id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17883 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.7.5-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/julienadeau/Downloads/MpIBP_R35figure.pdb Summary of feedback from opening /Users/julienadeau/Downloads/MpIBP_R35figure.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 30 LYS A 41 1 12 Start residue of secondary structure not found: HELIX 2 2 THR A 65 GLY A 72 1 8 Start residue of secondary structure not found: HELIX 3 3 SER A 73 LEU A 78 1 6 Start residue of secondary structure not found: SHEET 1 1 1 LEU A 17 THR A 24 0 Start residue of secondary structure not found: SHEET 2 2 1 ALA A 45 ALA A 49 0 End residue of secondary structure not found: SHEET 3 3 1 TYR A 54 GLY A 57 0 Start residue of secondary structure not found: SHEET 4 4 1 ASP A 87 LEU A 98 0 Start residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110 0 Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A 117 0 Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A 125 0 Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A 135 0 71 messages similar to the above omitted End residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110 0 Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A 117 0 Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A 125 0 Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A 135 0 Start residue of secondary structure not found: SHEET 9 9 1 PHE A 139 ILE A 141 0 Start residue of secondary structure not found: SHEET 10 10 1 GLY A 145 ASP A 155 0 17 messages similar to the above omitted 80 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 25 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for MpIBP_R35figure.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.3/A | No description available 1.4/A | No description available 1.5/A | No description available 1.6/A | No description available 1.7/A | No description available 1.8/A | No description available > hide #1.8 models > show #1.8 models > hide #1.7 models > show #1.7 models > rename #1.7 MpIBP_AlphaFold > hide #1.7 models > select add #1 17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected > select subtract #1 Nothing selected > select add #1.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > select subtract #1.1 Nothing selected > select add #1.2 722 atoms, 720 bonds, 15 pseudobonds, 109 residues, 2 models selected > select subtract #1.2 Nothing selected > select add #1.2 722 atoms, 720 bonds, 15 pseudobonds, 109 residues, 2 models selected > rename #1.2 RIII_1 > select subtract #1.2 Nothing selected > select add #1.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > select subtract #1.1 Nothing selected > select add #1.3 652 atoms, 661 bonds, 9 pseudobonds, 88 residues, 2 models selected > rename #1.3 RIII_2 > select subtract #1.3 Nothing selected > select add #1.4 1621 atoms, 1648 bonds, 28 pseudobonds, 216 residues, 2 models selected > rename #1.4 RIII_# > rename #1.4 RIII_3 > select subtract #1.4 Nothing selected > select add #1.5 782 atoms, 788 bonds, 10 pseudobonds, 114 residues, 3 models selected > rename #1.5 RIII_4 > select subtract #1.5 Nothing selected > select add #1.6 1190 atoms, 1010 bonds, 52 pseudobonds, 326 residues, 2 models selected > select subtract #1.6 Nothing selected > select add #1.8 627 atoms, 631 bonds, 87 residues, 1 model selected > select subtract #1.8 Nothing selected > select add #1.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > rename #1.1 RIII_5 > select add #1.6 2943 atoms, 2483 bonds, 105 pseudobonds, 827 residues, 4 models selected > select subtract #1.6 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > select add #1.8 2380 atoms, 2104 bonds, 53 pseudobonds, 588 residues, 3 models selected > rename #1.8 missingdomain > select subtract #1.8 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > select subtract #1.1 Nothing selected > select add #1.6 1190 atoms, 1010 bonds, 52 pseudobonds, 326 residues, 2 models selected > rename #1.6 RV > select subtract #1.6 Nothing selected > open /Users/julienadeau/Downloads/MpIBP_R35figure.pdb format pdb Summary of feedback from opening /Users/julienadeau/Downloads/MpIBP_R35figure.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 30 LYS A 41 1 12 Start residue of secondary structure not found: HELIX 2 2 THR A 65 GLY A 72 1 8 Start residue of secondary structure not found: HELIX 3 3 SER A 73 LEU A 78 1 6 Start residue of secondary structure not found: SHEET 1 1 1 LEU A 17 THR A 24 0 Start residue of secondary structure not found: SHEET 2 2 1 ALA A 45 ALA A 49 0 End residue of secondary structure not found: SHEET 3 3 1 TYR A 54 GLY A 57 0 Start residue of secondary structure not found: SHEET 4 4 1 ASP A 87 LEU A 98 0 Start residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110 0 Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A 117 0 Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A 125 0 Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A 135 0 71 messages similar to the above omitted End residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110 0 Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A 117 0 Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A 125 0 Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A 135 0 Start residue of secondary structure not found: SHEET 9 9 1 PHE A 139 ILE A 141 0 Start residue of secondary structure not found: SHEET 10 10 1 GLY A 145 ASP A 155 0 17 messages similar to the above omitted 80 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 25 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for MpIBP_R35figure.pdb --- Chain | Description 2.1/A | No description available 2.2/A | No description available 2.3/A | No description available 2.4/A | No description available 2.5/A | No description available 2.6/A | No description available 2.7/A | No description available 2.8/A | No description available > hide #2.8 models > show #2.8 models > select add #2.7 10003 atoms, 10119 bonds, 1390 residues, 1 model selected > select subtract #2.7 Nothing selected > select add #2.7 10003 atoms, 10119 bonds, 1390 residues, 1 model selected > delete sel > select add #2.8 627 atoms, 631 bonds, 87 residues, 1 model selected > select subtract #2.8 Nothing selected > select add #2 7347 atoms, 6931 bonds, 167 pseudobonds, 1441 residues, 15 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-17.137,0,1,0,40.382,0,0,1,119.14 > select subtract #2 Nothing selected > select add #2.2 722 atoms, 720 bonds, 15 pseudobonds, 109 residues, 2 models selected > rename #2.2 RIII_1 > select subtract #2.2 Nothing selected > hide #!2.2 models > hide #!1.2 models > select add #2.8 627 atoms, 631 bonds, 87 residues, 1 model selected > select add #2 7347 atoms, 6931 bonds, 167 pseudobonds, 1441 residues, 15 models selected > select subtract #2 Nothing selected > select add #2.8 627 atoms, 631 bonds, 87 residues, 1 model selected > delete sel > select add #2.6 1190 atoms, 1010 bonds, 52 pseudobonds, 326 residues, 2 models selected > select subtract #2.6 Nothing selected > hide #!2.6 models > select add #2.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > select subtract #2.1 Nothing selected > select add #2.4 1621 atoms, 1648 bonds, 28 pseudobonds, 216 residues, 2 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""rotate selected models"" > view matrix models > #2.4,0.69762,-0.1137,-0.70739,186.48,0.26489,0.9583,0.1072,-51.609,0.6657,-0.26216,0.69865,-5.2424 > view matrix models > #2.4,0.33073,-0.6945,-0.63897,334.36,0.76243,0.59565,-0.25279,-3.1966,0.55616,-0.40357,0.72651,31.981 > view matrix models > #2.4,-0.046131,0.036944,0.99825,-14.131,0.91589,0.40049,0.027503,-39.732,-0.39877,0.91556,-0.052312,77.428 > view matrix models > #2.4,-0.85109,0.21114,-0.4807,329.44,0.016306,0.92576,0.37776,-53.294,0.52477,0.31367,-0.79134,166.65 > view matrix models > #2.4,0.28901,-0.51163,-0.80914,337.2,-0.21999,0.7871,-0.57626,169.16,0.93171,0.34455,0.11493,-54.941 > view matrix models > #2.4,0.63035,-0.22191,-0.74391,222.2,-0.40996,0.71859,-0.56174,208.13,0.65923,0.65908,0.36199,-110.43 > ui mousemode right ""translate selected models"" > view matrix models > #2.4,0.63035,-0.22191,-0.74391,221.08,-0.40996,0.71859,-0.56174,202.26,0.65923,0.65908,0.36199,-110.98 > view matrix models > #2.4,0.63035,-0.22191,-0.74391,214.27,-0.40996,0.71859,-0.56174,194.89,0.65923,0.65908,0.36199,-100.92 > select subtract #2.4 Nothing selected > select add #2.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > view matrix models #2.1,1,0,0,-3.3535,0,1,0,4.3358,0,0,1,13.735 > ui mousemode right ""rotate selected models"" > view matrix models > #2.1,-0.062952,0.77855,-0.62441,145.49,-0.79048,0.34304,0.50741,167.19,0.60925,0.52553,0.59383,-112.6 > view matrix models > #2.1,-0.92154,0.3412,-0.18532,298.76,-0.29897,-0.31899,0.89937,126.58,0.24775,0.88421,0.39597,-76.108 > view matrix models > #2.1,-0.91653,0.38936,-0.091554,280.82,-0.25431,-0.39059,0.88474,130.18,0.30872,0.83417,0.45701,-86.775 > view matrix models > #2.1,-0.8666,0.49573,-0.057031,254.3,-0.30011,-0.42647,0.85326,146.3,0.39866,0.75656,0.51835,-98.732 > ui mousemode right ""translate selected models"" > view matrix models > #2.1,-0.8666,0.49573,-0.057031,260.98,-0.30011,-0.42647,0.85326,156.74,0.39866,0.75656,0.51835,-102.33 > view matrix models > #2.1,-0.8666,0.49573,-0.057031,260.87,-0.30011,-0.42647,0.85326,155.91,0.39866,0.75656,0.51835,-105.31 > view matrix models > #2.1,-0.8666,0.49573,-0.057031,260.24,-0.30011,-0.42647,0.85326,155.24,0.39866,0.75656,0.51835,-103.23 > ui mousemode right ""rotate selected models"" > view matrix models > #2.1,-0.86366,0.50391,0.013203,250.63,-0.26718,-0.47983,0.83569,158.75,0.42745,0.71822,0.54904,-106.53 > view matrix models > #2.1,-0.81653,0.54138,0.20045,216.25,-0.21813,-0.61082,0.76113,176.34,0.5345,0.57776,0.61684,-113.8 > view matrix models > #2.1,-0.90803,0.4056,-0.10473,284.65,-0.28788,-0.42258,0.85939,151.97,0.30431,0.8105,0.50048,-92.342 > ui mousemode right ""translate selected models"" > view matrix models > #2.1,-0.90803,0.4056,-0.10473,279.98,-0.28788,-0.42258,0.85939,154.01,0.30431,0.8105,0.50048,-79.428 > view matrix models > #2.1,-0.90803,0.4056,-0.10473,278.15,-0.28788,-0.42258,0.85939,151.43,0.30431,0.8105,0.50048,-75.033 > view matrix models > #2.1,-0.90803,0.4056,-0.10473,273.11,-0.28788,-0.42258,0.85939,157.98,0.30431,0.8105,0.50048,-70.726 > view matrix models > #2.1,-0.90803,0.4056,-0.10473,265.36,-0.28788,-0.42258,0.85939,147.03,0.30431,0.8105,0.50048,-92.793 > view matrix models > #2.1,-0.90803,0.4056,-0.10473,265.57,-0.28788,-0.42258,0.85939,147.52,0.30431,0.8105,0.50048,-92.974 > view matrix models > #2.1,-0.90803,0.4056,-0.10473,264.97,-0.28788,-0.42258,0.85939,144.99,0.30431,0.8105,0.50048,-92.492 > ui mousemode right ""translate selected models"" > view matrix models > #2.1,-0.90803,0.4056,-0.10473,268.04,-0.28788,-0.42258,0.85939,152.57,0.30431,0.8105,0.50048,-90.246 > ui mousemode right select > select clear > ui mousemode right translate > select add #2.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2.1,-0.90803,0.4056,-0.10473,274.96,-0.28788,-0.42258,0.85939,165.61,0.30431,0.8105,0.50048,-99.845 > ui mousemode right ""rotate selected models"" > view matrix models > #2.1,-0.86521,0.45995,-0.19966,271.34,-0.39086,-0.36924,0.84315,177.85,0.31408,0.80753,0.49924,-100.97 > view matrix models > #2.1,-0.90773,0.41518,-0.060466,268.57,-0.28065,-0.49372,0.82309,177.95,0.31188,0.76411,0.56469,-102.35 > view matrix models > #2.1,-0.68924,0.29214,-0.66303,316.65,-0.72204,-0.35276,0.59515,260.18,-0.060025,0.88894,0.45408,-43.338 > view matrix models > #2.1,-0.48798,0.85411,-0.17991,153.15,-0.86341,-0.4421,0.24305,336.24,0.12805,0.27394,0.95318,-51.17 > view matrix models > #2.1,-0.87896,0.46871,-0.088008,259.87,-0.46946,-0.81792,0.3326,308.96,0.083908,0.33365,0.93895,-49.966 > view matrix models > #2.1,-0.79545,0.47583,-0.37529,277.48,-0.40189,-0.8777,-0.261,373.63,-0.45358,-0.056792,0.8894,98.13 > view matrix models > #2.1,-0.94762,0.0091359,-0.31926,358.63,0.058283,-0.97786,-0.20098,302.1,-0.31403,-0.20906,0.92611,90.469 > ui mousemode right ""translate selected models"" > view matrix models > #2.1,-0.94762,0.0091359,-0.31926,360.91,0.058283,-0.97786,-0.20098,300.44,-0.31403,-0.20906,0.92611,105.26 > view matrix models > #2.1,-0.94762,0.0091359,-0.31926,360.95,0.058283,-0.97786,-0.20098,301.04,-0.31403,-0.20906,0.92611,103.59 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2.1,-0.94762,0.0091359,-0.31926,360.84,0.058283,-0.97786,-0.20098,308.79,-0.31403,-0.20906,0.92611,111.95 > view matrix models > #2.1,-0.94762,0.0091359,-0.31926,358.75,0.058283,-0.97786,-0.20098,301.55,-0.31403,-0.20906,0.92611,110.18 > ui mousemode right ""rotate selected models"" > view matrix models > #2.1,0.012894,0.77708,0.62927,-13.915,-0.99908,0.035703,-0.023619,326.32,-0.04082,-0.62839,0.77683,136.43 > view matrix models > #2.1,0.6359,0.36127,0.68199,-70.278,-0.76521,0.41011,0.49625,177.62,-0.10041,-0.83743,0.53724,201.63 > view matrix models > #2.1,0.65287,0.34072,0.67652,-69.804,-0.74944,0.42029,0.51157,171.84,-0.11003,-0.84099,0.52974,204.59 > ui mousemode right ""translate selected models"" > view matrix models > #2.1,0.65287,0.34072,0.67652,-77.3,-0.74944,0.42029,0.51157,153.76,-0.11003,-0.84099,0.52974,208.41 > view matrix models > #2.1,0.65287,0.34072,0.67652,-74.511,-0.74944,0.42029,0.51157,159.49,-0.11003,-0.84099,0.52974,204.23 > ui mousemode right ""rotate selected models"" > view matrix models > #2.1,0.66206,0.33462,0.6706,-74.584,-0.74138,0.42338,0.52068,156.67,-0.10969,-0.84189,0.52839,204.45 > view matrix models > #2.1,0.66739,0.31304,0.67572,-73.21,-0.73328,0.43464,0.52288,153.56,-0.13001,-0.84445,0.51961,209.24 > view matrix models > #2.1,0.50732,0.61012,0.60858,-77.661,-0.766,-0.0042599,0.64282,203.48,0.39479,-0.7923,0.46519,119.63 > view matrix models > #2.1,0.88892,-0.13047,0.43909,-24.974,-0.24857,0.66778,0.70163,20.053,-0.38476,-0.73283,0.56117,232.85 > ui mousemode right ""translate selected models"" > view matrix models > #2.1,0.88892,-0.13047,0.43909,-30.384,-0.24857,0.66778,0.70163,14.859,-0.38476,-0.73283,0.56117,238.4 > select subtract #2.1 Nothing selected > lighting simple > set bgColor white > show #1.8#!1.1,3-6#!2.1,3-5 cartoons > select add #2 6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected > show sel & #!2.1,3-5 cartoons > select subtract #2 Nothing selected > graphics silhouettes true > select add #2 6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected > view matrix models #2,1,0,0,7.4703,0,1,0,99.175,0,0,1,162.02 > select subtract #2 Nothing selected > select add #1 17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected > view matrix models #1,1,0,0,-10.641,0,1,0,-6.7046,0,0,1,60.639 > view matrix models #1,1,0,0,-14.341,0,1,0,-11.353,0,0,1,79.589 > view matrix models #1,1,0,0,-10.65,0,1,0,-2.656,0,0,1,84.174 > select subtract #1 Nothing selected > hide #!1.6 models > select add #1.7 10003 atoms, 10119 bonds, 1390 residues, 1 model selected > select subtract #1.7 Nothing selected > show #1.7 models > hide #!2 models > show #!2 models > hide #1.8 models > show #1.8 models > hide #1.7 models > open ""/Users/julienadeau/Desktop/Master's > degree/data/cryosparc/MpIBP/cryosparc_P43_J1976_006_volume_map_sharp.mrc"" > format mrc Opened cryosparc_P43_J1976_006_volume_map_sharp.mrc as #3, grid size 440,440,440, pixel 0.675, shown at level 0.00933, step 2, values float32 > volume #3 level 0.03011 > vop gaussian #3 sdev 2.03 Opened cryosparc_P43_J1976_006_volume_map_sharp.mrc gaussian as #4, grid size 440,440,440, pixel 0.675, shown at step 1, values float32 > transparency #4.1 50 > volume #!4 style mesh > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > volume #4 level 0.003749 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 9 atomic models, 1 maps. > select add #1 17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected > view matrix models #1,1,0,0,-4.9848,0,1,0,2.0599,0,0,1,-1.1115 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 9 atomic models, 1 maps. > select subtract #1 Nothing selected > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.003749 > volume #4 color #ffffb21b > volume #4 color #ffffb245 > volume #4 color #ffffb200 > volume #4 color #ffffb245 > hide #1.8#!1.1,3-5#!2.1,3-5 cartoons > show #1.8#!1.1,3-5#!2.1,3-5 surfaces > hide #!1.1,3-5,8#!2.1,3-5 surfaces > show #!1.1,3-5,8#!2.1,3-5 cartoons > ui tool show ""Side View"" > volume #4 color #fbfff845 > volume #4 color white > volume #4 color #ffffff32 > open /Users/julienadeau/Downloads/MpIBP_R35figure.pdb format pdb Summary of feedback from opening /Users/julienadeau/Downloads/MpIBP_R35figure.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 30 LYS A 41 1 12 Start residue of secondary structure not found: HELIX 2 2 THR A 65 GLY A 72 1 8 Start residue of secondary structure not found: HELIX 3 3 SER A 73 LEU A 78 1 6 Start residue of secondary structure not found: SHEET 1 1 1 LEU A 17 THR A 24 0 Start residue of secondary structure not found: SHEET 2 2 1 ALA A 45 ALA A 49 0 End residue of secondary structure not found: SHEET 3 3 1 TYR A 54 GLY A 57 0 Start residue of secondary structure not found: SHEET 4 4 1 ASP A 87 LEU A 98 0 Start residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110 0 Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A 117 0 Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A 125 0 Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A 135 0 71 messages similar to the above omitted End residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110 0 Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A 117 0 Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A 125 0 Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A 135 0 Start residue of secondary structure not found: SHEET 9 9 1 PHE A 139 ILE A 141 0 Start residue of secondary structure not found: SHEET 10 10 1 GLY A 145 ASP A 155 0 17 messages similar to the above omitted 80 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 25 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for MpIBP_R35figure.pdb --- Chain | Description 5.1/A | No description available 5.2/A | No description available 5.3/A | No description available 5.4/A | No description available 5.5/A | No description available 5.6/A | No description available 5.7/A | No description available 5.8/A | No description available > hide #5.7 models > hide #!5.6 models > show #!5.6 models > hide #!5.5 models > show #!5.5 models > hide #5.8 models > show #5.8 models > hide #!5.2 models > select add #5 17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected > view matrix models #5,1,0,0,-7.3432,0,1,0,12.188,0,0,1,124.46 > view matrix models #5,1,0,0,-23.356,0,1,0,-35.477,0,0,1,162.79 > select subtract #5 Nothing selected > select add #2 6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected > view matrix models #2,1,0,0,11.652,0,1,0,129.46,0,0,1,201.55 > view matrix models #2,1,0,0,12.894,0,1,0,162.66,0,0,1,255.33 > select subtract #2 4 models selected > select add #5 17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected > view matrix models #5,1,0,0,-4.3526,0,1,0,80.084,0,0,1,142.25 > show #!5.2 models > hide #!5.2 models > select subtract #5 Nothing selected > ui mousemode right ""rotate selected models"" > select add #2 6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected > show #1.7 models > hide #1.7 models > show #!1.6 models > hide #!1.6 models > select subtract #2 4 models selected > ui mousemode right ""translate selected models"" > show #!1.6 models > hide #!5.6 models > color #2.5 #c2c2c2ff > select add #2.5 782 atoms, 788 bonds, 10 pseudobonds, 114 residues, 3 models selected > color #2.5 skyblue > select subtract #2.5 1 model selected > select add #2.4 1621 atoms, 1648 bonds, 28 pseudobonds, 216 residues, 2 models selected > select subtract #2.4 1 model selected > select add #2.3 652 atoms, 661 bonds, 9 pseudobonds, 88 residues, 2 models selected > select subtract #2.3 1 model selected > select add #2.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > color #2.5 #ef574bff > color #2.5 skyblue > select add #2.3 2405 atoms, 2134 bonds, 62 pseudobonds, 589 residues, 5 models selected > select subtract #2.3 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 4 models selected > select add #2.3 2405 atoms, 2134 bonds, 62 pseudobonds, 589 residues, 5 models selected > select subtract #2.3 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 4 models selected > color #2.5 #ef574bff > color #2.5 skyblue > color #2.5 #ef574bff > color #2.5 skyblue > select subtract #2.1 1 model selected > select add #2.1 1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected > color #2.1 #ef574bff > select subtract #2.1 1 model selected > color #5.1 skyblue > color #5.1 #ef574bff > color #5.3 skyblue > color #5.4 #ef574bff > color #5.4 skyblue > hide #!5.5 models > show #!5.5 models > color #5.5 skyblue > select add #5.8 627 atoms, 631 bonds, 87 residues, 1 model selected > color #5.8 lightgrey > color #5.8 #11d1e1ff > color #5.8 #627be4ff > color #5.8 #4e41e4ff > select subtract #5.8 Nothing selected > hide #!1.6 models > color #1.1 skyblue > color #1.1 #ef574bff > select add #1.3 652 atoms, 661 bonds, 9 pseudobonds, 88 residues, 2 models selected > select subtract #1.3 1 model selected > color #1.3 skyblue > hide #!1.8 models > show #!1.8 models > color #1.8 #4e41e4ff > color #1.5 skyblue > color #1.4 skyblue > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right translate > ui mousemode right rotate > lighting simple > show #!1.2 models > hide #!1.2 models > show #!1.6 models > hide #!1.6 models > show #!1.6 models > hide #!1.6 models > show #1.7 models > ui mousemode right translate > show #!1.6 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.7.3 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 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: 529.140.2.0.0 OS Loader Version: 577.140.2~30 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 13.7.5 (22H527) Kernel Version: Darwin 22.6.0 Time since boot: 20 days, 4 hours, 12 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal VS278: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H4LMQS080476 Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX