id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17280 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000001f49acc00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at level 0.0284, step 1, values float32 Opened State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.00701, step 1, values float32 Log from Mon Mar 31 16:21:28 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at level 0.0284, step 1, values float32 Opened State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.00701, step 1, values float32 Log from Thu Mar 27 16:53:46 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at level 0.0284, step 1, values float32 Opened State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.00701, step 1, values float32 Log from Wed Mar 26 18:37:57 2025 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/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM > Maps/State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- > sharpened-highres.mrc"" format mrc Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at level 0.0049, step 2, values float32 > open > ""/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM > Maps/State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- > sharpened-highres.mrc"" Opened State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.00701, step 2, values float32 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc in map State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- sharpened-highres.mrc using 33671 points correlation = 0.8245, correlation about mean = 0.7206, overlap = 2069 steps = 60, shift = 0.77, angle = 1.48 degrees Position of State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) relative to State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer- sharpened-highres.mrc (#2) coordinates: Matrix rotation and translation 0.99987526 -0.01361448 -0.00800679 3.25328190 0.01377534 0.99969720 0.02038996 -4.19338540 0.00772676 -0.02049771 0.99976004 1.06230708 Axis -0.79135884 -0.30451436 0.53011526 Axis point 0.00000000 68.27155938 217.64147059 Rotation angle (degrees) 1.48033436 Shift along axis -0.73442213 > volume #1 level 0.0284 > volume #1 step 1 > volume #2 step 1 > surface dust #1 size 8.32 > surface dust #2 size 8.32 > lighting full > open /Users/justinvanriper/Desktop/2024-05-03_apply_ncs_56-coot-0_RNA- > WC_edited_modified_real_space_refined_061.pdb Chain information for 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb #3 --- Chain | Description A B | No description available C | No description available D | No description available > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) to map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) using 13483 atoms average map value = 0.03961, steps = 260 shifted from previous position = 3.36 rotated from previous position = 5.77 degrees atoms outside contour = 11091, contour level = 0.0284 Position of 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) relative to State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) coordinates: Matrix rotation and translation 0.99480463 -0.01991648 0.09983530 -7.78571490 0.01969956 0.99980096 0.00315823 -0.40546740 -0.09987833 -0.00117511 0.99499896 14.46516488 Axis -0.02127829 0.98066594 0.19452903 Axis point 135.56859660 0.00000000 84.49020469 Rotation angle (degrees) 5.84430165 Shift along axis 2.58193308 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) to map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) using 13483 atoms average map value = 0.03961, steps = 104 shifted from previous position = 0.00371 rotated from previous position = 0.00381 degrees atoms outside contour = 11092, contour level = 0.0284 Position of 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) relative to State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) coordinates: Matrix rotation and translation 0.99480232 -0.01990549 0.09986046 -7.78976604 0.01969464 0.99980125 0.00309692 -0.40019875 -0.09990226 -0.00111410 0.99499663 14.46298663 Axis -0.02067332 0.98070242 0.19441036 Axis point 135.51676875 0.00000000 84.52589260 Rotation angle (degrees) 5.84552505 Shift along axis 2.58031882 > ui mousemode right ""rotate selected models"" > select clear [Repeated 1 time(s)] > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > select #3 13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected > view matrix models > #3,0.97334,0.090641,0.2107,-32.528,-0.11231,0.98929,0.09323,6.0511,-0.19999,-0.11441,0.9731,43.281 > view matrix models > #3,0.96579,0.078425,0.24719,-34.703,-0.093033,0.99451,0.047964,8.7521,-0.24207,-0.06932,0.96778,43.581 > view matrix models > #3,0.49419,-0.86308,0.10426,159.83,0.86885,0.48624,-0.093138,-29.911,0.029689,0.13662,0.99018,-18.884 > view matrix models > #3,0.43314,-0.90103,0.022914,182.53,0.89896,0.43003,-0.083304,-27.905,0.065206,0.056681,0.99626,-14.115 > select clear > select #2 2 models selected > hide surfaces > hide cartoons > hide atoms > select clear > select #3 13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected > show sel cartoons > view clip false [Repeated 1 time(s)] > show target m > hide #!2 models > select clear > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) to map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) using 13483 atoms average map value = 0.3207, steps = 104 shifted from previous position = 3.68 rotated from previous position = 7.08 degrees atoms outside contour = 1877, contour level = 0.0284 Position of 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) relative to State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) coordinates: Matrix rotation and translation 0.53358153 -0.84510500 -0.03298910 167.85814131 0.84235537 0.53452686 -0.06869114 -38.99484238 0.07568479 0.00886377 0.99709240 -8.19795878 Axis 0.04581637 -0.06420023 0.99688474 Axis point 119.41582054 132.60810071 0.00000000 Rotation angle (degrees) 57.81867815 Shift along axis 2.02170861 > hide #!1 models > select #3:A/1-214 Nothing selected > select #3 13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected > A/1-214 Unknown command: A/1-214 > select #3/A:1-214 1578 atoms, 1602 bonds, 1 pseudobond, 196 residues, 2 models selected > select #3/A:1-351 2662 atoms, 2712 bonds, 1 pseudobond, 331 residues, 2 models selected > color sel cornflower blue > select #3/A:352-555 1322 atoms, 1350 bonds, 1 pseudobond, 165 residues, 2 models selected > color sel gold > select #3/A:556-912 khaki Expected a keyword > select #3/A:556-912 2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected > color sel khaki > color sel sienna > select #3/B:1-351 2662 atoms, 2712 bonds, 1 pseudobond, 331 residues, 2 models selected > color sel light blue > select #3/B:352-555 1322 atoms, 1350 bonds, 1 pseudobond, 165 residues, 2 models selected > color sel khaki > view matrix models > #3,0.17845,-0.98352,-0.029143,229.48,0.9838,0.17784,0.022506,-23.61,-0.016952,-0.032688,0.99932,7.7168 > select #3/B:556-912 2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected > color sel lightblue brown Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #3/B:556-912 2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected > color sel lightblue brown Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #3/B:556-912 2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected > color sel lightblue brown Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel lightblue brown Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel blue > color sel lightbrown Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel sandybrown > select clear > select #3/C 109 atoms, 121 bonds, 5 residues, 1 model selected > color sel light pink > select #3/D 106 atoms, 117 bonds, 5 residues, 1 model selected > color sel pale violet red > clear Unknown command: clear > select clear > hide #3.2 models > hide #3.1 models > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs > show #!1 models > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) to map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) using 13483 atoms average map value = 0.3207, steps = 172 shifted from previous position = 0.102 rotated from previous position = 21.7 degrees atoms outside contour = 1875, contour level = 0.0284 Position of 2024-05-03_apply_ncs_56-coot-0_RNA- WC_edited_modified_real_space_refined_061.pdb (#3) relative to State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#1) coordinates: Matrix rotation and translation 0.53357587 -0.84510873 -0.03298530 167.85658488 0.84235732 0.53452072 -0.06871500 -38.99499833 0.07570297 0.00887926 0.99709088 -8.19992537 Axis 0.04583939 -0.06420840 0.99688316 Axis point 119.41491024 132.60520438 0.00000000 Rotation angle (degrees) 57.81912908 Shift along axis 2.02388178 > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs > color zone #1 near #3 distance 4.99 > ui tool show ""Volume Viewer"" > ui tool show ""Show Volume Menu"" > morph map #1 #1 Missing or invalid ""structures"" argument: invalid structures specifier > morph map #1-2 Missing or invalid ""structures"" argument: invalid structures specifier > morph map #1 #2 Missing or invalid ""structures"" argument: invalid structures specifier > color #2 #929292ff models > color #2 darkgrey models > color #2 #919191ff models > color #2 #929292ff models > transparency #2 80 > transparency #2 20 > transparency #2 30 > set bgColor white > lighting simple > view name p2 > view p2 > rotate 90 x Unknown command: rotate 90 x > rotate x 90 Unknown command: rotate x 90 > roll x 90 > stop > roll x 1 90 [Repeated 1 time(s)] > view name p2 [Repeated 1 time(s)] > roll y 1 90 [Repeated 2 time(s)] > roll y 1 10 [Repeated 4 time(s)] > hide #!2 models > hide #!1 models > show #!1 models > view name p1 > roll y 1 90 > view name p2 > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs > roll y 1 90 > view name p3 > roll y 1 90 > view name p4 > roll y 1 90 > roll x 1 90 > view name p5 > roll x 2 90 > view name p6 > roll x 1 90 > lighting full > lighting soft > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs ——— End of log from Wed Mar 26 18:37:57 2025 ——— opened ChimeraX session > close #3 > show #!2 models > open > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited- > coot-15_real_space_refined_015.pdb Chain information for real_space_refined_036_edited- coot-15_real_space_refined_015.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > hide #!1 target m > hide #!2 target m > select #3/A:1-351 2616 atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected > color sel cornflower blue > select #3/A:352-555 1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected > color sel gold > select #3/A:556-912 2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected > color sel khaki > color sel sienna > select #3/B:1-351 2642 atoms, 2692 bonds, 1 pseudobond, 328 residues, 2 models selected > color sel light blue > select #3/B:352-555 1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected > color sel khaki > select #3/B:556-912 2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected > color sel lightblue brown Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #3/B:556-912 2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected > color sel lightblue brown Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #3/B:556-912 2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected > color sel blue > color sel sandybrown > select clear > select #3/C 111 atoms, 124 bonds, 5 residues, 1 model selected > color sel light pink > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > color sel pale violet red > select clear > show #!1 target m > color zone #1 near #3 distance 4.99 > transparency #1 50 > view p1 > transparency #1 100 > transparency #1 0 > hide #3.2 target m > hide #!3 target m > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs ——— End of log from Thu Mar 27 16:53:46 2025 ——— opened ChimeraX session > show #!3 models > hide #!1 models > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > color sel medium violet red > select clear > show #!1 models > color zone #1 near #3 distance 4.99 > select clear > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs ——— End of log from Mon Mar 31 16:21:28 2025 ——— opened ChimeraX session > hide #!1 models > select #3/C 111 atoms, 124 bonds, 5 residues, 1 model selected > color sel hot pink > select clear > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs > view p1 > show #!1 models > color zone #1 near #3 distance 4.99 > hide #!3 models > graphics silhouettes true > ui tool show ""Side View"" > view p1 > undo > view p1 > save /Users/justinvanriper/Desktop/image10.png supersample 3 > save /Users/justinvanriper/Desktop/image11.png supersample 3 > show #!3 models > hide #!1 models > select #3/C,D 253 atoms, 280 bonds, 12 residues, 1 model selected > show sel cartoons > nucleotides sel ladder > hide sel cartoons > show sel cartoons > select clear > cartoon style #3.1#!3 modeHelix tube sides 20 > save /Users/justinvanriper/Desktop/image12.png supersample 3 > lighting simple > lighting soft > view p1 > undo > select clear > view p1 > roll x 1 90 > show #!1 models > hide #!3 models > save /Users/justinvanriper/Desktop/image13.png supersample 3 > view p3 > view p5 > view p6 > view p7 Expected an objects specifier or a view name or a keyword > view p11 Expected an objects specifier or a view name or a keyword > view p22 Expected an objects specifier or a view name or a keyword > view p1 > roll x 1 10 > show #!3 models > hide #!3 models > hide #!1 models > show #!3 models > select #3/A,B:1-351 5258 atoms, 5358 bonds, 2 pseudobonds, 653 residues, 2 models selected > show sel surfaces Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. > color sel fromatoms target s > select clear > select #3/A,B 13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected > hide sel atoms > hide sel cartoons > select #3 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected > transparcency #3 50 Unknown command: transparcency #3 50 > transparancy #3 50 Unknown command: transparancy #3 50 > transparency #3 50 > transparency #3 90 > transparency #3 80 > transparency #3 80select clear Missing or invalid ""percent"" argument: Expected a number > select #3/A,B:30,38,78,86,39,127,213,206,211,212 192 atoms, 180 bonds, 20 residues, 1 model selected > show sel atoms > color (#!3 & sel) byhetero > color sel fromatoms target s > select clear > color sel fromatoms target s > select #3/A 6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected > color sel cornflower blue > select #3/B 6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected > color sel lightblue pale blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #3/B 6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected > color sel light blue > select clear > transparency #3 80 > select #3/A,B:30,38,78,86,39,127,213,206,211,212 192 atoms, 180 bonds, 20 residues, 1 model selected > color sel byhetero target a > select clear > select ::name=""MG"" 3 atoms, 3 residues, 1 model selected > show sel atoms > color sel byhetero target a > select clear > select backbone 6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected > hide sel atoms > select clear > select #3/C,D 253 atoms, 280 bonds, 12 residues, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > select clear > select #3/A,B:30,38,78,82,86,39,127,213,206,211,212 206 atoms, 192 bonds, 22 residues, 1 model selected > show sel atoms > select clear > select backbone 6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected > hide sel atoms > select clear > select #3/C,D 253 atoms, 280 bonds, 12 residues, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > select clear > view name p3 > view p2 > view p3 > select clear > save /Users/justinvanriper/Desktop/image14.png supersample 3 > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting flat > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > lighting flat > lighting soft > save /Users/justinvanriper/Desktop/image15.png supersample 3 > select #3/A,B:30,38,78,82,86,39,127,213,206,211,212, Expected an objects specifier or a keyword > select #3/A,B:30,38,78,82,86,39,127,213,206,211,212 206 atoms, 192 bonds, 22 residues, 1 model selected > ui mousemode right select > select clear > hide surfaces > view p3 > select #3/A,B:1-351 5258 atoms, 5358 bonds, 2 pseudobonds, 653 residues, 2 models selected > show sel surfaces > select clear > select #3/A,B:214,39,137,79 72 atoms, 64 bonds, 8 residues, 1 model selected > show sel atoms > color sel byhetero target a > select clear > select backbone 6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected > select clear > select backbone 6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected > hide sel cartoons > select clear > select #3/C,D 253 atoms, 280 bonds, 12 residues, 1 model selected > show sel cartoons > select clear > select backbone 6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected > hide sel atoms > select clear > select #3/C,D 253 atoms, 280 bonds, 12 residues, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > select clear > save /Users/justinvanriper/Desktop/image14.png supersample 3 > hide surfaces > select /A:82@CB 1 atom, 1 residue, 1 model selected > select clear > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure3C_session.cxs > select #3 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected > hide sel atoms > select ~sel & ##selected Nothing selected > select #3/C,D 253 atoms, 280 bonds, 12 residues, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > select clear > view p1 > select #3 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected > show sel cartoons > select clear > select#3/A:352-554 Unknown command: select#3/A:352-554 > select #3/A:352-554 1328 atoms, 1356 bonds, 1 pseudobond, 166 residues, 2 models selected > color sel gold [deleted to fit within ticket limits] > volume zone #2 nearAtoms sel range 2.3 > volume zone #2 nearAtoms sel range 2.4 > volume #2 level 0.165 > volume zone #2 nearAtoms sel range 2.5 > volume zone #2 nearAtoms sel range 2.2 > volume zone #2 nearAtoms sel range 2.5 > volume zone #2 nearAtoms sel range 2.5view p2 Invalid ""range"" argument: Expected a number > view p2 > ;ect c;ear Incomplete command: sequence > select clear > volume #2 level 0.1502 > view p2 > hide #!2 models > align #3 toAtoms #1.1 Unequal number of atoms to pair, 13446 and 13483 > matchmaker #3 to #1.1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker all_aligned_SLFN.cif, chain A (#1.1) with real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A (#3), sequence alignment score = 3964.3 RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs: 0.728) > show #!1.2 models > hide #!1.2 models > hide #!1.1 models > view p2 > view p3 Expected an objects specifier or a view name or a keyword > view name p3 > view p2 > view p3 > select clear > save /Users/justinvanriper/Desktop/image1.png supersample 3 > show #!1.1 models > show #!3#!1.1 atoms > show #!3#!1.1 cartoons > select #1.1 13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected > show sel cartoons [Repeated 1 time(s)] > undo [Repeated 4 time(s)] > select #1.1 13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected > hide sel cartoons > select clear > hide #!1.1 models > show #!1.2 models > select #1.2 10301 atoms, 10474 bonds, 16 pseudobonds, 1306 residues, 2 models selected > hide sel cartoons > select clear > save /Users/justinvanriper/Desktop/image2.png supersample 3 > hide #!1.2 models > show #!1.3 models > select #1.3 14346 atoms, 14642 bonds, 8 pseudobonds, 1774 residues, 2 models selected > show sel cartoons > hide sel cartoons > select clear > save /Users/justinvanriper/Desktop/image3.png supersample 3 > show #!1.4 models > hide #!1.3 models > select #1.4 13334 atoms, 13618 bonds, 6 pseudobonds, 1658 residues, 2 models selected > hide sel cartoons > select clear > save /Users/justinvanriper/Desktop/image4.png supersample 3 > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > show #!1.3 models > hide #!1.3 models > hide #!1.2 models > hide #!1.4 models > show #!1.5 models > select #11.5 Nothing selected > select #1.5 5162 atoms, 4961 bonds, 5 pseudobonds, 906 residues, 2 models selected > hide sel cartoons > select clear > save /Users/justinvanriper/Desktop/image5.png supersample 3 > hide #!1.5 models > select #3/A:1-351 2616 atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected > show sel cartoons > select clear > select add #3/A:133@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #3/A:190 12 atoms, 12 bonds, 2 residues, 1 model selected > select add #3/A:189 21 atoms, 20 bonds, 3 residues, 1 model selected > select add #3/A:206@CB 22 atoms, 20 bonds, 4 residues, 1 model selected > select subtract #3/A:189 13 atoms, 12 bonds, 3 residues, 1 model selected > select subtract #3/A:190 2 atoms, 1 bond, 2 residues, 1 model selected > select add #3/A:192 11 atoms, 9 bonds, 3 residues, 1 model selected > select add #3/A:211@CB 12 atoms, 9 bonds, 4 residues, 1 model selected > select subtract #3/A:192 3 atoms, 1 bond, 3 residues, 1 model selected > select add #3/D:7@OP1 4 atoms, 2 bonds, 4 residues, 1 model selected > select add #3/A:202 12 atoms, 9 bonds, 5 residues, 1 model selected > select subtract #3/A:202 4 atoms, 1 bond, 4 residues, 1 model selected > select add #3/A:202 12 atoms, 8 bonds, 5 residues, 1 model selected > select #3/A:202 8 atoms, 7 bonds, 1 residue, 1 model selected > view p1 > select clear > select #3/A:133,206,211,213,249,248 54 atoms, 49 bonds, 6 residues, 1 model selected > hide sel atoms > show sel atoms > select clear > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > show sel cartoons > show sel atoms > nucleotides sel fill > style nucleic & sel stick Changed 142 atom styles > nucleotides sel ladder > show sel cartoons > hide sel cartoons > show sel cartoons > select clear > save /Users/justinvanriper/Desktop/image1.png supersample 3 > view p22 > select #3/A 6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected > hide sel cartoons > hide (#!3 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!3 & sel-residues) > show (#!3 & sel-residues & backbone) target ab > hide sel atoms > select up 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected > select up 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 6 models selected > undo [Repeated 5 time(s)] > select backbone 34746 atoms, 34691 bonds, 57 pseudobonds, 8643 residues, 12 models selected > hide sel & #!3 atoms > select clear > view p22 > view p2 > view p22 > view p2 > select #3/D:7 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #3/D:7 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select clear Drag select of 4 atoms, 3 bonds, 2 shapes > select clear > select add #3/D:7@C5' 1 atom, 2 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3/D:7 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear Drag select of 3 atoms, 2 bonds, 2 shapes > hide sel atoms > undo > view p22 > view p2 > view p22 > select clear > nucleotides sel ladder [Repeated 3 time(s)] > nucleotides sel atoms > style nucleic & sel stick Changed 20 atom styles > select clear [Repeated 1 time(s)] > select #3/D:7@N1 1 atom, 1 residue, 1 model selected > select #3/D:7@C1' 1 atom, 1 residue, 1 model selected > select clear Drag select of 15 atoms, 16 bonds > hide sel atoms > view p22 > view p2 > view p1 > view p2 > view p22 > view p3 > save /Users/justinvanriper/Desktop/image1.png supersample 3 > open /Users/justinvanriper/Downloads/9ere.pdb 9ere.pdb title: SLFN11 dimer bound to TRNA-leu-taa [more info...] Chain information for 9ere.pdb #4 --- Chain | Description | UniProt A B | schlafen family member 11 | SLN11_HUMAN 1-901 T | RNA (76-mer) | U | RNA (5'-R(P*CP*CP*up*GP*GP*up*ap*CP*CP*A)-3') | Non-standard residues in 9ere.pdb #4 --- MG — magnesium ion MN — manganese (II) ion ZN — zinc ion > matchmaker #4 #2 Missing required ""to"" argument > matchmaker #4 #3 Missing required ""to"" argument > matchmaker #4 to #3 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A (#3) with 9ere.pdb, chain B (#4), sequence alignment score = 2189.5 RMSD between 442 pruned atom pairs is 1.346 angstroms; (across all 799 pairs: 3.355) > hide #4.1 models > hide #!4.2 models > select #4 14541 atoms, 14958 bonds, 32 pseudobonds, 1719 residues, 4 models selected > hide sel cartoons > hide sel atoms > select #4/A 6667 atoms, 6809 bonds, 11 pseudobonds, 829 residues, 3 models selected > show sel cartoons > select ::name=""MN"" 5 atoms, 5 residues, 2 models selected > show sel & #!4 cartoons > show sel & #!4 atoms > select clear > select #4/A:1002@MN 1 atom, 1 residue, 1 model selected > hide sel atoms > select #4/A 6667 atoms, 6809 bonds, 11 pseudobonds, 829 residues, 3 models selected > hide sel cartoons > select #4/B:135,214,216,209,252,251 54 atoms, 49 bonds, 6 residues, 1 model selected > show sel atoms > view p3 > select clear > select backbone 42034 atoms, 42022 bonds, 66 pseudobonds, 10353 residues, 14 models selected > select subtract #3/D:7@P 42033 atoms, 42018 bonds, 66 pseudobonds, 10353 residues, 14 models selected > select subtract #3/D:7@O5' 42032 atoms, 42017 bonds, 66 pseudobonds, 10353 residues, 14 models selected > select subtract #3/D:7@OP2 42031 atoms, 42017 bonds, 66 pseudobonds, 10353 residues, 14 models selected > select subtract #3/D:7@OP1 42030 atoms, 42017 bonds, 66 pseudobonds, 10353 residues, 14 models selected > hide sel & #!3-4 atoms > select clear > view p3 > show #!1.2 models > hide #!1.2 models > show #!1.3 models > hide #!1.3 models > show #!1.4 models > hide #!1.4 models > show #!1.4 models > select add #4 14541 atoms, 14958 bonds, 32 pseudobonds, 1719 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,0.50735,0.86168,0.0098541,-105.53,-0.86116,0.5074,-0.030957,188.4,-0.031675,0.0072203,0.99947,-48.483 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.51937,0.8476,0.10874,-118.71,-0.85399,0.5194,0.030262,176.55,-0.030827,-0.10858,0.99361,-26.909 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.51937,0.8476,0.10874,-119.41,-0.85399,0.5194,0.030262,176.13,-0.030827,-0.10858,0.99361,-26.965 > view matrix models > #4,0.51937,0.8476,0.10874,-119.38,-0.85399,0.5194,0.030262,176.16,-0.030827,-0.10858,0.99361,-26.984 > view p3 > select clear > hide #!1.4 models > show #!1.4 models > hide #!1.4 models > color #4 #bbbbbbff > color #3.1#!1,3-4 byhetero > undo > ui mousemode right select > select #4/B:1003@MN 1 atom, 1 residue, 1 model selected > select add #4/B:1002@MN 2 atoms, 2 residues, 1 model selected > select clear [Repeated 1 time(s)]Drag select of 68 atoms, 51 bonds > color sel byhetero > select clear > select #4/B:1003@MN 1 atom, 1 residue, 1 model selected > select add #4/B:1002@MN 2 atoms, 2 residues, 1 model selected > color sel #c3c3c3ff > select clear > view p3 > select #4/C Nothing selected > select #4/D Nothing selected > select #4/A 6667 atoms, 6809 bonds, 11 pseudobonds, 829 residues, 3 models selected > select #4/B 6668 atoms, 6809 bonds, 14 pseudobonds, 830 residues, 3 models selected > select #4/C Nothing selected > select #4/D Nothing selected > select #4/E Nothing selected > select #4/F Nothing selected > select ::name=""A""::name=""C""::name=""G""::name=""U"" 1670 atoms, 1858 bonds, 3 pseudobonds, 78 residues, 4 models selected > show sel & #!3-4 cartoons > select #4/U:77 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/U:76,77 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #4/U:76 Nothing selected > nucleotides #!3-4 atoms > style nucleic & #!3-4 stick Changed 1455 atom styles Drag select of 13 atoms, 13 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms > select add #4/U:77@C4' 1 atom, 1 bond, 1 residue, 1 model selected > select add #4/U:77@C5' 2 atoms, 1 bond, 1 residue, 1 model selected > select subtract #4/U:77@C5' 1 atom, 1 residue, 1 model selected > hide sel atoms [Repeated 2 time(s)] > select add #4/U:77@C5' 2 atoms, 2 bonds, 1 residue, 1 model selected > hide sel atoms > select #4/U:77@P 1 atom, 1 residue, 1 model selected > select clear Drag select of 20 atoms, 13 bonds > select subtract #4/B:1002@MN 19 atoms, 13 bonds, 7 residues, 2 models selected > select clear Drag select of 11 atoms, 8 bonds > color sel byhetero > select #4/U:77@P 1 atom, 1 residue, 1 model selected > color sel #cacacaff > select clear > view p3 > save /Users/justinvanriper/Desktop/image2.png supersample 3 > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session.cxs > save /Users/justinvanriper/Desktop/image3.png supersample 3 > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v2.cxs ——— End of log from Sun Mar 30 16:27:42 2025 ——— opened ChimeraX session > show #!2 models > view p21 Expected an objects specifier or a view name or a keyword > view name p1 > select clear > hide #!2 models > select #4/U:77@P 1 atom, 1 residue, 1 model selected Drag select of 6 atoms, 5 bonds > select clear Drag select of 8 atoms, 6 bonds > show sel atoms [Repeated 1 time(s)] > select clear > select #3/D:7 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #4/U:77 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!2 models > hide #!4 models > select clear Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc , 52 atoms, 45 bonds > volume zone #1 nearAtoms sel range 5 minimalBounds false > volume zone #2 nearAtoms sel range 5 minimalBounds false > volume zone #2 nearAtoms sel range 2minimalBounds false Invalid ""range"" argument: Expected a number > volume zone #2 nearAtoms sel range 2 minimalBounds false > volume zone #2 nearAtoms sel range 20 minimalBounds false > volume #2 level 0.06773 > volume #2 style mesh > volume #2 level 0.3939 > volume #2 style surface > show #!4 models > hide #!1 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > select #4/B:1002@MN 1 atom, 1 residue, 1 model selected > select add #4/B:1003@MN 2 atoms, 2 residues, 1 model selected > color sel byhetero > select clear > select #4/U:66,65 Nothing selected > select #4/U:77,78 40 atoms, 43 bonds, 2 residues, 1 model selected > show sel atoms > select #4/U:77,78,76 40 atoms, 43 bonds, 2 residues, 1 model selected > show sel atoms [Repeated 1 time(s)] > show sel cartoons > show sel atoms [Repeated 1 time(s)] > hide sel cartoons > select #4/U:77,78,76 40 atoms, 43 bonds, 2 residues, 1 model selected > show sel atoms > select #4/U:77,78,76,75 40 atoms, 43 bonds, 2 residues, 1 model selected > show sel atoms [Repeated 1 time(s)] > select #4/U:77,78,76,75,78 40 atoms, 43 bonds, 2 residues, 1 model selected > show sel cartoons > show sel atoms [Repeated 1 time(s)] > hide sel cartoons > select clear > select #4/U 83 atoms, 91 bonds, 4 residues, 1 model selected > show sel atoms > select #4/T 1123 atoms, 1249 bonds, 6 pseudobonds, 56 residues, 3 models selected > show sel atoms > hide sel atoms > select #4/T:76 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #4/U:77 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/U:78-90 63 atoms, 69 bonds, 3 residues, 1 model selected > hide sel atoms > show #!3 models > select clear > select #4/T:76 20 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > show #!2 models > select clear Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc , 104 atoms, 90 bonds > volume zone #2 nearAtoms sel range 20 minimalBounds false > volume zone #2 nearAtoms sel range 200 minimalBounds false > volume #2 level 0.0284 > volume #2 level 0.1858 > hide #!4 models > volume #2 level 0.1334 > select #3/C:7-5 Nothing selected > select #3/D:7-5 Nothing selected > select #3/D:5-7 60 atoms, 65 bonds, 3 residues, 1 model selected > show sel atoms > color sel byhetero target a > color sel orange > color sel byhetero > select clear Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc > select #2 4 models selected > select #2 4 models selected Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc > select #2 4 models selected > select #2 4 models selected > select clear > select #2 4 models selected > select #2 4 models selected > select #2 4 models selected > select #2 4 models selected > select #2 4 models selected > select #2 4 models selected > select clear > volume #2 level 0.2908 > volume #2 level 0.1184 > volume #2 level 0.3695 > open > ""/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM > Maps/State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- > sharpened-highres.mrc"" Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc as #5, grid size 300,300,300, pixel 0.832, shown at level 0.0049, step 2, values float32 > open > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited- > coot-15_real_space_refined_015.pdb Chain information for real_space_refined_036_edited- coot-15_real_space_refined_015.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > hide #!5 models > align #6 #3 Missing required ""to_atoms"" argument > matchMaker #6 #3 Unknown command: matchMaker #6 #3 > matchMaker #6 to #3 Unknown command: matchMaker #6 to #3 > matchmaker #6 to #3 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain B (#3) with real_space_refined_036_edited- coot-15_real_space_refined_015.pdb, chain B (#6), sequence alignment score = 4287.2 RMSD between 823 pruned atom pairs is 0.000 angstroms; (across all 823 pairs: 0.000) > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!5 models > fitMap #5 #2 Unknown command: fitMap #5 #2 > fitMap #5 to #2 Unknown command: fitMap #5 to #2 > fitMap #5 inMap #2 Unknown command: fitMap #5 inMap #2 > fitmap #5 inMap #2 Fit map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer- sharpened-highres.mrc in map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc using 33671 points correlation = 0.2174, correlation about mean = 0.04112, overlap = 237.1 steps = 80, shift = 0.594, angle = 1.18 degrees Position of State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#5) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#2) coordinates: Matrix rotation and translation 0.49093697 -0.86901817 -0.06154935 180.57446509 0.85839817 0.49458163 -0.13616756 -28.14054668 0.14877326 0.01401584 0.98877201 -18.53097395 Axis 0.08598408 -0.12041542 0.98899285 Axis point 115.25822066 140.21594117 0.00000000 Rotation angle (degrees) 60.84687762 Shift along axis 0.58808435 > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > select add #5 3 models selected > view matrix models > #5,0.86956,0.28743,0.40156,-77.867,-0.36997,0.91778,0.14421,37.739,-0.32709,-0.27397,0.90441,92.416 > view matrix models > #5,0.93675,0.31834,-0.14547,-14.538,-0.31142,0.94778,0.068705,36.682,0.15974,-0.019057,0.98697,-15.975 > view matrix models > #5,0.9119,0.36696,0.18378,-63.838,-0.39413,0.90789,0.14284,42.361,-0.11444,-0.20269,0.97253,46.091 > view matrix models > #5,0.83191,0.18763,0.52222,-76.207,-0.3153,0.93425,0.16662,25.403,-0.45662,-0.30327,0.83638,122.4 > view matrix models > #5,0.80642,0.251,0.53543,-83.467,-0.30673,0.95167,0.015837,42.909,-0.50558,-0.177,0.84443,110.24 > view matrix models > #5,0.58595,0.6547,0.47753,-102.55,-0.73093,0.68143,-0.037369,141.33,-0.34987,-0.32714,0.87782,106.29 > view matrix models > #5,0.55983,0.70952,0.42799,-99.825,-0.77263,0.63361,-0.039764,153.52,-0.29939,-0.30842,0.90291,93.808 > view matrix models > #5,0.56832,0.70324,0.42716,-99.932,-0.7727,0.63456,-0.016629,150.18,-0.28275,-0.32061,0.90402,93.202 > volume #5 level 0.07792 > volume #5 step 1 > transparency #6 50 > transparency #5 50 > hide #!2 models > select add #3 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 6 models selected > show sel cartoons > view matrix models > #3,0.72097,0.44589,-0.53046,47.646,-0.54116,0.84042,-0.029076,86.505,0.43284,0.30802,0.84721,-86.27,#5,0.59849,0.71718,0.35702,-96.718,-0.76798,0.64047,0.00080783,146.6,-0.22808,-0.27467,0.9341,76.454 > view matrix models > #3,0.71289,0.45635,-0.53247,47.56,-0.54968,0.83513,-0.020195,86.962,0.43547,0.30709,0.84621,-86.325,#5,0.58873,0.72613,0.35515,-96.319,-0.77632,0.63033,-0.0018491,149.32,-0.2252,-0.27462,0.93481,75.977 > view matrix models > #3,0.71287,0.45638,-0.53248,47.56,-0.5497,0.83512,-0.020173,86.963,0.43548,0.30709,0.8462,-86.325,#5,0.58871,0.72615,0.35514,-96.318,-0.77634,0.63031,-0.0018557,149.33,-0.2252,-0.27462,0.93481,75.976 > select subtract #3 3 models selected > view matrix models > #5,0.64532,0.75454,-0.11929,-46.01,-0.73531,0.65587,0.17073,118.84,0.20706,-0.022467,0.97807,-15.117 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.64532,0.75454,-0.11929,-33.098,-0.73531,0.65587,0.17073,117.84,0.20706,-0.022467,0.97807,-17.108 > view matrix models > #5,0.64532,0.75454,-0.11929,-31.521,-0.73531,0.65587,0.17073,112.2,0.20706,-0.022467,0.97807,-17.91 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.6506,0.75522,-0.079794,-37.34,-0.75574,0.65419,0.029836,133.07,0.074734,0.040893,0.99636,-11.503 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.6506,0.75522,-0.079794,-37.908,-0.75574,0.65419,0.029836,135.06,0.074734,0.040893,0.99636,-14.225 > fitmap #3 inMap #5 Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb (#3) to map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#5) using 13446 atoms average map value = 0.3504, steps = 116 shifted from previous position = 2.36 rotated from previous position = 9.54 degrees atoms outside contour = 2689, contour level = 0.077924 Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb (#3) relative to State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc (#5) coordinates: Matrix rotation and translation 0.85608006 -0.45325355 -0.24837099 110.20658380 0.30092060 0.82781164 -0.47347089 41.63304292 0.42020676 0.33058905 0.84506637 -85.76061070 Axis 0.62364205 -0.51855984 0.58494982 Axis point 0.00000000 250.94986784 -6.64552907 Rotation angle (degrees) 40.13933325 Shift along axis -3.02541784 > select clear > ui mousemode right zoom > transparency #5 90 > hide #!3 cartoons > volume #5 level 0.5427 > volume #5 level 0.2616 > volume #5 level 0.1192 > select #3/D: Expected an objects specifier or a keyword > select #3/D:5 20 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > matchmaker #2 #3 Missing required ""to"" argument > matchmaker #2 to #3 No molecules/chains to match specified > show #!2 models > hide #!2 models > show #!4 models > matchmaker #4 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A (#3) with 9ere.pdb, chain B (#4), sequence alignment score = 2189.5 RMSD between 442 pruned atom pairs is 1.346 angstroms; (across all 799 pairs: 3.355) > select clear > hide #!4 models > volume #5 level 0.1491 > show #!3 cartoons > hide #!3 cartoons > show #!3 cartoons > hide #!3 cartoons > ui mousemode right select Drag select of 72 atoms, 67 bonds, 5 State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened- highres.mrc > select clear > show #!3 cartoons > select backbone 48750 atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected > show sel & #!3 atoms > select clear > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > color sel medium violet red > hide sel atoms > show sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > color sel byhetero > select clear > volume #5 level 0.1379 > hide sel cartoons [Repeated 1 time(s)] > hide sel atoms > select clear > select #5 4 models selected > select #3/C:1@C1' 1 atom, 1 residue, 1 model selected > hide sel cartoons > select clear > select #3/C 111 atoms, 124 bonds, 5 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > hide sel atoms > select clear [Repeated 1 time(s)] > ui mousemode right zoom > volume #5 level 0.1267 > volume #5 level 0.1342 > volume #5 level 0.1491 > volume #5 level 0.1229 > volume #5 level 0.1941 > volume #5 level 0.2429 > volume #5 level 0.1267 > show #!4 models > volume #5 level 0.09292 > volume #5 level 0.2541 > size stickRadius 0.3 sidechain Expected a keyword > stickRadius 0.3 sidechain Unknown command: stickRadius 0.3 sidechain > size stickRadius 0.2 Changed 99913 bond radii > size stickRadius 0.1 Changed 99913 bond radii > size stickRadius 0.15 Changed 99913 bond radii > hide #!4 models > select #3/A:251 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A:248 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:251-252 15 atoms, 14 bonds, 2 residues, 1 model selected > select #3/A:251-254 31 atoms, 30 bonds, 4 residues, 1 model selected > select #3/A:251-255 38 atoms, 37 bonds, 5 residues, 1 model selected > select #3/A:251-256 42 atoms, 41 bonds, 6 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide sel cartoons [Repeated 1 time(s)] > ui mousemode right select > select clear > hide #!3 cartoons > select backbone 48750 atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected > hide sel & #!3 atoms > select clear > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > select #3/D backbone Expected a keyword > select #3/D, Expected an objects specifier or a keyword > select backbone & sel 84 atoms, 90 bonds, 7 residues, 1 model selected > select backbone & sel 84 atoms, 90 bonds, 7 residues, 1 model selected > show sel atoms > select clear > view name p11 > select clear > volume #5 level 0.2316 > view p11 > select backbone 48750 atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected > show sel & #!3 atoms > show sel & #!3 cartoons > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > hide sel cartoons > select clear > hide #!5 models > show #!4 models > show #!3-4 cartoons > select #4/U 83 atoms, 91 bonds, 4 residues, 1 model selected > hide sel cartoons > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > hide sel cartoons > select #4/T 1123 atoms, 1249 bonds, 6 pseudobonds, 56 residues, 3 models selected > hide sel cartoons > select #3/D:1-6 122 atoms, 134 bonds, 6 residues, 1 model selected > hide sel atoms > select clear > select #3/C:1@C1' 1 atom, 1 residue, 1 model selected > select #3/C 111 atoms, 124 bonds, 5 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #4/B:254 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/B:251 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > select clear > view p11 > select #4/B:136 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > select #4/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B:135 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > select clear [Repeated 1 time(s)] > hide #!3-4 cartoons > view p1 > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!5 models > volume #5 level 0.2277 > view p11 > select clear > ui mousemode right zoom > select #3/A 6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected > show sel cartoons > ;ect c;ear Incomplete command: sequence > select clear > select #3/A:140 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:135140 Nothing selected > select #3/A:135-140 41 atoms, 40 bonds, 6 residues, 1 model selected > hide sel cartoons > hide sel atoms > select clear > volume #5 level 0.1143 > size stickRadius 0.1 Changed 99913 bond radii > size stickRadius 0.15 Changed 99913 bond radii > size stickRadius 0.2 Changed 99913 bond radii > size stickRadius 0.17 Changed 99913 bond radii > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v3.cxs > ui tool show ""Side View"" > volume #5 level 0.1964 > volume #5 level 0.1377 > volume #5 level 0.1416 > volume #5 level 0.1534 > select #3/D:5-7 60 atoms, 65 bonds, 3 residues, 1 model selected > show sel atoms > select ~sel & ##selected 13386 atoms, 13677 bonds, 20 pseudobonds, 1657 residues, 3 models selected > select ~sel & ##selected 60 atoms, 65 bonds, 3 residues, 1 model selected > select #3/D:4-7 82 atoms, 90 bonds, 4 residues, 1 model selected > show sel atoms > select clear > volume #5 level 0.1456 > volume #5 level 0.1495 > volume #5 level 0.1143 > hide #!5 models > ui mousemode right select > select clear [Repeated 3 time(s)] > select #3/A:383 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > show #!3 atoms > hide #!3 atoms > undo [Repeated 1 time(s)] > select clear [Repeated 2 time(s)] > select #3/c 111 atoms, 124 bonds, 5 residues, 1 model selected > show sel surfaces > hide sel surfaces > hide sel cartoons > hide sel atoms > select clear > select #3/A 6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected > show sel cartoons > select clear > hide #!3 models > show #!3 models > hide #!3 atoms > select #3/A:133,206,211,213,248,249 54 atoms, 49 bonds, 6 residues, 1 model selected > show sel atoms > select clear > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > show sel atoms > select clear > show #!6 models > hide #!6 models > show #!5 models > select ::name=""MG"" 16 atoms, 16 residues, 6 models selected > show sel & #!3 atoms > select clear > volume #5 level 0.1338 > volume #5 level 0.1808 > volume #5 level 0.1064 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > select clearviewname p0402 Expected an objects specifier or a keyword > viewname p0402 Unknown command: viewname p0402 > view name p0402 > volume #5 level 0.1338 > lighting flat [Repeated 1 time(s)] > lighting full [Repeated 1 time(s)] > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting flat [Repeated 1 time(s)] > lighting full > lighting soft > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > view p0402 > select #3 13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected > color sel cornflower blue > select #3/A 6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected > color sel cornflowerblue bloue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel cornflower blue > cor sel byHetero target a Unknown command: cor sel byHetero target a > color sel byhetero target a > select clear > volume #2 level 0.3969 > volume mask #1 atomSpec sel distance 5 softEdge 2 modelId #4 Expected a keyword > select #3/D 142 atoms, 156 bonds, 7 residues, 1 model selected > volume mask #5 atomSpec sel distance 5 softEdge 2 modelId #4 Expected a keyword > volume mask #5 atomSpec sel distance 5 softEdge 2 Expected a keyword > volume zone #5 nearAtoms sel range 6 minimalBounds false > volume zone #5 nearAtoms sel range 2 > hide #!5 models > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > volume zone #5 nearAtoms sel range 2 > select #3/D & select #3/A:206,211,213, Expected a keyword > select #3/D, #3/A:206,211,213, Expected an objects specifier or a keyword > select #3/D, #3/A:206,211,213 Expected an objects specifier or a keyword > select #3/D #3/A:206,211,213 169 atoms, 180 bonds, 10 residues, 1 model selected > volume zone #5 nearAtoms sel range 2 > select #3/D #3/A:206,211,213,133 180 atoms, 190 bonds, 11 residues, 1 model selected > select #3/D #3/A:206,211,213,133.24,249 Expected a keyword > select #3/D #3/A:206,211,213,133,248,249 196 atoms, 205 bonds, 13 residues, 1 model selected > volume zone #5 nearAtoms sel range 2 > volume zone #5 nearAtoms sel range 4 > volume zone #5 nearAtoms sel range 6 > volume zone #5 nearAtoms sel range 8 > select #3/D #3/A:200-249 548 atoms, 571 bonds, 57 residues, 1 model selected > volume zone #5 nearAtoms sel range 8 > select #3/D #3/A:140-249 855 atoms, 881 bonds, 1 pseudobond, 94 residues, 2 models selected > volume zone #5 nearAtoms sel range 8 > select clear > ui tool show ""Side View"" > volume #5 level 0.1495 > save /Users/justinvanriper/Desktop/image24.png supersample 3 > save > /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v4.cxs ——— End of log from Wed Apr 2 14:23:23 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 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: MacBookPro17,1 Model Number: MYD92LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 8 days, 5 hours, 18 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Acer XF270H B: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 144.00Hz 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