id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17347 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-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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""factorPackIds"" : { }, ""deploymentId"" : 240000032 }, { ""rolloutId"" : ""658361a603dc58766bab2d2a"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6736733a26c1270f5a9ef53d"" }, ""deploymentId"" : 240000045 } ], ""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/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/chimerasessions/ApoandPIP_HBCcomparison.cxs"" format session Opened Apo_Emready.mrc as #1, grid size 440,440,440, pixel 0.65, shown at level 5.06, step 1, values float32 Opened PIP_Emready.mrc as #4, grid size 440,440,440, pixel 0.65, shown at level 4.03, step 1, values float32 opened ChimeraX session > show #!1 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!1 models > hide #!4 models > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Apo/cryosparc_P256_J1166_008_volume_map_sharp.mrc Opened cryosparc_P256_J1166_008_volume_map_sharp.mrc as #5, grid size 440,440,440, pixel 0.65, shown at level 0.0436, step 2, values float32 > volume #5 step 1 > volume #5 level 0.08382 > volume #5 level 0.09052 > show #!2 models > ui tool show Toolbar > select add #2 9206 atoms, 9444 bonds, 36 pseudobonds, 1222 residues, 4 models selected > show sel & #!2 cartoons > ui tool show ""Fit in Map"" > fitmap #2 inMap #5 Fit molecule apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2) to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) using 8726 atoms average map value = 0.3494, steps = 120 shifted from previous position = 4.18 rotated from previous position = 7.05 degrees atoms outside contour = 1481, contour level = 0.090521 Position of apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2) relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.99997494 0.00707934 0.00002711 -1.01256812 -0.00707933 0.99997493 -0.00017045 1.03163649 -0.00002831 0.00017025 0.99999999 0.78746983 Axis 0.02405541 0.00391298 -0.99970297 Axis point 145.67275394 140.80305016 0.00000000 Rotation angle (degrees) 0.40573999 Shift along axis -0.80755690 > select clear > surface dust #5 size 6.5 > volume #5 style mesh > hide #!5 models > show #!5 models > volume #5 level 0.1205 > select #2/A:50 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:55 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/A:53 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:53-70 147 atoms, 153 bonds, 18 residues, 1 model selected > select #2/A:53-75 192 atoms, 201 bonds, 23 residues, 1 model selected > select #2/A:53-77 211 atoms, 221 bonds, 25 residues, 1 model selected > select #2/A:53-80 233 atoms, 243 bonds, 28 residues, 1 model selected > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > ui tool show ""Surface Zone"" > surface zone #5 nearAtoms #2 distance 3.9 > surface zone #5 nearAtoms #2 distance 4.1 > surface zone #5 nearAtoms #2 distance 1.77 > surface zone #5 nearAtoms sel distance 1.78 > surface zone #5 nearAtoms sel distance 1.86 > surface zone #5 nearAtoms sel distance 2.29 > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > show sel cartoons > show sel atoms > volume #5 style surface > fitmap #2 inMap #5 Fit molecule apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2) to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) using 8726 atoms average map value = 0.3494, steps = 40 shifted from previous position = 0.00559 rotated from previous position = 0.0109 degrees atoms outside contour = 2074, contour level = 0.12055 Position of apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2) relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.99997481 0.00709769 -0.00004926 -1.00538528 -0.00709769 0.99997481 0.00000200 1.01711711 0.00004927 -0.00000165 1.00000000 0.80377550 Axis -0.00025765 -0.00694035 -0.99997588 Axis point 142.00535630 142.18303541 0.00000000 Rotation angle (degrees) 0.40668096 Shift along axis -0.81055623 > color #5 #d6d6d6ff models > color #5 #d6d6d600 models > color #5 #d6d6d634 models > color #5 #d6d6d633 models > color sel byhetero > select clear > volume #5 level 0.09427 No atoms selected for zoning > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > surface zone #5 nearAtoms sel distance 2.76 > surface zone #5 nearAtoms sel distance 1.4 > select clear > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > surface zone #5 nearAtoms sel distance 1.4 > surface zone #5 nearAtoms sel distance 1.5 > surface zone #5 nearAtoms sel distance 1.6 > surface zone #5 nearAtoms sel distance 1.7 > surface zone #5 nearAtoms sel distance 1.8 > volume #5 level 0.1243 > volume #5 level 0.1506 > volume #5 level 0.09803 > show #!1 models > resample #1 onGrid #5 Unknown command: resample #1 onGrid #5 > vop resample #1 onGrid #5 Opened Apo_Emready.mrc resampled as #6, grid size 440,440,440, pixel 0.65, shown at step 1, values float32 > surface zone #1 nearAtoms sel distance 5.78 > surface zone #1 nearAtoms sel distance 5.71 > surface zone #1 nearAtoms sel distance 0.98 > surface zone #6 nearAtoms sel distance 3.9 > surface zone #6 nearAtoms sel distance 4.03 > surface zone #6 nearAtoms sel distance 1.54 > volume #6 color #d6d6d6 > volume #6 color #d6d6d633 > surface zone #6 nearAtoms sel distance 1.52 > surface zone #6 nearAtoms sel distance 1.9 > volume #6 level 1.359 > volume #6 level 7.281 > volume #6 level 4.038 > volume #6 level 2.117 > surface dust #5 size 6.5 > surface zone #6 nearAtoms sel distance 1.9 > surface zone #5 nearAtoms sel distance 3.9 > surface zone #5 nearAtoms sel distance 3.8 > surface zone #5 nearAtoms sel distance 3.7 > surface zone #5 nearAtoms sel distance 3.6 > surface zone #5 nearAtoms sel distance 3.5 > surface zone #5 nearAtoms sel distance 3.4 > surface zone #5 nearAtoms sel distance 3.3 > surface zone #5 nearAtoms sel distance 3.2 > surface zone #5 nearAtoms sel distance 3.1 > surface zone #5 nearAtoms sel distance 3 > surface zone #5 nearAtoms sel distance 2.9 > surface zone #5 nearAtoms sel distance 2.8 > surface zone #5 nearAtoms sel distance 2.7 > surface zone #5 nearAtoms sel distance 2.6 > surface zone #5 nearAtoms sel distance 2.5 > surface zone #5 nearAtoms sel distance 2.4 > surface zone #5 nearAtoms sel distance 2.3 > surface zone #5 nearAtoms sel distance 2.2 > surface zone #5 nearAtoms sel distance 2.1 > surface zone #5 nearAtoms sel distance 2 > surface zone #5 nearAtoms sel distance 1.9 > surface zone #5 nearAtoms sel distance 1.8 > surface zone #5 nearAtoms sel distance 1.7 > surface zone #5 nearAtoms sel distance 1.6 > surface zone #5 nearAtoms sel distance 1.5 > vop zone #5 near #2 range 5 > vop resample > volume resample Missing or invalid ""volumes"" argument: empty atom specifier > surface > hide #!2 models > show #!2 models > undo > hide #!2 surfaces > show #!2 cartoons > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > surface zone #5 nearAtoms sel distance 1.5 > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > show sel cartoons > hide sel atoms > show sel atoms > ui tool show ""Side View"" > surface zone #5 nearAtoms sel distance 1.43 > surface zone #5 nearAtoms sel distance 1.83 > surface zone #5 nearAtoms sel distance 1.84 > surface zone #5 nearAtoms sel distance 1.93 > volume #5 level 0.1281 > volume #5 style mesh > select clear > graphics silhouettes false > volume #5 level 0.2031 > volume #5 style surface > volume #5 level 0.09427 > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > color zone #5 near sel [dist 3] Expected a keyword > color zone #5 near sel [dist ] Expected a keyword > color zone #5 near sel [dist ] Expected a keyword > color zone #5 near sel > color #2 #d6d6d6ff > color #2 #d6d6d61b > hide #!5 models > show #!5 models > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide #!2 models > show #!2 models > select add #5 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 8 models selected > show sel surfaces > color #5 silver models > color #5 #d6d6d6ff models > color #2 #d6d6d61c > select subtract #5 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 6 models selected > ui tool show ""Color Actions"" > color sel orchid > color #5 #d6d6d620 models > color #5 #d6d6d621 models > hide sel surfaces > show sel cartoons > hide #!5 models > show #!5 models > color #2 orchid > surface unzone #5 > select up 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 6 models selected > select up 17969 atoms, 18445 bonds, 8 pseudobonds, 2358 residues, 15 models selected > select down 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 10 models selected > select down 8 pseudobonds, 5 models selected > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > color zone #5 near sel > hide #!5 models > show #!5 models > undo > show #!5 models > color #5 #d6d6d6ff models > color #5 #d6d6d629 models > color #5 #d6d6d631 models > color #5 #d6d6d634 models > color #5 #d6d6d633 models > surface zone #5 nearAtoms sel distance 1.93 > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > show sel cartoons > show sel atoms > select clear > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > surface zone #5 nearAtoms sel distance 1.93 > surface zone #5 nearAtoms sel distance 1.94 > surface zone #5 nearAtoms sel distance 1.95 > surface zone #5 nearAtoms sel distance 1.96 > surface zone #5 nearAtoms sel distance 1.95 > surface zone #5 nearAtoms sel distance 1.94 > surface zone #5 nearAtoms sel distance 1.93 > surface zone #5 nearAtoms sel distance 1.92 > surface zone #5 nearAtoms sel distance 1.93 > ui tool show ""Volume Viewer"" > volume #5 style mesh > select clear > select #2/A:53-82 249 atoms, 259 bonds, 30 residues, 1 model selected > color (#!2 & sel) byhetero > select clear > select #2/A:53-85 269 atoms, 279 bonds, 33 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #5 nearAtoms sel distance 1.93 > color (#!2 & sel) byhetero > select clear > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting flat > lighting simple > lighting soft > lighting full > undo > redo > graphics silhouettes false > lighting shadows false > lighting simple > lighting full > lighting simple > lighting shadows true > lighting shadows false > lighting simple > lighting soft > lighting simple > lighting full > lighting simple > volume #1 step 1 > volume #5 step 1 > volume #5 level 0.09427 > volume #5 transparency 0.5 > set raytracing true Expected a keyword > graphics silhouettes true > set silhouetteWidth 2 > select ~sel & ##selected Nothing selected > 1 Unknown command: 1 > set silhouetteWidth 1 > set silhouetteWidth 0.5 > set silhouetteWidth 0.75 > graphics silhouettes true > set silhouetteWidth 1 > select ~sel & ##selected Nothing selected > set silhouetteWidth 2 > set silhouetteWidth 4 > set silhouetteWidth 0 > set silhouetteWidth 0.5 > set silhouetteWidth 0.9 > set silhouetteWidth 1 > set silhouetteWidth 0 > volume #5 transparency 0.5 > volume #5 transparency 1 > volume #5 transparency 0.2 > volume #5 transparency 0.3 > volume #5 transparency 0.4 > volume #5 transparency 0.7 > volume #5 transparency 0 > volume #5 transparency 0.5 > volume #5 transparency 0.1 > ui tool show ""Side View"" > graphics silhouettes false > graphics silhouettes true > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > set silhouetteWidth 1 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_TM1.cxs"" > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_TM1.tif"" width 3000 height 2775 > supersample 3 transparentBackground true > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_TM1_opaque.tif"" width 3000 height 2775 > supersample 3 > select #2/A:86-90 36 atoms, 36 bonds, 5 residues, 1 model selected > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2/A:86-90 36 atoms, 36 bonds, 5 residues, 1 model selected > show sel cartoons > select #2/A:86-95 72 atoms, 74 bonds, 10 residues, 1 model selected > show sel cartoons > select #2/A:86-100 110 atoms, 113 bonds, 15 residues, 1 model selected > show sel cartoons > select #2/A:86-110 191 atoms, 197 bonds, 25 residues, 1 model selected > show sel cartoons > select #2/A:86-104 146 atoms, 150 bonds, 19 residues, 1 model selected > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > select #2/A:86-104 146 atoms, 150 bonds, 19 residues, 1 model selected > show sel cartoons > surface zone #5 nearAtoms sel distance 1.93 > show sel atoms > color (#!2 & sel) byhetero > select clear No atoms selected for zoning > select #2/A:86-104 146 atoms, 150 bonds, 19 residues, 1 model selected > surface zone #5 nearAtoms sel distance 1.65 > surface zone #5 nearAtoms sel distance 1.89 > surface zone #5 nearAtoms sel distance 1.9 > surface zone #5 nearAtoms sel distance 2.33 > surface dust #5 size 6.5 > surface zone #5 nearAtoms sel distance 2.33 > select clear > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > show sel cartoons > hide sel cartoons > select #2/A:86-104 146 atoms, 150 bonds, 19 residues, 1 model selected > show sel cartoons > select clear > volume #5 level 0.1543 > undo > volume #5 level 0.09427 > select clear > select #2/A:86-103 139 atoms, 143 bonds, 18 residues, 1 model selected > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2/A:86-103 139 atoms, 143 bonds, 18 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #5 nearAtoms sel distance 2.33 > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2/A:87-103 134 atoms, 138 bonds, 17 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #5 nearAtoms sel distance 2.33 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_Turret.tif"" width 3000 height 2775 > supersample 3 > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_Turret.cxs"" > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_Turretotherside.tif"" width 3000 height > 2775 supersample 3 > volume #5 level 0.1243 > volume #5 level 0.1281 > surface unzone #5 > volume #5 level 0.09427 > hide #!5 models > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > hide sel atoms > show sel cartoons > hide sel cartoons > select #2/A:87-125-160 Nothing selected > show #!2 cartoons > select #2/A:87-125-160 Nothing selected > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > hide sel cartoons > select #2/A:125-160 260 atoms, 264 bonds, 36 residues, 1 model selected > show sel cartoons > show sel atoms > hide sel cartoons > hide sel atoms > select #2/A:130-163 247 atoms, 250 bonds, 34 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #5 nearAtoms sel distance 2.33 > show #!5 models > surface zone #5 nearAtoms sel distance 2.33 > color (#!2 & sel) byhetero > select clear No atoms selected for zoning > select #2/A:130-163 247 atoms, 250 bonds, 34 residues, 1 model selected > surface zone #5 nearAtoms sel distance 0.94 > surface zone #5 nearAtoms sel distance 2.17 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_TM2.tif"" width 3000 height 2775 > supersample 3 > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_TM2.cxs"" > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #2/A:170-185 115 atoms, 117 bonds, 16 residues, 1 model selected > show sel cartoons > select #2/A:170-190 159 atoms, 162 bonds, 21 residues, 1 model selected > show sel cartoons > surface zone #5 nearAtoms sel distance 2.17 > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > show sel cartoons > select #2/A:272-283 80 atoms, 79 bonds, 12 residues, 1 model selected > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2/A:272-283 80 atoms, 79 bonds, 12 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #5 nearAtoms sel distance 2.17 > color (#!2 & sel) byhetero > surface zone #5 nearAtoms sel distance 2.2 > surface zone #5 nearAtoms sel distance 1.78 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_Gloop.tif"" width 3000 height 2775 > supersample 3 > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Apo_density_Gloop.cxs"" > volume #5 style surface > color #5 #d6d6d62d models > color #5 #d6d6d64b models > color #5 #d6d6d632 models > color #5 #d6d6d633 models > color #5 #ebebebff models > color #5 #ebebeb1d models > hide #!2 models > show #!2 models > surface unzone #5 No atoms selected for zoning > select #2/A:272-283 80 atoms, 79 bonds, 12 residues, 1 model selected > surface zone #5 nearAtoms sel distance 1.78 > select add #2 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected > select subtract #2 4 models selected > color #5 #ebebeb1c models > color #5 #ebebebff models > hide #!5 models > hide #!2 models > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/R162W/25041/Map_deposted_R162W.mrc Opened Map_deposted_R162W.mrc as #7, grid size 200,200,200, pixel 1.3, shown at level 0.147, step 1, values float32 > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/R162W/PreparePDBDeposition_9/R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif Summary of feedback from opening /Users/omallen/Library/CloudStorage/OneDrive- TheFrancisCrickInstitute/PhD/R162W/PreparePDBDeposition_9/R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 590 Skipping entity category: Missing column 'type' on line 17346 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""6"" on line 140 Invalid residue range for struct_conf ""7"": invalid entity ""B"", on line 141 Invalid residue range for struct_conf ""8"": invalid entity ""B"", on line 142 Invalid residue range for struct_conf ""9"": invalid entity ""B"", on line 143 Invalid residue range for struct_conf ""10"": invalid entity ""B"", on line 144 Invalid residue range for struct_conf ""11"": invalid entity ""B"", on line 145 7 messages similar to the above omitted Bad residue range for struct_conf ""24"" on line 159 Invalid sheet range for struct_sheet_range ""15 1"" on line 542 Invalid sheet range for struct_sheet_range ""16 1"": invalid entity ""B"", on line 543 Invalid sheet range for struct_sheet_range ""17 1"": invalid entity ""B"", on line 544 Invalid sheet range for struct_sheet_range ""18 1"": invalid entity ""B"", on line 545 Invalid sheet range for struct_sheet_range ""19 1"": invalid entity ""B"", on line 546 27 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' on line 17807 Chain information for R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif #8 --- Chain | Description A B C D | No description available > dssp Computing secondary structure > color #8 #76d6ffff > vop resample #8 onGrid #7 > ui mousemode right ""move picked models"" > view matrix models #7,1,0,0,8.596,0,1,0,14.611,0,0,1,11.771 > volume #7 color #d6d6d6 > volume #7 color #d6d6d62a > volume #7 color #d6d6d62b > volume #7 level 0.3069 > volume #7 color #d6d6d67d > ui tool show ""Fit in Map"" > fitmap #8 inMap #7 Fit molecule R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms average map value = 0.1643, steps = 56 shifted from previous position = 1.65 rotated from previous position = 2.59 degrees atoms outside contour = 12511, contour level = 0.30691 Position of R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) relative to Map_deposted_R162W.mrc (#7) coordinates: Matrix rotation and translation 0.99904039 0.04364511 0.00365979 -16.07766265 -0.04368355 0.99898289 0.01117760 -10.04576712 -0.00316822 -0.01132675 0.99993083 -8.28604144 Axis -0.24883231 0.07549772 -0.96559959 Axis point -256.35165071 298.63577796 0.00000000 Rotation angle (degrees) 2.59179413 Shift along axis 11.24320770 > view matrix models #7,1,0,0,8.5273,0,1,0,14.028,0,0,1,13.751 > fitmap #8 inMap #7 Fit molecule R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms average map value = 0.1643, steps = 64 shifted from previous position = 2.07 rotated from previous position = 0.0113 degrees atoms outside contour = 12512, contour level = 0.30691 Position of R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) relative to Map_deposted_R162W.mrc (#7) coordinates: Matrix rotation and translation 0.99904562 0.04353748 0.00351236 -16.03551677 -0.04357403 0.99898849 0.01110417 -10.05050367 -0.00302536 -0.01124662 0.99993218 -8.31277280 Axis -0.24787267 0.07250403 -0.96607572 Axis point -256.34646527 298.49329793 0.00000000 Rotation angle (degrees) 2.58406990 Shift along axis 11.27683237 > fitmap #8 inMap #7 Fit molecule R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms average map value = 0.1643, steps = 48 shifted from previous position = 0.00116 rotated from previous position = 0.00158 degrees atoms outside contour = 12512, contour level = 0.30691 Position of R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) relative to Map_deposted_R162W.mrc (#7) coordinates: Matrix rotation and translation 0.99904494 0.04355420 0.00349802 -16.03495196 -0.04359064 0.99898758 0.01112082 -10.05091747 -0.00301012 -0.01126268 0.99993204 -8.31191031 Axis -0.24813042 0.07214536 -0.96603641 Axis point -256.17698253 298.26223636 0.00000000 Rotation angle (degrees) 2.58516437 Shift along axis 11.28324034 > view matrix models > #8,0.96041,-0.26456,0.087263,29.605,0.26449,0.96431,0.012559,-34.45,-0.087471,0.011019,0.99611,12.072 > fitmap #8 inMap #7 Fit molecule R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms average map value = 0.4305, steps = 116 shifted from previous position = 3.55 rotated from previous position = 16.7 degrees atoms outside contour = 7787, contour level = 0.30691 Position of R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif (#8) relative to Map_deposted_R162W.mrc (#7) coordinates: Matrix rotation and translation 0.99995381 0.00960961 0.00017168 -14.39763100 -0.00960963 0.99995382 0.00013001 -11.64595909 -0.00017042 -0.00013166 0.99999998 -14.00600694 Axis -0.01361154 0.01779507 -0.99974900 Axis point -1244.88982642 1472.45187575 0.00000000 Rotation angle (degrees) 0.55073751 Shift along axis 13.99122468 > save /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/R162W/25041/Map_deposited_R162W_inlinewithmodel.mrc > models #7 > color #7-8 byhetero > hide #8.1 models > hide #8.2 models > select add #8 16710 atoms, 16948 bonds, 272 pseudobonds, 1134 residues, 3 models selected > hide sel atoms > hide sel cartoons > select #8/A:53-82 522 atoms, 534 bonds, 24 pseudobonds, 30 residues, 2 models selected > show sel cartoons > show sel atoms > delete H > surface zone #7 nearAtoms sel distance 7.8 > volume #7 style mesh > surface zone #7 nearAtoms sel distance 7.59 > surface zone #7 nearAtoms sel distance 2.99 > select clear No atoms selected for zoning > select #8/A:53-82 264 atoms, 276 bonds, 24 pseudobonds, 30 residues, 2 models selected > surface zone #7 nearAtoms sel distance 2.92 > surface zone #7 nearAtoms sel distance 2.59 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Mut_density_TM1.tif"" width 3000 height 2951 > supersample 3 > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Mut_density_TM1.cxs"" > select add #8 8578 atoms, 8816 bonds, 272 pseudobonds, 1134 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #8/A:87-103 137 atoms, 141 bonds, 17 residues, 1 model selected > show sel cartoons > show sel atoms > surface zone #7 nearAtoms sel distance 2.59 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Mut_density_Turret.cxs"" > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Mut_density_Turret.tif"" width 3000 height 2951 > supersample 3 > select add #8 8578 atoms, 8816 bonds, 272 pseudobonds, 1134 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #8/A:130-163 250 atoms, 255 bonds, 27 pseudobonds, 34 residues, 2 models selected > show sel atoms > show sel cartoons > surface zone #7 nearAtoms sel distance 2.59 > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper > work/Revision_Figures/Mut_density_TM2.tif"" width 3000 height 2951 > 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 - 89.3 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: 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: Mac14,9 Model Number: MPHE3B/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 20 days, 23 hours, 4 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL U2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 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: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 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: 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 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 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 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