1330 3.2.127 | | 267.41 | 196.08 | 1238 3.2.19 | | 265.25 | 246.76 | 1228 3.2.149 | | 254.66 | 197.86 | 1179 3.2.119 | | 239.98 | 215.93 | 1111 3.2.2 | | 237.17 | 169.72 | 1098 3.2.56 | | 222.48 | 197.57 | 1030 3.2.65 | | 217.3 | 223.92 | 1006 3.2.80 | | 217.3 | 252.08 | 1006 3.2.96 | | 216.86 | 160.57 | 1004 3.2.81 | | 203.04 | 235 | 940 3.2.29 | | 163.3 | 239.44 | 756 3.2.133 | | 158.11 | 154.66 | 732 3.2.59 | | 140.4 | 126.57 | 650 3.2.76 | | 129.38 | 117.17 | 599 3.2.108 | | 128.95 | 116.28 | 597 3.2.101 | | 114.48 | 120.7 | 530 3.2.102 | | 99.79 | 103.8 | 462 3.2.116 | | 97.63 | 100.11 | 452 3.2.85 | | 94.18 | 105.1 | 436 3.2.28 | | 81.22 | 91.64 | 376 3.2.120 | | 81.22 | 115.67 | 376 3.2.125 | | 79.49 | 95.85 | 368 3.2.70 | | 78.62 | 89.41 | 364 3.2.107 | | 77.98 | 87.95 | 361 3.2.91 | | 75.82 | 105.55 | 351 3.2.104 | | 74.09 | 95.42 | 343 3.2.20 | | 71.5 | 78.19 | 331 3.2.97 | | 71.06 | 90.89 | 329 3.2.11 | | 68.69 | 92.51 | 318 3.2.110 | | 63.07 | 89.74 | 292 3.2.124 | | 60.91 | 110.18 | 282 3.2.114 | | 60.7 | 87.89 | 281 3.2.7 | | 48.38 | 64.66 | 224 3.2.130 | | 48.38 | 68.94 | 224 3.2.60 | | 47.74 | 57.39 | 221 3.2.146 | | 47.74 | 62.71 | 221 3.2.6 | | 46.01 | 57.15 | 213 3.2.150 | | 43.63 | 61.99 | 202 3.2.42 | | 42.34 | 55.79 | 196 3.2.109 | | 42.34 | 68.31 | 196 3.2.62 | | 41.9 | 62.43 | 194 3.2.145 | | 41.69 | 54.72 | 193 3.2.14 | | 41.47 | 61.78 | 192 3.2.35 | | 40.39 | 53.98 | 187 3.2.16 | | 38.66 | 49.47 | 179 3.2.32 | | 38.02 | 55.01 | 176 3.2.23 | | 37.8 | 53.51 | 175 3.2.152 | | 37.8 | 58.72 | 175 3.2.38 | | 34.78 | 57.43 | 161 3.2.144 | | 34.78 | 50.38 | 161 3.2.1 | | 34.56 | 53.71 | 160 3.2.141 | | 34.13 | 43.42 | 158 3.2.88 | | 33.48 | 50.84 | 155 3.2.95 | | 33.48 | 47.02 | 155 3.2.139 | | 31.97 | 63.31 | 148 3.2.51 | | 31.32 | 44.68 | 145 3.2.37 | | 30.46 | 49.12 | 141 3.2.33 | | 28.94 | 46.13 | 134 3.2.143 | | 28.94 | 46.13 | 134 3.2.18 | | 28.73 | 37.55 | 133 3.2.41 | | 28.73 | 48.41 | 133 3.2.47 | | 28.51 | 38.59 | 132 3.2.27 | | 28.3 | 50.22 | 131 3.2.151 | | 27 | 38.44 | 125 3.2.103 | | 26.78 | 43.97 | 124 3.2.137 | | 24.62 | 45.13 | 114 3.2.135 | | 23.76 | 52.37 | 110 3.2.73 | | 23.33 | 41.55 | 108 3.2.94 | | 23.33 | 39.8 | 108 3.2.34 | | 23.11 | 40.33 | 107 3.2.68 | | 23.11 | 33.54 | 107 3.2.142 | | 20.95 | 29.21 | 97 3.2.36 | | 20.3 | 35.08 | 94 3.2.90 | | 19.22 | 34.5 | 89 3.2.113 | | 19.01 | 38.34 | 88 3.2.117 | | 19.01 | 38.34 | 88 3.2.58 | | 18.36 | 31.48 | 85 3.2.140 | | 18.36 | 26.35 | 85 3.2.79 | | 18.14 | 33.85 | 84 3.2.21 | | 17.06 | 35.72 | 79 3.2.64 | | 16.85 | 32.3 | 78 3.2.134 | | 16.85 | 32.3 | 78 3.2.98 | | 15.55 | 25.45 | 72 3.2.26 | | 15.34 | 26.6 | 71 3.2.3 | | 13.82 | 27.81 | 64 3.2.78 | | 12.74 | 22.92 | 59 3.2.15 | | 12.31 | 29.54 | 57 3.2.30 | | 12.31 | 29.54 | 57 3.2.43 | | 12.31 | 29.54 | 57 3.2.45 | | 12.31 | 29.54 | 57 3.2.46 | | 12.31 | 29.54 | 57 3.2.54 | | 12.31 | 29.54 | 57 3.2.71 | | 12.31 | 29.54 | 57 3.2.75 | | 12.31 | 29.54 | 57 3.2.84 | | 12.31 | 29.54 | 57 3.2.87 | | 12.31 | 29.54 | 57 3.2.89 | | 12.31 | 29.54 | 57 3.2.92 | | 12.31 | 29.54 | 57 3.2.99 | | 12.31 | 29.54 | 57 3.2.111 | | 12.31 | 29.54 | 57 3.2.126 | | 12.31 | 29.54 | 57 3.2.131 | | 12.31 | 21.78 | 57 3.2.136 | | 12.31 | 29.54 | 57 3.2.153 | | 12.31 | 29.54 | 57 3.2.49 | | 12.1 | 17.38 | 56 3.2.57 | | 11.66 | 19.36 | 54 3.2.25 | | 11.45 | 17.42 | 53 3.2.123 | | 11.45 | 26.1 | 53 3.2.138 | | 11.45 | 18.21 | 53 3.2.5 | | 11.23 | 24.74 | 52 3.2.115 | | 11.23 | 20 | 52 3.2.121 | | 10.58 | 19.65 | 49 3.2.39 | | 9.5 | 20.92 | 44 3.2.53 | | 9.5 | 17.04 | 44 3.2.74 | | 9.07 | 14.34 | 42 3.2.44 | | 8.64 | 19.12 | 40 3.2.93 | | 8.64 | 20.22 | 40 3.2.106 | | 7.78 | 18.22 | 36 3.2.129 | | 7.78 | 13.69 | 36 3.2.112 | | 7.56 | 13.14 | 35 3.2.10 | | 7.34 | 15.99 | 34 3.2.12 | | 7.13 | 13.14 | 33 3.2.17 | | 6.7 | 11.68 | 31 3.2.118 | | 6.26 | 15.22 | 29 3.2.63 | | 6.05 | 14.9 | 28 3.2.83 | | 6.05 | 11.67 | 28 3.2.86 | | 6.05 | 12.92 | 28 3.2.22 | | 5.83 | 13.64 | 27 3.2.128 | | 5.83 | 14.77 | 27 3.2.66 | | 5.62 | 13.93 | 26 3.2.67 | | 5.62 | 11.34 | 26 3.2.69 | | 5.62 | 12.9 | 26 3.2.55 | | 5.4 | 12.81 | 25 3.2.24 | | 5.18 | 10.2 | 24 3.2.147 | | 5.18 | 13.81 | 24 3.2.148 | | 5.18 | 12.05 | 24 Populating font family aliases took 116 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > view #3.2.13 @ zoom 0.75 moved plane near -92.38150187515349 [ 0.63441866 -0.77278985 -0.017591 ] moved plane far -92.38150187515349 [ 0.63441866 -0.77278985 -0.017591 ] > surface #3.2 > transparency #3.2 50 > ~surface #3.2 > surface #3.2.13 > show #!3 & (#3.2.13 : show #!3#!3.2.1-153 surfaces > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting soft > hide #!3#!3.2.1-153 surfaces > close session > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250522-pdb6U7K-PEDV-CoV-S2-res771-1242.pdb"" Chain information for 20250522-pdb6U7K-PEDV-CoV-S2-res771-1242.pdb #1 --- Chain | Description A B C | No description available > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"" Chain information for 20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb #2 --- Chain | Description A B C | No description available > hide #!1 models > select #2/A-C:736-760 519 atoms, 525 bonds, 75 residues, 1 model selected > select #2/A-C:736-765 642 atoms, 654 bonds, 90 residues, 1 model selected > select #2/A-C:736-764 615 atoms, 627 bonds, 87 residues, 1 model selected > delete sel > save ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250523-pdb6U7K-PEDV-CoV-S2-res765-1242.pdb"" models #2 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #2/A-C:736-770 150 atoms, 150 bonds, 18 residues, 1 model selected > select #2/A-C:736-760 Nothing selected > close #1 > close #2 > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"" format pdb Chain information for 20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb #1 --- Chain | Description A B C | No description available > color light gray > select #1/A-C:736-765 642 atoms, 654 bonds, 90 residues, 1 model selected > color sel blue > ~select Nothing selected > hide psuedobonds Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide pseudobonds > select #1/A-C:766-1242 10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 2 models selected > color sel dim gray > ~select Nothing selected > turn x 90 > turn x 270 > save /Users/adonisrubio/Desktop/image36.png supersample 3 > turn x 90 > save /Users/adonisrubio/Desktop/image37.png supersample 3 > turn x 270 > select #1/A-C:736-755 435 atoms, 441 bonds, 60 residues, 1 model selected > delete sel > save /Users/adonisrubio/Desktop/image38.png supersample 3 > save /Users/adonisrubio/Desktop/image39.png supersample 3 > turn x 90 > turn x 270 > turn x 90 > turn x 270 > save /Users/adonisrubio/Desktop/image40.png supersample 3 > turn x 90 > save /Users/adonisrubio/Desktop/image41.png supersample 3 > select #1/A-C:736-755 Nothing selected > select #1/A-C:736-765 207 atoms, 210 bonds, 30 residues, 1 model selected > delete sel > save ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250523-pdb6U7K-PEDV-CoV-S2-res766-1242.pdb"" > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C Alignment identifier is 1 Could not find virtual screen for QCocoaScreen(0x6000026ec0b0, ""HDMI (1)"", QRect(-1920,0 1920x1080), dpr=1, displayId=8, ) with displayId 8 > select #1/A-C:766-780 324 atoms, 327 bonds, 45 residues, 1 model selected > select #1/A-C:1073-1074 48 atoms, 45 bonds, 6 residues, 1 model selected > select #1/A-C:1072-1073 48 atoms, 45 bonds, 6 residues, 1 model selected > select ~sel & ##selected 10593 atoms, 10767 bonds, 3 pseudobonds, 1389 residues, 2 models selected > select #1/A-C:1214 21 atoms, 18 bonds, 3 residues, 1 model selected > show > hide atoms > select #1/A-C:1242 36 atoms, 36 bonds, 3 residues, 1 model selected > close session > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/AlphaFold-models/20250524-Tamarind-AlphaFoldresult-PEDV- > CoV-S2-766-1242-postfusiontemplates/20250524-PEDV-CoV-S2-766-1319-unrelaxed- > Alphafold2-multimer-rank-1-model-4-renumbered.pdb"" Chain information for 20250524-PEDV-CoV-S2-766-1319-unrelaxed- Alphafold2-multimer-rank-1-model-4-renumbered.pdb #1 --- Chain | Description A B C | No description available Computing secondary structure > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250523pdb6U7KPEDVS2res766to1319.pdb"" Chain information for 20250523pdb6U7KPEDVS2res766to1319.pdb #2 --- Chain | Description A B C | No description available > select #2 10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-199.61,0,1,0,-294.61,0,0,1,-219.36 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.85316,-0.51564,-0.078914,366.51,-0.21402,0.48397,-0.84851,95.212,0.47572,-0.70703,-0.52327,231.91 > view matrix models > #2,-0.99223,-0.12163,0.026228,280.4,-0.081474,0.47579,-0.87578,73.692,0.094044,-0.87111,-0.482,346.79 > ~select Nothing selected > select #2/A-C:1069-1089 486 atoms, 483 bonds, 63 residues, 1 model selected > color sel goldenrod > select #2 10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 3 models selected > color sel dim gray > select #2/A-C:1069-1089 486 atoms, 483 bonds, 63 residues, 1 model selected > color sel goldenrod > select #2/A-C:892-910 423 atoms, 423 bonds, 57 residues, 1 model selected > color sel red > ~select Nothing selected > hide pseudobonds > color #1 dimgray > color #1/A-C:1069-1089 goldenrod > color #1/A-C:892-910 red > select #2 10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.99223,-0.12163,0.026228,303.82,-0.081474,0.47579,-0.87578,47.346,0.094044,-0.87111,-0.482,377.62 > ~select Nothing selected > save /Users/adonisrubio/Desktop/image42.png supersample 3 > open > /Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/input_4920176801590624244.pdb Summary of feedback from opening /Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/input_4920176801590624244.pdb --- warning | Ignored bad PDB record found on line 10643 Chain information for input_4920176801590624244.pdb #3 --- Chain | Description A B C | No description available Computing secondary structure > open > /Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/cavity_4920176801590624244.pdb Summary of feedback from opening /Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/cavity_4920176801590624244.pdb --- warning | Ignored bad PDB record found on line 46927 > hide #!3 models > hide #4 models > select #1/A-C:1241 #2/A-C:1241 48 atoms, 42 bonds, 6 residues, 2 models selected > view matrix models > #1,1,0,0,-8.7051,0,1,0,-14.602,0,0,1,-24.547,#2,-0.99223,-0.12163,0.026228,295.12,-0.081474,0.47579,-0.87578,32.744,0.094044,-0.87111,-0.482,353.07 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.9694,0.010769,0.24524,-10.842,0.0035832,0.99831,-0.058,-14.209,-0.24545,0.057104,0.96773,-21.191,#2,-0.93968,-0.32642,-0.10221,376.8,-0.090346,0.52507,-0.84625,12.244,0.3299,-0.78597,-0.52289,272.37 > view matrix models > #1,0.87307,-0.1924,0.44802,-10.4,0.25535,0.96319,-0.083978,-22.908,-0.41538,0.18772,0.89007,-11.638,#2,-0.80848,-0.58801,-0.024548,414.93,-0.33974,0.50037,-0.79637,68.566,0.48056,-0.63551,-0.60431,207.16 > color dim gray > color sel red > show sel atoms > style sel sphere Changed 48 atom styles > view matrix models > #1,0.74147,-0.27295,0.61295,-19.609,0.17971,0.96093,0.21052,-26.41,-0.64647,-0.045945,0.76155,-11.548,#2,-0.65583,-0.75401,-0.036949,424.21,-0.2368,0.25195,-0.93832,153.18,0.71681,-0.60663,-0.34379,77.442 > close #3 > close #4 > view matrix models > #1,0.86755,-0.46791,0.16858,-26.363,0.48848,0.86536,-0.11197,-29.131,-0.093489,0.17949,0.97931,-6.7903,#2,-0.80683,-0.475,0.35128,278.72,-0.56572,0.44985,-0.69108,117.97,0.17024,-0.75631,-0.63167,343.11 > hide #!2 models > show #!2 models > hide #1 models > view matrix models > #1,0.20104,-0.6117,0.76512,-46.806,0.61843,0.68499,0.38514,-88.78,-0.75969,0.39574,0.51601,82.694,#2,-0.07769,-0.98199,0.17219,274.24,-0.63321,-0.084804,-0.76932,276.98,0.77007,-0.1688,-0.61522,65.474 > close session > open ""/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV- > CoV/20250523-pdb6U7K-PEDV-CoV-S2-res766-1319.pdb"" Chain information for 20250523-pdb6U7K-PEDV-CoV-S2-res766-1319.pdb #1 --- Chain | Description A B C | No description available > hide pseudobonds > select #1/A-C:1241 24 atoms, 21 bonds, 3 residues, 1 model selected > color dim gray > color sel red > show sel atoms sphere Expected ',' or a keyword > show sel atoms > style sel sphere Changed 24 atom styles > ~select Nothing selected > save /Users/adonisrubio/Desktop/image43.png supersample 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2J3LL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 3 days, 20 hours, 8 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: C305W-2560UN: Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array) UI Looks like: 2560 x 1080 @ 85.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.3 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 narwhals: 1.40.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 2.2.6 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 plotly: 6.0.1 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.8.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomlkit: 0.13.2 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX