id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16746 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.3-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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""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000083 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/akw/Desktop/session-6.cxs Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876, shown at level 0.118, step 1, values float32 Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size 256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values float32 Log from Thu Dec 12 01:43:15 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/akw/Desktop/session-6.cxs Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876, shown at level 0.118, step 1, values float32 Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size 256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values float32 Log from Wed Dec 11 17:42:09 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/akw/Desktop/session-4.cxs Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876, shown at level 0.0576, step 1, values float32 Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size 256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values float32 Log from Wed Dec 11 00:35:51 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Volumes/LabUSB/CryoEM-Structure/khg-paper-cryoem-structure-3.cxs Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876, shown at level 0.142, step 1, values float32 Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size 256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values float32 Log from Fri Dec 6 16:57:31 2024UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/neherlab/Desktop/khg-paper-cryoem-structure.cxs Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876, shown at level 0.116, step 2, values float32 Log from Fri Oct 11 15:38:55 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Volumes/LabUSB/CryoEM-Structure/egelman-helix-300box.mrc Opened egelman-helix-300box.mrc as #1, grid size 300,300,300, pixel 0.876, shown at level 0.192, step 2, values float32 > volume #1 level 0.1156 > open /Volumes/LabUSB/CryoEM-Structure/IandJ.pdb Summary of feedback from opening /Volumes/LabUSB/CryoEM-Structure/IandJ.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 64 HIS A 71 1 8 Start residue of secondary structure not found: HELIX 2 2 TRP A 94 GLU A 106 1 13 Start residue of secondary structure not found: HELIX 3 3 PRO A 125 PHE A 149 1 25 Start residue of secondary structure not found: HELIX 4 4 TYR A 161 ALA A 171 1 11 Start residue of secondary structure not found: HELIX 5 5 ASP A 262 LYS A 268 1 7 427 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (57 ) Cannot find LINK/SSBOND residue CYS (246 ) Cannot find LINK/SSBOND residue CYS (294 ) Cannot find LINK/SSBOND residue CYS (308 ) Cannot find LINK/SSBOND residue CYS (448 ) 75 messages similar to the above omitted Chain information for IandJ.pdb #2 --- Chain | Description I J | No description available > select add #2 13594 atoms, 13782 bonds, 868 residues, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.76629,-0.62579,0.14558,151.31,0.63634,0.7705,-0.037475,-109.76,-0.088718,0.12136,0.98864,1.3347 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.76629,-0.62579,0.14558,29.699,0.63634,0.7705,-0.037475,-202.73,-0.088718,0.12136,0.98864,-143.58 > view matrix models > #2,0.76629,-0.62579,0.14558,41.34,0.63634,0.7705,-0.037475,-220.86,-0.088718,0.12136,0.98864,-144.45 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule IandJ.pdb (#2) to map egelman-helix-300box.mrc (#1) using 13594 atoms average map value = 0.07346, steps = 204 shifted from previous position = 2.41 rotated from previous position = 19.9 degrees atoms outside contour = 9988, contour level = 0.11563 Position of IandJ.pdb (#2) relative to egelman-helix-300box.mrc (#1) coordinates: Matrix rotation and translation 0.93052266 -0.36618758 0.00585159 -15.31543785 0.36604431 0.93043576 0.01734523 -198.88648151 -0.01179613 -0.01399819 0.99983244 -140.05885987 Axis -0.04275375 0.02407225 0.99879560 Axis point 504.53247009 -154.36497997 0.00000000 Rotation angle (degrees) 21.50346116 Shift along axis -144.02302456 > select subtract #2 Nothing selected > color #2 #9437ffff > color zone #1 near #2 distance 4 > color zone #1 near #2 distance 3 > select add #2 13594 atoms, 13782 bonds, 868 residues, 1 model selected > view matrix models > #2,0.93052,-0.36619,0.0058516,-15.291,0.36604,0.93044,0.017345,-198.66,-0.011796,-0.013998,0.99983,-144.86 > fitmap #2 inMap #1 Fit molecule IandJ.pdb (#2) to map egelman-helix-300box.mrc (#1) using 13594 atoms average map value = 0.1375, steps = 56 shifted from previous position = 1.5 rotated from previous position = 2.05 degrees atoms outside contour = 6748, contour level = 0.11563 Position of IandJ.pdb (#2) relative to egelman-helix-300box.mrc (#1) coordinates: Matrix rotation and translation 0.94076379 -0.33860304 0.01764840 -26.86855672 0.33865095 0.94091203 0.00029064 -188.53442556 -0.01670400 0.00570323 0.99984421 -149.04283603 Axis 0.00798146 0.05065634 0.99868425 Axis point 504.40694109 -163.85487466 0.00000000 Rotation angle (degrees) 19.82041430 Shift along axis -158.61164696 > color zone #1 near #2 distance 3 > color zone #1 near #2 distance 2.8 > color zone #1 near #2 distance 2.5 > color zone #1 near #2 distance 2.3 > color zone #1 near #2 distance 2 > color zone #1 near #2 distance 2.2 > color zone #1 near #2 distance 2.3 > hide #2 models > set bgColor white > lighting full > view > view orient > turn x 90 > turn y 90 [Repeated 1 time(s)] > turn y 15 [Repeated 1 time(s)] > turn y 5 > save /Users/neherlab/Desktop/khg-paper-cryoem-structure.cxs ——— End of log from Fri Oct 11 15:38:55 2024 ——— opened ChimeraX session > show #2 models > hide #2 models > select subtract #2 Nothing selected > select add #2 13594 atoms, 13782 bonds, 868 residues, 1 model selected > show #2 models > hide #!1 models > graphics silhouettes true > select subtract #2 Nothing selected > select #2/I,J:246-269 718 atoms, 718 bonds, 48 residues, 1 model selected > color #2/I,J:246-269 yellow > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color #2/I,J:246-269 gold > select clear > turn y 180 > open /Volumes/LabUSB/CryoEM-Structure/20231130_dimer-segmented-from-helix- > MAP-256box.mrc Opened 20231130_dimer-segmented-from-helix-MAP-256box.mrc as #3, grid size 256,256,256, pixel 0.876,0.876,0.876, shown at level 0.00805, step 1, values float32 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit map 20231130_dimer-segmented-from-helix-MAP-256box.mrc in map egelman- helix-300box.mrc using 167699 points correlation = 0.4491, correlation about mean = 0.08124, overlap = 1078 steps = 260, shift = 28.8, angle = 21.1 degrees Position of 20231130_dimer-segmented-from-helix-MAP-256box.mrc (#3) relative to egelman-helix-300box.mrc (#1) coordinates: Matrix rotation and translation 0.93520941 0.32888530 -0.13121668 6.84267416 -0.33690918 0.94051345 -0.04389371 30.32792885 0.10897506 0.08525791 0.99038150 -21.06759020 Axis 0.17950636 -0.33383977 -0.92538018 Axis point 99.70475446 4.62128701 -0.00000000 Rotation angle (degrees) 21.08429426 Shift along axis 10.59916523 > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.93521,0.32889,-0.13122,19.207,-0.33691,0.94051,-0.043894,38.214,0.10898,0.085258,0.99038,-15.453 > fitmap #3 inMap #1 Fit map 20231130_dimer-segmented-from-helix-MAP-256box.mrc in map egelman- helix-300box.mrc using 167699 points correlation = 1, correlation about mean = 1, overlap = 3307 steps = 148, shift = 7.6, angle = 21.1 degrees Position of 20231130_dimer-segmented-from-helix-MAP-256box.mrc (#3) relative to egelman-helix-300box.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 -0.00010603 -0.00006061 39.43083226 0.00010604 0.99999999 0.00008940 -15.79518287 0.00006060 -0.00008941 0.99999999 7.00577045 Axis -0.59068847 -0.40040599 0.70054420 Axis point 194523.93940707 304687.20038210 0.00000000 Rotation angle (degrees) 0.00867223 Shift along axis -12.05900032 > color zone #3 near #2 distance 2.3 > color zone #3 near #2 distance 4 > color zone #3 near #2 distance 4.5 > color zone #3 near #2 distance 5 > color zone #3 near #2 distance 6 > transparency sel 50 > select subtract #3 Nothing selected > turn y 180 [Repeated 1 time(s)] > turn y 90 > ui mousemode right translate > turn y 90 [Repeated 2 time(s)] > hide #!3 models > graphics silhouettes true width 5 color black > graphics silhouettes true width 3 color black > color #2/I,J:420-424 tomato > color #2/I,J:412-427 tomato > graphics silhouettes true width 3.5 color black > graphics silhouettes true width 4color black Invalid ""width"" argument: Expected a number > graphics silhouettes true width 4 color black > save /Volumes/LabUSB/CryoEM-Structure/khg-paper-cryoem-structure-2.cxs > color #2/I,J:413-427 tomato > open /Volumes/LabUSB/CryoEM- > Structure/RSR80_chainsrenamed_real_space_refined_083.pdb Chain information for RSR80_chainsrenamed_real_space_refined_083.pdb #4 --- Chain | Description A B C D E F G H I J K L M N O P Q R | No description available > show #!1 models > select add #4 122346 atoms, 124038 bonds, 7812 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-93.156,0,1,0,-94.185,0,0,1,-2.6872 > view matrix models #4,1,0,0,-92.208,0,1,0,-95.587,0,0,1,-93.689 > fitmap #4 inMap #1 Fit molecule RSR80_chainsrenamed_real_space_refined_083.pdb (#4) to map egelman-helix-300box.mrc (#1) using 122346 atoms average map value = 0.1296, steps = 60 shifted from previous position = 2.94 rotated from previous position = 0.0246 degrees atoms outside contour = 66485, contour level = 0.11563 Position of RSR80_chainsrenamed_real_space_refined_083.pdb (#4) relative to egelman-helix-300box.mrc (#1) coordinates: Matrix rotation and translation 0.99999991 -0.00037639 0.00016867 -92.80659779 0.00037641 0.99999992 -0.00011613 -92.90413739 -0.00016862 0.00011619 0.99999998 -92.83846069 Axis 0.27108294 0.39357404 0.87841534 Axis point 96981.13632418 -143405.54567079 0.00000000 Rotation angle (degrees) 0.02455089 Shift along axis -143.27367059 > hide sel atoms > show sel cartoons > surface dust #1 size 8.76 > volume #1 step 1 > select clear > select #4/R 6797 atoms, 6891 bonds, 434 residues, 1 model selected > hide sel > hide #2 models > hide #!1 models > hide select Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel > select hide Expected an objects specifier or a keyword > hide sel cartoons > show #!1 models > hide #!1 models > color #4 darkgrey > select #4/I,J 13594 atoms, 13782 bonds, 868 residues, 1 model selected > color #4 #531b93ff > undo > select add #4 122346 atoms, 124038 bonds, 7812 residues, 1 model selected > select subtract #4 Nothing selected > select #4/I,J 13594 atoms, 13782 bonds, 868 residues, 1 model selected > color #4 #9437ffff > color #4/I,J #9437ffff > select clear > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #4 models > show #!1 models > transparency #1.1 50 > show #4 models > ui mousemode right ""rotate selected models"" > select add #4 122346 atoms, 124038 bonds, 7812 residues, 1 model selected > view matrix models > #4,0.24737,-0.96822,0.036881,285.57,0.95913,0.23929,-0.15104,-103.8,0.13741,0.072735,0.98784,-137.36 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.24737,-0.96822,0.036881,286.95,0.95913,0.23929,-0.15104,-101.22,0.13741,0.072735,0.98784,-149.95 > fitmap #4 inMap #1 Fit molecule RSR80_chainsrenamed_real_space_refined_083.pdb (#4) to map egelman-helix-300box.mrc (#1) using 122346 atoms average map value = 0.1296, steps = 192 shifted from previous position = 12.1 rotated from previous position = 13.3 degrees atoms outside contour = 60380, contour level = 0.11563 Position of RSR80_chainsrenamed_real_space_refined_083.pdb (#4) relative to egelman-helix-300box.mrc (#1) coordinates: Matrix rotation and translation 0.40715860 -0.91335746 0.00013720 244.88878665 0.91335746 0.40715861 0.00011883 -164.75881347 -0.00016440 0.00007693 0.99999998 -116.53246470 Axis -0.00002294 0.00016510 0.99999999 Axis point 249.34556201 106.27136078 0.00000000 Rotation angle (degrees) 65.97353305 Shift along axis -116.56528249 > select subtract #4 Nothing selected > select #4/R 6797 atoms, 6891 bonds, 434 residues, 1 model selected > show sel cartoons > select clear > select #4/A 6797 atoms, 6891 bonds, 434 residues, 1 model selected > hide sel cartoons > view matrix models > #4,0.40716,-0.91336,0.0001372,219.39,0.91336,0.40716,0.00011883,-179.67,-0.0001644,7.6929e-05,1,-130.93 > undo > ui mousemode right translate > volume #1 level 0.1423 > hide #!1 models > show #!1 models > transparency #1.1 50 > hide #!1 models > select #4/R 6797 atoms, 6891 bonds, 434 residues, 1 model selected > hide sel cartoons > lighting flat > undo > lighting full > select #4/Q,R 13594 atoms, 13782 bonds, 868 residues, 1 model selected > color #4 #5e5e5eff > color #4/Q,R #5e5e5eff > undo > select clear > save /Volumes/LabUSB/CryoEM-Structure/khg-paper-cryoem-structure-3.cxs ——— End of log from Fri Dec 6 16:57:31 2024 ——— opened ChimeraX session > show #!1 models > hide #4 models > show #4 models > hide #4 models > show #2 models > hide #2 models > show #!3 models > hide #!3 models > color #1 #919191ff models > color #1 #797979ff models > color #1 #919191ff models > show #2 models > hide #!1 models > show #!1 models > color zone #1 near #2 distance 6 > color zone #1 near #2 distance 4 > color zone #1 near #2 distance 3.5 > ui tool show ""Side View"" > hide #2 models > hide #!1 models > show #4 models > show #2 models > hide #4 models > save test1.png transparentBackground true > select add #2 13594 atoms, 13782 bonds, 868 residues, 1 model selected > select subtract #2 Nothing selected > color #2 #9437ffff > color #2/I,J: 246-269 gold > hide #2 models > show #4 models > color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R: 246-269 gold > turn x 90 > hide #4 models > show #!1 models > color zone #1 near #2 distance 3.5 > view [Repeated 1 time(s)] > view orient > select ~sel & ##selected Nothing selected > color zone #1 near #4 distance 3.5 > volume #1 level 0.09592 > transparency #1.1 50 > show #4 models > volume #1 level 0.07834 > color zone #1 near #4 distance 3.5 > volume #1 level 0.06235 > color zone #1 near #4 distance 3.5 > turn y 90 [Repeated 1 time(s)] > show #!3 models > hide #!3 models > undo [Repeated 2 time(s)] > transparency #1.1 50 > transparency #1.1 0 > save /Users/akw/Desktop/session-4.cxs > save session-4-yellow-lid-helix.png transparentBackground true [Repeated 1 time(s)] > volume #1 level 0.09592 > color zone #1 near #4 distance 3.5 > volume #1 level 0.05756 > surface dust #1 size 8.76 > surface dust #1 size 9 > surface dust #1 size 10 > surface dust #1 size 11 > save /Users/akw/Desktop/session-4.cxs ——— End of log from Wed Dec 11 00:35:51 2024 ——— opened ChimeraX session > hide #!1 models > ui tool show ""Side View"" > show #!3 models > hide #!3 models > show #2 models > hide #2 models > show #2 models > hide #2 models > hide #4 models > show #4 models > color #4 #919191ff > color #4 #929292ff > color #4 #919191ff > color #4 #929292ff > color #4 darkgrey > color #4/I,J #9437ffff > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > color #1 #929292ff models > color #1 darkgrey models > color #1 #929292ff models > volume #1 level 0.1295 > volume #1 level 0.1183 > hide #4 models > hide #!1 models > show #4 models > color #4/I,J #9437ffff > show #!1 models > color zone #1 near #4 distance 3.5 > hide #4 models > save session-4-purple-dimer-helix-2.png transparentBackground true > hide #!1 models > show #4 models > save session-4-purple-dimer-helix-model-2.png transparentBackground true > hide #4 models > show #4 models > turn x 90 > save session-4-purple-dimer-helix-model-top-2.png transparentBackground true > hide #4 models > show #!1 models > show #4 models > hide #!1 models > show #!1 models > hide #4 models > save session-4-purple-dimer-helix-top-2.png transparentBackground true > save /Users/akw/Desktop/session-4-2.cxs > hide #!1 models > show #2 models > hide #2 models > show #4 models > turn x 90 [Repeated 2 time(s)] > select add #4 122346 atoms, 124038 bonds, 7812 residues, 1 model selected > color #4 silver > color #4 darkgrey > hide #4 models > show #4 models > select subtract #4 Nothing selected > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R: > 309,310,312,326,327,433,435,437,443,444 royalblue > color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R: > 309,310,312,326,327,433,435,437,443,444 limegreen > color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R: > 309,310,312,326,327,433,435,437,443,444 turquiose Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R: > 309,310,312,326,327,433,435,437,443,444 turquoise > show #!1 models > hide #4 models > color #1 darkgrey models > color zone #1 near #4 distance 3.5 > turn y 90 [Repeated 5 time(s)] > save /Users/akw/Desktop/session-6.cxs ——— End of log from Wed Dec 11 17:42:09 2024 ——— opened ChimeraX session > ui tool show ""Side View"" > view orient > turn x 90 > lighting flat > hide #!1 models > show #4 models > show #!1 models > hide #4 models > show #4 models > hide #4 models > show #2 models > hide #2 models > show #!3 models > hide #!3 models > lighting full > color #3 darkgrey models > show #!3 models > hide #!1 models > undo [Repeated 2 time(s)] > save session-6-heparins.png transparentBackground true > save /Users/akw/Desktop/session-6.cxs ——— End of log from Thu Dec 12 01:43:15 2024 ——— opened ChimeraX session > turn y 20 > turn y 5 > turn y 3 > undo > show #2 models > turn y 30 > turn y 15 > turn y -5 > hide #2 models > ui tool show ""Side View"" > turn y 90 > turn y 45 > ui tool show ""Side View"" > lighting soft > show #4 models > hide #!1 models > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color #4/A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R: > 309,310,312,326,327,433,435,437,443,444 dark blue > show #!1 models > color zone #1 near #4 distance 3 > color zone #1 near #4 distance 2.5 > color zone #1 near #4 distance 4 > hide #4 models > volume #1 level 0.1631 > open /Volumes/LabUSB/CryoEM- > Structure/RSR80_chainsrenamed_real_space_refined_083.pdb Chain information for RSR80_chainsrenamed_real_space_refined_083.pdb #5 --- Chain | Description A B C D E F G H I J K L M N O P Q R | No description available > hide #5 models > save /Users/akw/Desktop/session-6.cxs > save hep-darkblue.png transparentBackground true > view orient > turn x -90 > save /Users/akw/Desktop/session-6.cxs > save hep-darkblue.png transparentBackground true > ui tool show ""Scale Bar"" > scalebar color #000000 > save hep-darkblue.png transparentBackground true ===== 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 ATI-4.8.13 OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine OpenGL vendor: ATI Technologies 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: iMac Model Identifier: iMac20,1 Processor Name: 8-Core Intel Core i7 Processor Speed: 3.8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14242.0.0,0) OS Loader Version: 540.100.7~14 Software: System Software Overview: System Version: macOS 12.3 (21E230) Kernel Version: Darwin 21.4.0 Time since boot: 68 days 10:11 Graphics/Displays: AMD Radeon Pro 5500 XT: Chipset Model: AMD Radeon Pro 5500 XT Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0041 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XT-012 Option ROM Version: 113-D322A1XT-012 EFI Driver Version: 01.01.231 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL S2421HGF: 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: HXYS973 Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort 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