id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9706 Crash saving session including maps chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. 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backing stores 4288K 8 \nCG image 52K 13 \nColorSync 228K 26 \nCoreAnimation 76K 15 \nCoreGraphics 16K 3 \nCoreUI image data 1528K 23 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.1G 94 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 784.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1440K 357 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 740K 74 \nRosetta Thread Context 740K 74 \nSTACK GUARD 40K 10 \nStack 169.1M 37 \nStack Guard 56.1M 27 \nVM_ALLOCATE 101.1M 194 \nVM_ALLOCATE (reserved) 160.1M 13 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 44.5M 672 \n__DATA_CONST 31.0M 341 \n__DATA_DIRTY 1644K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 737.4M 149 \n__OBJC_RO 82.7M 1 \n__OBJC_RW 3200K 2 \n__TEXT 797.1M 669 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 5.2G 1152 \nshared memory 3004K 21 \nunshared pmap 11.6M 8 \n=========== ======= ======= \nTOTAL 9.7G 4240 \nTOTAL, minus reserved VM space 8.5G 4240 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000614 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { ""NETWORK_SERVICE_PROXY_CONFIG_UPDATE"" : ""6401414cc679dd6bc5828183"" }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_D5.cxs"" Opened postprocess_D5.mrc as #3, grid size 80,80,80, pixel 3.26, shown at level 4.63, step 1, values float32 Log from Fri Sep 1 13:16:38 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_C1.cxs"" Opened postprocess.mrc as #2, grid size 80,80,80, pixel 3.26, shown at level 6.48, step 1, values float32 Log from Fri Aug 4 16:39:05 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/houghtf/Documents/Documents/barrel > paper/Data/Tomography/Barrel_fitted_final_map_job178.cxs"" Opened postprocess.mrc as #2, grid size 80,80,80, pixel 3.26, shown at level 6.79, step 1, values float32 Log from Tue Aug 1 11:09:11 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/houghtf/Documents/Documents/barrel paper/Data/Figure 1/Colour > barrel.cxs"" Log from Mon Jul 31 17:27:57 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/houghtf/Documents/Documents/barrel paper/Data/Figure > 1/barrel.pdb"" Chain information for barrel.pdb #1 --- Chain | Description A | No description available B | No description available C M | No description available D F J | No description available E | No description available G | No description available H L | No description available I | No description available K | No description available N P R T | No description available O | No description available Q | No description available S | No description available > set bgColor white > select add #1 46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected > cartoon (#!1 & sel) > hide (#!1 & sel) target a > select clear > select /A 3128 atoms, 3168 bonds, 207 residues, 1 model selected > ui tool show ""Color Actions"" > color sel green > select /B 1508 atoms, 1526 bonds, 98 residues, 1 model selected > color sel sandy brown > select /C 3111 atoms, 3153 bonds, 206 residues, 1 model selected > color sel green > select /D 1607 atoms, 1627 bonds, 101 residues, 1 model selected > color sel sandy brown > select /E 3101 atoms, 3142 bonds, 206 residues, 1 model selected > color sel green > select /F 1594 atoms, 1614 bonds, 101 residues, 1 model selected > color sel sandy brown > select /G 3100 atoms, 3141 bonds, 205 residues, 1 model selected > color sel green > select /H 1572 atoms, 1592 bonds, 99 residues, 1 model selected > color sel sandy brown > select /I 3069 atoms, 3109 bonds, 1 pseudobond, 202 residues, 2 models selected > color sel green > select /J 1571 atoms, 1590 bonds, 100 residues, 1 model selected > color sel khaki > select /L 1520 atoms, 1538 bonds, 97 residues, 1 model selected > color sel khaki > select /N 1555 atoms, 1574 bonds, 97 residues, 1 model selected > color sel khaki > select /P 1540 atoms, 1559 bonds, 97 residues, 1 model selected > color sel khaki > select /R 1529 atoms, 1547 bonds, 96 residues, 1 model selected > color sel khaki > select /T 1516 atoms, 1534 bonds, 96 residues, 1 model selected > color sel khaki > select /S 3087 atoms, 3128 bonds, 204 residues, 1 model selected > color sel green > select /Q 3061 atoms, 3101 bonds, 1 pseudobond, 203 residues, 2 models selected > color sel green > select /O 3131 atoms, 3173 bonds, 207 residues, 1 model selected > color sel green > select /M 3100 atoms, 3141 bonds, 205 residues, 1 model selected > color sel green > select ::name=""FUC""::name=""HOH""::name=""NAG"" 698 atoms, 690 bonds, 48 residues, 1 model selected > show sel target ab > color sel byhetero > select H 22664 atoms, 3013 residues, 1 model selected > hide sel target a > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:149-150 36 atoms, 35 bonds, 2 residues, 1 model selected > select /A:149-225 1174 atoms, 1189 bonds, 77 residues, 1 model selected > select /A:149-150 36 atoms, 35 bonds, 2 residues, 1 model selected > select /A:149-224 1163 atoms, 1178 bonds, 76 residues, 1 model selected > color sel lime target a > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > sequence chain /E Alignment identifier is 1/E > sequence chain /G Alignment identifier is 1/G > sequence chain /I Alignment identifier is 1/I > sequence chain /K Alignment identifier is 1/K > sequence chain /M Alignment identifier is 1/M > sequence chain /O Alignment identifier is 1/O > sequence chain /Q Alignment identifier is 1/Q > sequence chain /S Alignment identifier is 1/S > select /S:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /S:151-224 1126 atoms, 1141 bonds, 74 residues, 1 model selected > color sel lime target a > select /Q:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /Q:151-224 1118 atoms, 1133 bonds, 1 pseudobond, 73 residues, 2 models selected > color sel lime target a > select /O:150-151 20 atoms, 19 bonds, 2 residues, 1 model selected > select /O:150-224 1129 atoms, 1144 bonds, 75 residues, 1 model selected > color sel lime target a > select /M:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /M:151-225 1137 atoms, 1152 bonds, 75 residues, 1 model selected > color sel lime target a > select /K:150 14 atoms, 13 bonds, 1 residue, 1 model selected > select /K:150-224 1141 atoms, 1156 bonds, 75 residues, 1 model selected > color sel lime target a > select /I:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /I:151-224 1106 atoms, 1120 bonds, 1 pseudobond, 72 residues, 2 models selected > color sel lime target a > select /G:150-151 28 atoms, 27 bonds, 2 residues, 1 model selected > select /G:150-224 1141 atoms, 1156 bonds, 75 residues, 1 model selected > color sel lime target a > select /E:150-151 28 atoms, 27 bonds, 2 residues, 1 model selected > select /E:150-224 1141 atoms, 1156 bonds, 75 residues, 1 model selected > color sel lime target a > select /C:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /C:151-224 1126 atoms, 1141 bonds, 74 residues, 1 model selected > color sel lime target a > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /C Alignment identifier is 1/C > sequence chain /E Alignment identifier is 1/E > sequence chain /G Alignment identifier is 1/G > sequence chain /I Alignment identifier is 1/I > sequence chain /K Alignment identifier is 1/K > sequence chain /M Alignment identifier is 1/M > sequence chain /O Alignment identifier is 1/O > sequence chain /Q Alignment identifier is 1/Q > sequence chain /S Alignment identifier is 1/S > select /S:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /S:151-224 1126 atoms, 1141 bonds, 74 residues, 1 model selected > color sel lime target c > select clear > select /Q:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /Q:151-224 1118 atoms, 1133 bonds, 1 pseudobond, 73 residues, 2 models selected > color sel lime target c > select /O:150 6 atoms, 5 bonds, 1 residue, 1 model selected > select /O:150-224 1129 atoms, 1144 bonds, 75 residues, 1 model selected > color sel lime target c [Repeated 1 time(s)] > select /M:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /M:151-224 1126 atoms, 1141 bonds, 74 residues, 1 model selected > color sel lime target c > select /K:150-151 28 atoms, 27 bonds, 2 residues, 1 model selected > select /K:150-224 1141 atoms, 1156 bonds, 75 residues, 1 model selected > color sel lime target c > select /I:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /I:151-224 1106 atoms, 1120 bonds, 1 pseudobond, 72 residues, 2 models selected > color sel lime target c > select /G:150-151 28 atoms, 27 bonds, 2 residues, 1 model selected > select /G:150-224 1141 atoms, 1156 bonds, 75 residues, 1 model selected > color sel lime target c > select /E:150-151 28 atoms, 27 bonds, 2 residues, 1 model selected > select /E:150-225 1152 atoms, 1167 bonds, 76 residues, 1 model selected > color sel lime target c > select /C:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /C:151-224 1126 atoms, 1141 bonds, 74 residues, 1 model selected > color sel lime target c > select /A:149 21 atoms, 20 bonds, 1 residue, 1 model selected > select /A:149-236 1361 atoms, 1378 bonds, 88 residues, 1 model selected > color sel lime target c > lighting shadows false > select /A:225-227 50 atoms, 49 bonds, 3 residues, 1 model selected > select /A:225-237 209 atoms, 209 bonds, 13 residues, 1 model selected > color sel crimson target c > color sel lime target c [Repeated 1 time(s)] > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /C Alignment identifier is 1/C > sequence chain /E Alignment identifier is 1/E > sequence chain /G Alignment identifier is 1/G > sequence chain /I Alignment identifier is 1/I > sequence chain /K Alignment identifier is 1/K > sequence chain /M Alignment identifier is 1/M > sequence chain /O Alignment identifier is 1/O > sequence chain /Q Alignment identifier is 1/Q > sequence chain /S Alignment identifier is 1/S > select /A:149 21 atoms, 20 bonds, 1 residue, 1 model selected > select /A:149-236 1361 atoms, 1378 bonds, 88 residues, 1 model selected > color sel lime target c > select /S:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /S:151-236 1324 atoms, 1341 bonds, 86 residues, 1 model selected > color sel lime target c > select /Q:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /Q:151-236 1316 atoms, 1333 bonds, 1 pseudobond, 85 residues, 2 models selected > color sel lime target c > select /O:150-151 20 atoms, 19 bonds, 2 residues, 1 model selected > select /O:150-236 1327 atoms, 1344 bonds, 87 residues, 1 model selected > color sel lime target c > select /M:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /M:151-236 1324 atoms, 1341 bonds, 86 residues, 1 model selected > color sel lime target c > select /K:150 14 atoms, 13 bonds, 1 residue, 1 model selected > select /K:150-236 1339 atoms, 1356 bonds, 87 residues, 1 model selected > color sel lime target c > select /I:151 13 atoms, 12 bonds, 1 residue, 1 model selected > select /I:151-236 1304 atoms, 1320 bonds, 1 pseudobond, 84 residues, 2 models selected > color sel lime target c > select /G:150-151 28 atoms, 27 bonds, 2 residues, 1 model selected > select /G:150-236 1339 atoms, 1356 bonds, 87 residues, 1 model selected > color sel lime target c > select /E:150 14 atoms, 13 bonds, 1 residue, 1 model selected > select /E:150-236 1339 atoms, 1356 bonds, 87 residues, 1 model selected > color sel lime target c > select /C:151-152 27 atoms, 26 bonds, 2 residues, 1 model selected > select /C:151-236 1324 atoms, 1341 bonds, 86 residues, 1 model selected > color sel lime target c > save ""/Users/houghtf/Documents/Documents/barrel paper/Data/Figure 1/Colour > barrel.cxs"" ——— End of log from Mon Jul 31 17:27:57 2023 ——— opened ChimeraX session > select /W:5@O 1 atom, 1 residue, 1 model selected > select /W:10@O 1 atom, 1 residue, 1 model selected > select /W:10@O 1 atom, 1 residue, 1 model selected > select /W:5@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:10@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:23@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:12@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:22@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:11@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:14@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:3@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:25@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:7@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:17@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:4@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:16@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:6@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:1@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:2@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:15@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:9@O 1 atom, 1 residue, 1 model selected > hide sel target a > select /W:8@O 1 atom, 1 residue, 1 model selected > hide sel target a > ui tool show ""Show Sequence Viewer"" > sequence chain /K Alignment identifier is 1/K > select /K:237 11 atoms, 10 bonds, 1 residue, 1 model selected > select /K:237-354 1704 atoms, 1725 bonds, 1 pseudobond, 115 residues, 2 models selected > ui tool show ""Color Actions"" > color sel green > select clear > save ""/Users/houghtf/Documents/Documents/barrel paper/Data/Figure 1/Colour > barrel.cxs"" > open ""/Users/houghtf/Documents/Documents/barrel > paper/Data/Tomography/Relion4 > jobs/Job178_Tomo_reconstruct/PostProcess/postprocess.mrc"" Opened postprocess.mrc as #2, grid size 80,80,80, pixel 3.26, shown at level 14.5, step 1, values float32 > volume #2 level 3.236 > tile 2 models tiled > ui tool show ""Model Panel"" > hide #!1 models > show #!1 models > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.78642,0.61676,-0.033974,-178.25,-0.6172,0.78242,-0.082895,-187.42,-0.024544,0.086159,0.99598,-91.525 > view matrix models > #2,0.46935,0.81933,-0.32927,-121.09,-0.49735,0.55341,0.66812,-275.69,0.72963,-0.14982,0.66723,-120 > volume #2 level 6.304 > transparency #2.1 70 > select add #1 46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 4 models selected > select subtract #2 46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected > ui mousemode right ""move picked models"" [Repeated 1 time(s)] > view matrix models #1,1,0,0,-27.091,0,1,0,-200.08,0,0,1,-2.1825 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.99521,-0.00043184,0.09773,-31.977,0.00083095,0.99999,-0.0040431,-199.89,-0.097727,0.0041049,0.9952,0.41268 > view matrix models > #1,0.97583,-0.19657,0.095468,-26.269,0.19334,0.98023,0.042091,-206.58,-0.10185,-0.022616,0.99454,1.2458 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms average map value = 12.17, steps = 60 shifted from previous position = 10.2 rotated from previous position = 8.31 degrees atoms outside contour = 5212, contour level = 6.3038 Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates: Matrix rotation and translation 0.40034478 -0.62961202 0.66581736 96.61861426 0.89139750 0.43602363 -0.12366848 104.13230329 -0.21244895 0.64301796 0.73579436 84.17677080 Axis 0.40006376 0.45828712 0.79367620 Axis point -1.59484684 57.64046084 0.00000000 Rotation angle (degrees) 73.37650062 Shift along axis 153.18519836 > select clear > volume #2 level 6.795 > fitmap #1 inMap #2 Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms average map value = 12.17, steps = 44 shifted from previous position = 0.0518 rotated from previous position = 0.0326 degrees atoms outside contour = 6052, contour level = 6.7948 Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates: Matrix rotation and translation 0.40003055 -0.62940740 0.66619958 96.61067856 0.89145208 0.43599686 -0.12336906 104.06639494 -0.21281153 0.64323640 0.73549860 84.18577427 Axis 0.39998184 0.45863029 0.79351924 Axis point -1.50101650 57.58528401 0.00000000 Rotation angle (degrees) 73.39553772 Shift along axis 153.17354966 > select add #2 2 models selected > select subtract #2 Nothing selected > lighting full > lighting soft > transparency 70 > transparency 60 > transparency 70 > save ""/Users/houghtf/Documents/Documents/barrel > paper/Data/Tomography/Barrel_fitted_final_map_job178.cxs"" ——— End of log from Tue Aug 1 11:09:11 2023 ——— opened ChimeraX session > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes true > lighting full > lighting soft > transparency 60 > lighting full > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting full > transparency 50 > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > volume #2 level 7.419 > lighting shadows false > volume #2 level 7.169 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_side.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map.cxs"" includeMaps true > select add #2 2 models selected > ui tool show ""Color Actions"" > color sel gold > color sel indian red > color sel coral > color sel chocolate > color sel olive > color sel lawn green > color sel light gray > color sel light steel blue > color sel light blue > color sel sky blue > color sel light cyan > color sel seashell > color sel blanched almond > color sel bisque > color sel navajo white > color sel aquamarine > color sel purple > color sel dark slate gray > color sel dark olive green > color sel sandy brown > color sel goldenrod > color sel green yellow > color sel dark orange > color sel gold > color sel indian red > color sel fire brick > color sel maroon > color sel dark red > color sel crimson > color sel orange red [Repeated 1 time(s)] > color sel peru > color sel light salmon > color sel dark goldenrod > color sel dark turquoise > color sel cornflower blue > color sel teal > color sel steel blue > color sel cadet blue > color sel light slate gray > color sel slate gray > color sel light slate gray > select clear > lighting full > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top2.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > select add #1 46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected > transparency (#!1 & sel) 60 > select clear > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top2.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > select add #1 46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected > transparency (#!1 & sel) 70 > select clear > select add #2 2 models selected > transparency #2.1 60 > select clear > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top2.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > volume #2 level 6.483 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_side2.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top2.tif"" width 2500 height 2094 supersample 3 > transparentBackground true > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map.cxs"" ——— End of log from Fri Aug 4 16:39:05 2023 ——— opened ChimeraX session > graphics silhouettes true width 1 > graphics silhouettes false > open ""/Users/houghtf/Documents/Documents/barrel paper/Data/Figure > 3/Tomography/postprocess_D5.mrc"" Opened postprocess_D5.mrc as #3, grid size 80,80,80, pixel 3.26, shown at level 15.6, step 1, values float32 > volume #3 level 5.6 > hide #!2 models > hide #!1 models > volume #3 color #919191 > volume #3 color #797979 > volume #3 color #919191 > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Figure 4 supplementary/D5_map_top_view.png"" width 2000 height 1474 > supersample 3 transparentBackground true [Repeated 1 time(s)] > volume #3 level 4.011 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Figure 4 supplementary/D5_map_top_view.png"" width 2000 height 1474 > supersample 3 transparentBackground true > volume #3 level 6.318 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Figure 4 supplementary/D5_map_side_view.png"" width 2000 height 1474 > supersample 3 transparentBackground true > volume #3 level 4.729 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Figure 4 supplementary/D5_map_top_view.png"" width 2000 height 1474 > supersample 3 transparentBackground true > transparency #3 40 > transparency #3 60 > hide #!3 models > show #!3 models > show #!1 models > ui mousemode right ""translate selected models"" > hide #!3 models > show #!3 models > select add #1 46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected > view matrix models > #1,0.99963,-0.0030275,-0.027213,110.16,0.0040774,0.99925,0.038609,101.69,0.027075,-0.038706,0.99888,-29.384 > view matrix models > #1,0.99963,-0.0030275,-0.027213,108.61,0.0040774,0.99925,0.038609,109.69,0.027075,-0.038706,0.99888,80.045 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.99823,-0.0045389,0.059253,104.25,0.0025678,0.99944,0.0333,109.99,-0.059371,-0.033089,0.99769,82.132 > view matrix models > #1,0.98492,0.0033303,0.173,98.539,0.022103,0.9892,-0.14488,118.92,-0.17161,0.14652,0.97421,81.487 > view matrix models > #1,0.99277,-0.017764,0.11868,101.68,0.012706,0.99898,0.043241,109.24,-0.11933,-0.041421,0.99199,84.143 > view matrix models > #1,0.75562,-0.6496,0.084038,125.79,0.63782,0.7589,0.13136,95.233,-0.14911,-0.045661,0.98777,85.218 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 46489, contour level = 6.4828 Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates: Matrix rotation and translation -0.19827520 -0.73775716 0.64529165 40.29012050 0.96933156 -0.24512634 0.01759003 355.31075172 0.14520081 0.62898923 0.76373377 317.87111077 Axis 0.32504447 0.26586846 0.90755719 Axis point -133.46374530 96.89250027 0.00000000 Rotation angle (degrees) 109.86675385 Shift along axis 396.04821469 > fitmap #1 inMap #2 Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 46489, contour level = 6.4828 Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates: Matrix rotation and translation -0.19827520 -0.73775716 0.64529165 40.29012050 0.96933156 -0.24512634 0.01759003 355.31075172 0.14520081 0.62898923 0.76373377 317.87111077 Axis 0.32504447 0.26586846 0.90755719 Axis point -133.46374530 96.89250027 0.00000000 Rotation angle (degrees) 109.86675385 Shift along axis 396.04821469 > fitmap #1 inMap #3 Fit molecule barrel.pdb (#1) to map postprocess_D5.mrc (#3) using 46489 atoms average map value = 12.98, steps = 52 shifted from previous position = 6.1 rotated from previous position = 3.64 degrees atoms outside contour = 2262, contour level = 4.7286 Position of barrel.pdb (#1) relative to postprocess_D5.mrc (#3) coordinates: Matrix rotation and translation 0.76128068 -0.64307053 0.08313854 127.23977321 0.63943948 0.76580601 0.06825179 92.55169719 -0.10755871 0.00120330 0.99419801 81.39406835 Axis -0.05164161 0.14687748 0.98780572 Axis point -43.68057914 221.09846877 0.00000000 Rotation angle (degrees) 40.47914099 Shift along axis 87.42442058 > select subtract #1 Nothing selected > fitmap #1 inMap #3 Fit molecule barrel.pdb (#1) to map postprocess_D5.mrc (#3) using 46489 atoms average map value = 12.98, steps = 28 shifted from previous position = 0.0663 rotated from previous position = 0.0344 degrees atoms outside contour = 2265, contour level = 4.7286 Position of barrel.pdb (#1) relative to postprocess_D5.mrc (#3) coordinates: Matrix rotation and translation 0.76119496 -0.64324100 0.08260293 127.25214416 0.63962916 0.76566310 0.06807753 92.62301550 -0.10703627 0.00101497 0.99425460 81.38018517 Axis -0.05164442 0.14603989 0.98792976 Axis point -43.85158218 221.12303548 0.00000000 Rotation angle (degrees) 40.48673266 Shift along axis 87.35269780 > volume #3 color #6c6091 > volume #3 color #6c6091c3 > volume #3 color #6d7691c3 > volume #3 color #6d76919d > volume #3 color #7683919d > volume #2 level 5.776 > volume #2 level 4.877 > volume #3 level 3.293 > volume #3 level 4.575 > hide #!2 models > close #2 > volume #3 level 5.446 > volume #3 level 4.216 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top_D5.tif"" width 2000 height 1474 supersample 3 > volume #3 color #95a2b29d > volume #3 color #95a2b280 > volume #3 color #8995a380 > volume #3 color #8995a371 > volume #3 color #828d9b71 > volume #3 color #828d9b6a > volume #3 color #828d9b6b > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top_D5.tif"" width 936 height 690 supersample 3 > transparentBackground true > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_top_D5.tif"" width 2000 height 1474 supersample 3 > transparentBackground true > select /R 1529 atoms, 1547 bonds, 96 residues, 1 model selected > select /L 1520 atoms, 1538 bonds, 97 residues, 1 model selected > ui tool show ""Color Actions"" > color sel sandy brown > select clear > volume #3 level 4.216 > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_side_D5_1.tif"" width 2000 height 1474 supersample > 3 transparentBackground true > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_side_D5_2.tif"" width 2000 height 1474 supersample > 3 transparentBackground true > hide #!1 models > volume #3 level 4.626 > show #!1 models > save ""/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure > 4/Barrel_fitted_cryoET_map_D5.cxs"" includeMaps true ——— End of log from Fri Sep 1 13:16:38 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 16 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 90 days 4:56 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 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 U2415: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 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1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Sessions can't reproduce all ChimeraX