id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15836 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. 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}, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x14D732944)"" ] } ===== Log before crash start ===== > camera ortho > cofr centerOfView > mousemode rightMode zoom > mousemode alt rightMode ""contour level"" > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias open_vseries ""open browse vseries true"" > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/raop/Documents/Presentations/Postdoc RIP/Year > 1/images/brownpgd2_newchirality2.cxs"" format session Opened TM_focused map_sharpen.mrc as #2, grid size 392,392,392, pixel 0.808, shown at level 0.33, step 1, values float32 Opened TM-focused-3.32A-sharp.mrc as #1, grid size 392,392,392, pixel 0.808, shown at level 0.333, step 1, values float32 Opened TM-focused-3.70A-Class1-sharp.mrc as #3, grid size 392,392,392, pixel 0.808, shown at level 0.355, step 1, values float32 Opened TM-focused-3.72A-Class2-sharp.mrc as #4, grid size 392,392,392, pixel 0.808, shown at level 0.483, step 1, values float32 Opened TM_focused map_sharpen.mrc gaussian as #6, grid size 392,392,392, pixel 0.808, shown at level 0.197, step 1, values float32 Opened TM-focused-3.32A-sharp.mrc gaussian as #7, grid size 392,392,392, pixel 0.808, shown at level 0.183, step 1, values float32 Opened volume difference.mrc as #8, grid size 392,392,392, pixel 0.808, shown at level 0.125, step 1, values float32 Opened volume difference.mrc as #10, grid size 392,392,392, pixel 0.808, shown at level 0.126, step 1, values float32 opened ChimeraX session > close session > open /Users/raop/Documents/Manuscripts/PGD2/images/PGD2_molecule_fit.pdb > format pdb > close session > open > /Users/raop/Documents/Manuscripts/PGD2/images/lipiddensity_overlay_PGD2_PS_fit3.cxs > format session Opened A2AR_zm_pgd2_class2.mrc as #2, grid size 392,392,392, pixel 0.808, shown at level 0.383, step 1, values float32 Opened A2AR_zm.mrc as #3, grid size 392,392,392, pixel 0.808, shown at level 0.798, step 1, values float32 Opened TM-focused-3.32A-sharp.mrc as #5, grid size 392,392,392, pixel 0.808, shown at level 0.445, step 1, values float32 Opened A2AR_zm_pgd2_TMfocused.mrc as #9, grid size 392,392,392, pixel 0.808, shown at level 0.391, step 1, values float32 Opened emd_4390.map as #13, grid size 150,150,150, pixel 1.07, shown at level 0.0605, step 1, values float32 opened ChimeraX session > show #8 models > close session > open ""/Users/raop/Documents/Presentations/Postdoc RIP/Year > 1/images/brownpgd2_newchirality2.cxs"" format session Opened TM_focused map_sharpen.mrc as #2, grid size 392,392,392, pixel 0.808, shown at level 0.33, step 1, values float32 Opened TM-focused-3.32A-sharp.mrc as #1, grid size 392,392,392, pixel 0.808, shown at level 0.333, step 1, values float32 Opened TM-focused-3.70A-Class1-sharp.mrc as #3, grid size 392,392,392, pixel 0.808, shown at level 0.355, step 1, values float32 Opened TM-focused-3.72A-Class2-sharp.mrc as #4, grid size 392,392,392, pixel 0.808, shown at level 0.483, step 1, values float32 Opened TM_focused map_sharpen.mrc gaussian as #6, grid size 392,392,392, pixel 0.808, shown at level 0.197, step 1, values float32 Opened TM-focused-3.32A-sharp.mrc gaussian as #7, grid size 392,392,392, pixel 0.808, shown at level 0.183, step 1, values float32 Opened volume difference.mrc as #8, grid size 392,392,392, pixel 0.808, shown at level 0.125, step 1, values float32 Opened volume difference.mrc as #10, grid size 392,392,392, pixel 0.808, shown at level 0.126, step 1, values float32 opened ChimeraX session > color #8 #ffd70034 models > color #9 gold > select add #9 54 atoms, 54 bonds, 1 residue, 1 model selected > color sel byhetero > hide #!8 models > select clear > hide #!5 models > show #!5 models > hide #!5 models > ui tool show ""Side View"" > show #!5 models > select add #9/A:1@H201 1 atom, 1 residue, 1 model selected > select add #9/A:1@H203 2 atoms, 1 residue, 1 model selected > select add #9/A:1@H191 3 atoms, 1 residue, 1 model selected > select add #9/A:1@H192 4 atoms, 1 residue, 1 model selected > select add #9/A:1@H181 5 atoms, 1 residue, 1 model selected > select add #5/A:77 11 atoms, 5 bonds, 2 residues, 2 models selected > select subtract #5/A:77 5 atoms, 1 residue, 1 model selected > select add #9/A:1@H171 6 atoms, 1 residue, 1 model selected > select add #9/A:1@H172 7 atoms, 1 residue, 1 model selected > select add #9/A:1@H161 8 atoms, 1 residue, 1 model selected > select add #9/A:1@H15 9 atoms, 1 residue, 1 model selected > select add #9/A:1@H14 10 atoms, 1 residue, 1 model selected > select add #9/A:1@H13 11 atoms, 1 residue, 1 model selected > select add #9/A:1@H12 12 atoms, 1 residue, 1 model selected > select add #9/A:1@H101 13 atoms, 1 residue, 1 model selected > select add #9/A:1@H102 14 atoms, 1 residue, 1 model selected > select add #14/A:1@HO3 15 atoms, 2 residues, 2 models selected > select add #9/A:1@H8 16 atoms, 2 residues, 2 models selected > select add #9/A:1@H71 17 atoms, 2 residues, 2 models selected > hide sel atoms > select add #9/A:1@H6 18 atoms, 2 residues, 2 models selected > select add #9/A:1@H5 19 atoms, 2 residues, 2 models selected > select add #9/A:1@H41 20 atoms, 2 residues, 2 models selected > select add #9/A:1@H42 21 atoms, 2 residues, 2 models selected > select add #9/A:1@H31 22 atoms, 2 residues, 2 models selected > select add #9/A:1@H32 23 atoms, 2 residues, 2 models selected > select add #9/A:1@H21 24 atoms, 2 residues, 2 models selected > select add #9/A:1@HO1 25 atoms, 2 residues, 2 models selected > hide sel atoms > select add #9/A:1@H202 26 atoms, 2 residues, 2 models selected > select add #9/A:1@H162 27 atoms, 2 residues, 2 models selected > select add #9/A:1@H182 28 atoms, 2 residues, 2 models selected > select add #9/A:1@HO5 29 atoms, 2 residues, 2 models selected > hide sel atoms > select add #9/A:1@H72 30 atoms, 2 residues, 2 models selected > select add #9/A:1@H22 31 atoms, 2 residues, 2 models selected > hide sel atoms > color #14 gold > select add #14 33 atoms, 2 bonds, 2 residues, 2 models selected > color sel byhetero > select clear > select add #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select add #5/A:75 19 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select add #5/A:163@NE2 1 atom, 1 residue, 1 model selected > select add #9/A:1@O4 2 atoms, 2 residues, 2 models selected > ui tool show Distances > show #!12 models > select add #9/A:1@O1 3 atoms, 2 residues, 2 models selected > select add #5/A:75@NE2 4 atoms, 3 residues, 2 models selected Exactly two atoms must be selected! > select #9/A:1@O1 1 atom, 1 residue, 1 model selected > select add #5/A:75@NE2 2 atoms, 2 residues, 2 models selected > distance #9/A:1@O1 #5/A:75@NE2 Distance between PGD2_updatedpos2.pdb #9/A PG2 1 O1 and Calico01-model.pdb #5/A HIS 75 NE2: 4.291Å > distance style decimalPlaces 2 > distance style decimalPlaces 1 > distance style color #ffd500 > distance style color #ffc600 > distance style color #ff9900 > distance style color #ff6900 > distance style color #ff5600 > distance style color #ff4b00 > distance style color #ff4400 > distance style color #ff4300 > distance style color #ff4200 > distance style color #ff4100 > distance style color #ff3f00 > distance style color #ff3e00 > distance style color #ff3d00 > distance style color #ff3e00 > distance style color #ff3f00 > distance style color #ff4700 > distance style color #ff4b00 > distance style color #ff5200 > distance style color #ff5600 > distance style color #ff5700 > distance style color #ff5900 > distance style color #ff5d00 > distance style color #ff6300 > distance style color #ff7600 > distance style color #ff8100 > distance style color #ff8200 > distance style color #ff8202 > distance style color #ff820a > distance style color #ff820f > distance style color #ff821d > distance style color #ff8240 > distance style color #ff8267 > distance style color #ff8281 > distance style color #ff8293 > distance style color #ff8297 > distance style color #ff82a1 > distance style color #ff82a3 > distance style color #ff82a6 > distance style color #ff82af > distance style color #ff82b3 > distance style color #ff82b4 > distance style color #ff82b8 > distance style color #ff82bd > distance style color #ff82c0 > distance style color #ff82c1 > distance style color #ff82c2 > distance style color #ff82c4 > distance style color #ff82c5 > distance style color #ff82c6 > distance style color #ff82c7 > distance style color #ff82c8 > distance style color #ff82c9 > distance style color #ff82ca > distance style color #ff82cb > distance style color #ff82cf > distance style color #ff82d0 > distance style color #ff82d2 > distance style color #ff82d5 > distance style color #ff82da > distance style color #ff82db > distance style color #ff82de > select clear > select #5/A:75@ND1 1 atom, 1 residue, 1 model selected > select add #9/A:1@O1 2 atoms, 2 residues, 2 models selected > distance #5/A:75@ND1 #9/A:1@O1 Distance between Calico01-model.pdb #5/A HIS 75 ND1 and PGD2_updatedpos2.pdb #9/A PG2 1 O1: 3.8Å > undo > hide #!12 models > show #!12 models > ~distance #9/A:1@O1 #5/A:75@NE2 > ~distance #5/A:75@ND1 #9/A:1@O1 > ~distance #13/A:1@O3 #5/A:163@NE2 > select #9/A:1@O1 1 atom, 1 residue, 1 model selected > select add #5/A:75@ND1 2 atoms, 2 residues, 2 models selected > distance #9/A:1@O1 #5/A:75@ND1 Distance between PGD2_updatedpos2.pdb #9/A PG2 1 O1 and Calico01-model.pdb #5/A HIS 75 ND1: 3.8Å > distance style color gold > distance style decimalPlaces 3 > ~distance #9/A:1@O1 #5/A:75@ND1 > ~distance #9/A:1@O4 #5/A:163@NE2 > select #9/A:1@O4 1 atom, 1 residue, 1 model selected > select add #5/A:163@NE2 2 atoms, 2 residues, 2 models selected > distance #9/A:1@O4 #5/A:163@NE2 Distance between PGD2_updatedpos2.pdb #9/A PG2 1 O4 and Calico01-model.pdb #5/A GLN 163 NE2: 3.541Å > select #9/A:1@O1 1 atom, 1 residue, 1 model selected > select add #5/A:75@ND1 2 atoms, 2 residues, 2 models selected > select #5/A:75@ND1 1 atom, 1 residue, 1 model selected > select #5/A:75@ND1 1 atom, 1 residue, 1 model selected > select #5/A:75@ND1 1 atom, 1 residue, 1 model selected > select #5/A:75@ND1 1 atom, 1 residue, 1 model selected > select #9/A:1@O1 1 atom, 1 residue, 1 model selected > select add #5/A:75@ND1 2 atoms, 2 residues, 2 models selected > distance #9/A:1@O1 #5/A:75@ND1 Distance between PGD2_updatedpos2.pdb #9/A PG2 1 O1 and Calico01-model.pdb #5/A HIS 75 ND1: 3.796Å > show #!10 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!5 models > show #!5 models > show #!8 models > volume #8 level 0.06638 > ui tool show ""Fit in Map"" > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.02392, steps = 72 shifted from previous position = 2.63 rotated from previous position = 0.499 degrees atoms outside contour = 1416, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985151 -0.01355130 -0.01064526 2.94801584 0.01348797 0.99989104 -0.00599791 -0.75773938 0.01072538 0.00585344 0.99992535 -4.83221537 Axis 0.32517945 -0.58637093 0.74190799 Axis point 153.20977798 268.22837495 0.00000000 Rotation angle (degrees) 1.04414696 Shift along axis -2.18210865 > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.02391, steps = 44 shifted from previous position = 0.00273 rotated from previous position = 0.0197 degrees atoms outside contour = 1414, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985477 -0.01347105 -0.01043853 2.89689705 0.01341171 0.99989362 -0.00573426 -0.79411785 0.01051467 0.00559343 0.99992908 -4.76072519 Axis 0.31538452 -0.58337734 0.74846743 Axis point 156.40983342 264.54657743 0.00000000 Rotation angle (degrees) 1.02900361 Shift along axis -2.18634089 > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.02395, steps = 48 shifted from previous position = 0.0152 rotated from previous position = 0.00725 degrees atoms outside contour = 1416, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985298 -0.01351114 -0.01055824 2.92521403 0.01345104 0.99989304 -0.00574310 -0.79976670 0.01063470 0.00560023 0.99992777 -4.76543876 Axis 0.31403167 -0.58671070 0.74642794 Axis point 156.18401484 265.22206990 0.00000000 Rotation angle (degrees) 1.03486429 Shift along axis -2.16921510 > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.02394, steps = 40 shifted from previous position = 0.00213 rotated from previous position = 0.00624 degrees atoms outside contour = 1415, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985355 -0.01347741 -0.01054694 2.91769277 0.01341628 0.99989291 -0.00584574 -0.77496926 0.01062460 0.00570338 0.99992729 -4.78225696 Axis 0.31971452 -0.58609235 0.74449875 Axis point 154.83276859 266.36202248 0.00000000 Rotation angle (degrees) 1.03490996 Shift along axis -2.17335202 > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.0239, steps = 48 shifted from previous position = 0.0151 rotated from previous position = 0.0128 degrees atoms outside contour = 1414, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985523 -0.01344120 -0.01043334 2.89085222 0.01338270 0.99989444 -0.00565708 -0.80361384 0.01050827 0.00551664 0.99992957 -4.74957292 Axis 0.31195874 -0.58466813 0.74889580 Axis point 157.60219585 264.09445089 0.00000000 Rotation angle (degrees) 1.02616323 Shift along axis -2.18526120 > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.02395, steps = 48 shifted from previous position = 0.019 rotated from previous position = 0.026 degrees atoms outside contour = 1415, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985295 -0.01348174 -0.01059854 2.92806657 0.01341784 0.99989150 -0.00607813 -0.73247429 0.01067933 0.00593503 0.99992536 -4.82358711 Axis 0.33056978 -0.58550965 0.74020408 Axis point 151.61368164 268.83094387 0.00000000 Rotation angle (degrees) 1.04114345 Shift along axis -2.17363776 > fitmap #5 inMap #8 Fit molecule Calico01-model.pdb (#5) to map volume difference.mrc (#8) using 2104 atoms average map value = 0.02396, steps = 48 shifted from previous position = 0.0047 rotated from previous position = 0.0244 degrees atoms outside contour = 1419, contour level = 0.066384 Position of Calico01-model.pdb (#5) relative to volume difference.mrc (#8) coordinates: Matrix rotation and translation 0.99985089 -0.01358992 -0.01065409 2.95638996 0.01353006 0.99989238 -0.00567077 -0.82595391 0.01073001 0.00552577 0.99992716 -4.76221735 Axis 0.30839235 -0.58899427 0.74698053 Axis point 157.14154113 264.81398071 0.00000000 Rotation angle (degrees) 1.04015128 Shift along axis -2.15907347 > volume #8 level 0.1652 > volume #8 level 0.1423 > hide #!10 models > hide #!8 models > ~distance #9/A:1@O1 #5/A:75@ND1 > ~distance #9/A:1@O4 #5/A:163@NE2 > distance #9/A:1@O1 #5/A:75@ND1 Distance between PGD2_updatedpos2.pdb #9/A PG2 1 O1 and Calico01-model.pdb #5/A HIS 75 ND1: 3.789Å > select #9/A:1@O4 1 atom, 1 residue, 1 model selected > select add #5/A:163@NE2 2 atoms, 2 residues, 2 models selected > distance #9/A:1@O4 #5/A:163@NE2 Distance between PGD2_updatedpos2.pdb #9/A PG2 1 O4 and Calico01-model.pdb #5/A GLN 163 NE2: 3.224Å > distance style decimalPlaces 2 > distance style decimalPlaces 1 > distance style color #ffd702 > distance style color #ffd715 > distance style color #ffd784 > distance style color #ffd7ab > distance style color #ffd7b9 > distance style color #ffd7bf > distance style color #ffd7c5 > distance style color #ffd7cc > distance style color #ffd7dc > distance style color #ffd7dd > distance style color #ffd7de > distance style color #ffd7df > distance style color #ffd7e0 > distance style color #ffd7e1 > distance style color #ffd7e2 > distance style color #ffd7e4 > distance style color #ffd7e6 > distance style color #ffd7e7 > distance style color #ffd7e8 > distance style color #ffd6e8 > distance style color #ffd2e8 > distance style color #ffbae8 > distance style color #fface8 > distance style color #ffa7e8 > distance style color #ff9ce8 > distance style color #ff9be8 > distance style color #ff9ae8 > distance style color #ff95e8 > distance style color #ff92e8 > distance style color #ff90e8 > distance style color #ff8fe8 > distance style color #ff8ee8 > distance style color #ff8de8 > distance style color #ff8ce8 > distance style color #ff8be8 > distance style color #ff8ae8 > distance style color #ff88e8 > distance style color #ff87e8 > distance style color #ff85e8 > distance style color #ff84e8 > select clear > distance style symbol false > distance style symbol true > hide #12.1 models > show #12.1 models > hide #12.1 models ===== Log before crash end ===== Log: > camera ortho > cofr centerOfView > mousemode rightMode zoom > mousemode alt rightMode ""contour level"" > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias open_vseries ""open browse vseries true"" > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,10 Model Number: Z1740017JLL/A Chip: Unknown Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 6 days, 14 hours, 59 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX