id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16159 Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.9.dev202410220943 (2024-10-22 09:43:07 UTC) Description Last time you used ChimeraX it crashed. 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ChimeraX version: 1.9.dev202410220943 (2024-10-22) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/IFS/Figure3b-withextracellularparts.cxs Log from Fri Oct 18 17:00:10 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/IFS/lipid-binding-site-chicken1.cxs Opened emd_23883.map as #2, grid size 360,360,360, pixel 0.83, shown at level 0.253, step 1, values float32 Log from Thu Oct 17 16:10:12 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/oct15.cxs format session Log from Tue Oct 15 18:31:46 2024 Startup Messages --- note | available bundle cache has not been initialized yet > camera ortho > cofr centerOfView > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > mousemode rightMode clip > 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 7,0.25 > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > 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 volume unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel > minimalBounds true range 15; close #10000 > alias map_unsphere volume 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_residuesalias 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 rock_movie cofr showpivot false; movie record; rock y 30; wait 136; > movie encode ~/Desktop/rock_movie.mp4; stop > alias open_vseries ""open browse vseries true"" > alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask > #10000 spacing 1 border -0.5 > buttonpanel Shortcuts rows 3 columns 5 > 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 > radius 1"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > buttonpanel Shortcuts add reset_mouse command ""mousemode alt right contour ; > mousemode right clip ; mousemode alt left 'translate selected models' ; > mousemode shift left 'rotate selected models' ; mousemode alt control left > 'pick blobs'; help https://github.com/olibclarke/chimerax- > trimmings/blob/main/default_mousemodes.md"" > buttonpanel Shortcuts add previous_model command prevmodel > buttonpanel Shortcuts add next_model command nextmodel > runscript //Users/aysenur/chimerax_startup.py 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/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/PDB_files/7mjs-CHICKEN.pdb 7mjs-CHICKEN.pdb title: Single-particle cryo-em structure of major facilitator superfamily domain containing 2A In complex with LPC-18:3 [more info...] Chain information for 7mjs-CHICKEN.pdb #1 --- Chain | Description | UniProt H | 2AG3 fab heavy chain | L | 2AG3 fab light chain | X | major facilitator superfamily domain containing 2A | F1NCD6_CHICK 1-528 Non-standard residues in 7mjs-CHICKEN.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) ZGS — [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$L^{4}-azanyl)ethoxy]phosphoryl]oxy- propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate (lysopc(18:3(9Z,12Z,15Z))) > select ::name=""NAG"" 28 atoms, 28 bonds, 2 residues, 1 model selected > hide sel atoms > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > select /H 1018 atoms, 1045 bonds, 132 residues, 1 model selected > hide sel cartoons > select /L 863 atoms, 883 bonds, 113 residues, 1 model selected > hide sel atoms > hide sel cartoons > ui mousemode right select Drag select of 4 atoms, 3 bonds Drag select of 12 atoms, 12 bonds > hide sel atoms Drag select of 14 atoms, 23 residues, 11 bonds > hide sel atoms > select clear > alias rainbow_rosie rainbow $1 palette > #03256C:#277da1:#577590:#4d908e:#43aa8b:#90be6d:#f9c74f:#F9A64C:#F9844A:#F96347:#f94144:#9a031e Drag select of 80 atoms, 458 residues, 1 pseudobonds, 73 bonds > rainbow_rosie sel > select clear > ui mousemode right translate > select ::name=""NAG"" 28 atoms, 28 bonds, 2 residues, 1 model selected > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > hide sel atoms > ui mousemode right select Drag select of 45 atoms, 457 residues, 1 pseudobonds, 39 bonds > hide sel atoms > select clear > alias savepng $1 format png width $2 transparentBackground true > Missing or invalid first argument: Expected a text string Drag select of 458 residues, 1 pseudobonds > Missing or invalid second argument: Expected a text string > select savepng Expected an objects specifier or a keyword > Missing or invalid second argument: Expected a text string > select clear > Missing or invalid second argument: Expected a text string > Missing or invalid second argument: Expected a text string > Missing or invalid second argument: Expected a text string Drag select of 408 residues Drag select of 458 residues, 1 pseudobonds > select up 3620 atoms, 3720 bonds, 1 pseudobond, 460 residues, 2 models selected > select up 3655 atoms, 3754 bonds, 1 pseudobond, 461 residues, 2 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > savepng sel 3 > select format png width 3 transparentBackground true Expected an objects specifier or a keyword > select clear > save image my_structure.png supersample 2 dpi 300 Cannot determine format for 'image' > save /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/oct15.cxs ——— End of log from Tue Oct 15 18:31:46 2024 ——— opened ChimeraX session > lighting soft > lighting multiShadow 512 > lighting default > save /Users/aysenur/Desktop/chickenrainbowrosieribbon.png format png width > 2048 transparentBackground true > open /Users/aysenur/Documents/PostDoc-Files/Manuscripts/MFSD2A_Review/Files- > from-pdb/emd_23883.map Opened emd_23883.map as #2, grid size 360,360,360, pixel 0.83, shown at level 0.0536, step 1, values float32 > volume #2 level 0.1896 > volume #2 level 0.2427 > fitmap #1 inMap #2 Fit molecule 7mjs-CHICKEN.pdb (#1) to map emd_23883.map (#2) using 5536 atoms average map value = 0.3382, steps = 40 shifted from previous position = 0.00806 rotated from previous position = 0.00889 degrees atoms outside contour = 2106, contour level = 0.24267 Position of 7mjs-CHICKEN.pdb (#1) relative to emd_23883.map (#2) coordinates: Matrix rotation and translation 0.99999999 0.00014185 -0.00006257 -0.01095348 -0.00014185 0.99999999 -0.00000699 0.02299878 0.00006257 0.00000700 1.00000000 -0.01831794 Axis 0.04506116 -0.40314712 -0.91402511 Axis point 181.95656038 79.44962357 0.00000000 Rotation angle (degrees) 0.00889202 Shift along axis 0.00697759 > volume zone #2 nearAtoms #1/A range 2.5 no atoms specified for zone > surface zone #2 nearAtoms #1/A distance 2.5 maxComponents 7 No atoms specified > ui mousemode right translate > select add #2 2 models selected > select /H 1018 atoms, 1045 bonds, 132 residues, 1 model selected > select add #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > select add #2 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 4 models selected > select subtract #1 2 models selected > volume #2 level 0.2526 > select up 5536 atoms, 5682 bonds, 706 residues, 3 models selected > volume zone #2 nearAtoms #1/A range 2.5 no atoms specified for zone > volume zone #2 nearAtoms #1 range 2.5 > surface zone #2 nearAtoms #1 distance 2.5 maxComponents 7 > surface zone #2 nearAtoms #1 distance 3 maxComponents 7 > surface zone #2 nearAtoms #1 distance 4 maxComponents 7 > surface zone #2 nearAtoms #1 distance 2.5 maxComponents 7 > volume zone #2 nearAtoms #1 range 2.5 > ui mousemode right select > select clear Drag select of 2 emd_23883.map [Repeated 1 time(s)] > select clear > volume zone #2 nearAtoms #1/X range 2.5 [Repeated 1 time(s)] > surface zone #2 nearAtoms #1/X distance 2.5 maxComponents 7 > volume zone #2 nearAtoms #1/X range 2.5 > coulombic protein surfaces #2 key true The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /X :36 CD1 /X :36 CD2 /X :36 CG /X :280 OG Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for surface #2.1: minimum, -3723.30, mean -3.95, maximum 4878.84 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > key border false > ui mousemode right select > ui mousemode right translate > transparency #2 40 > transparency #2 30 > transparency #2 10 > transparency #2 50 > transparency #2 30 > turn y 180 [Repeated 1 time(s)] > save /Users/aysenur/Desktop/chickenelectrostatic.png format png width 2048 > transparentBackground true > turn y 180 > hide #3 models > save /Users/aysenur/Desktop/chickenelectrostatic180y.png format png width > 2048 transparentBackground true > turn y 180 > volume zone #2 nearAtoms #1/X:36-277 range 2.5 > select #1/X:36-277 1810 atoms, 1861 bonds, 232 residues, 1 model selected > select #1/X:278-511 1782 atoms, 1828 bonds, 226 residues, 1 model selected > cartoon hide sel > transparency #2 0 > transparency #2 70 > transparency #2 40 > transparency #2 600 > transparency #2 60 > transparency #2 55 > transparency #2 15 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > transparency #2 45 [Repeated 1 time(s)] > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume zone #2 nearAtoms #1/X range 2.5 > select up 1811 atoms, 1856 bonds, 229 residues, 1 model selected > select ~sel & ##selected 3725 atoms, 3826 bonds, 477 residues, 1 model selected > transparency #2 20 > select add #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > select subtract #1 Nothing selected > hide #!2 models > select #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > cartoon (#!1 & sel) > show #!2 models > select subtract #1 Nothing selected > select /H 1018 atoms, 1045 bonds, 132 residues, 1 model selected > cartoon hide sel > select /L 863 atoms, 883 bonds, 113 residues, 1 model selected > cartoon hide sel > hide #!2 models > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > surface sel > show (#!1 & sel) target ab > surface style #1 mesh > surface style #1 dot > select add #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 3 models selected > show #!2 models > hide #!2 models > select #1:ZGS 35 atoms, 34 bonds, 1 residue, 1 model selected > surface hidePatches (#!1 & sel) > size #1 stickRadius 0.3 Changed 5682 bond radii > select add #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 3 models selected > select subtract #1 1 model selected > alias TM5 #1:170-211 > alias TM8 #1:324-354 > select #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > cartoon hide (#!1 & sel) > select TM1 Expected an objects specifier or a keyword > cartoon (#!1 & sel) > select TM1 Expected an objects specifier or a keyword > select TM5 Expected an objects specifier or a keyword > select #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > cartoon hide (#!1 & sel) > ribbon #1:170-211 > ribbon #1:324-354 > ribbon #1:212-279 > ribbon #1:212-279 transparency 60 > cartoon #1:212-279 transparency 60 Expected a keyword > select #1:212-279 420 atoms, 426 bonds, 56 residues, 1 model selected > select transparency 60 Expected an objects specifier or a keyword > transparency #1:212-279 60 > transparency #1:212-279 90 > select add #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > transparency #1:212-279 0 > transparency #1:212-279 80 target r > transparency #1:212-279 90 target r > transparency #1:280-323 90 target r > ribbon #1:280-323 > ribbon #1:355-511 > transparency #1:355-511 90 target r > ribbon #1:36-169 > transparency #1:36-169 90 target r > show #!2 models > select ~sel & ##selected Nothing selected > transparency #2 90 > transparency #2 80 > transparency #2 95 > ui mousemode right select > select #2 2 models selected > select #2 2 models selected > select subtract #2 Nothing selected > select add #1 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 2 models selected > select subtract #1 1 model selected > select #2 2 models selected > select #2 2 models selected > select subtract #2 Nothing selected > hide #!2 models > select /X:338 8 atoms, 7 bonds, 1 residue, 1 model selected > select /X:349 14 atoms, 15 bonds, 1 residue, 1 model selected > select /X:179 5 atoms, 4 bonds, 1 residue, 1 model selected > select /X:183 7 atoms, 6 bonds, 1 residue, 1 model selected > select /X:345 7 atoms, 7 bonds, 1 residue, 1 model selected > select /X:179 5 atoms, 4 bonds, 1 residue, 1 model selected > atoms #1:186,182 Unknown command: atoms #1:186,182 > atom #1:186,182 Unknown command: atom #1:186,182 > select #1:186,182 15 atoms, 13 bonds, 2 residues, 1 model selected > show sel target ab > ui mousemode right select > select clear > select /L 863 atoms, 883 bonds, 113 residues, 1 model selected > cartoon hide sel > select /L 863 atoms, 883 bonds, 113 residues, 1 model selected > cartoon hide sel > select /H 1018 atoms, 1045 bonds, 132 residues, 1 model selected > cartoon hide sel > alias select_lipid_binding_residues select > #1:186,182,311,315,391,395,399,344,400,348,403,336,337 > select_lipid_binding_residues 112 atoms, 105 bonds, 13 residues, 1 model selected > show sel ab Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show sel > ui mousemode right label > label #1/X:311 > label #1/X:315 > label #1/X:395 > label #1/X:389 > hide #1:389 > label #1/X:390 > select up 1021 atoms, 1043 bonds, 130 residues, 1 model selected > select down 112 atoms, 105 bonds, 13 residues, 1 model selected > alias select_TM4 select #1:135-169 > select_TM4 299 atoms, 308 bonds, 36 residues, 1 model selected > transparency sel 90 target r > transparency sel 0 target r > transparency sel 90 target r > alias select_TM10 select #378-420 > select_TM10 Nothing selected > alias select_TM10 select #1:378-420 > select_TM10 325 atoms, 333 bonds, 43 residues, 1 model selected > transparency sel 0 target r > label #1/X:315 > alias select_TM7 select #1:280-323 > select_TM7 352 atoms, 361 bonds, 44 residues, 1 model selected > transparency sel 0 target r > ui mousemode right select > select clear > ui mousemode right translate > select_lipid_binding_residues 112 atoms, 105 bonds, 13 residues, 1 model selected > color sel pink > color sel red > color sel black > color sel salmon > color sel purple > color sel salmon > ui tool show ""Color Actions"" > color sel orchid > color sel violet > color sel pale violet red > color sel purple > color sel medium orchid > color sel orchid > color sel hot pink > color sel blue violet > color sel deep pink > color sel magenta > color sel thistle > color sel sky blue > color sel navy > color sel slate gray > color sel dark olive green > color sel pink > color sel violet > color sel plum > color sel light coral > color sel saddle brown > color sel pale violet red > color sel purple > color sel dark magenta > color sel dark orchid > color sel medium orchid > color sel orchid > color sel hot pink > ui mousemode right select > select clear > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > style sel stick ringFill thick Changed 35 atom styles, 1 residue ring style > select clear > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > style sel sphere ringFill thin Changed 35 atom styles, 1 residue ring style > style sel stick ringFill thick Changed 35 atom styles, 1 residue ring style > style sel stick ringFill thin Changed 35 atom styles, 1 residue ring style > size sel stickRadius 1 Changed 34 bond radii > size sel stickRadius 0.5 Changed 34 bond radii > size sel stickRadius 0.8 Changed 34 bond radii > size sel stickRadius 0.45 Changed 34 bond radii > size sel stickRadius 0.65 Changed 34 bond radii > select clear > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > size sel stickRadius 0.4 Changed 34 bond radii > select clear > ui mousemode right translate > save /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/IFS/chicken-lipid-site1.png format > png width 2048 transparentBackground true > ui mousemode right label > label #1/X:186 > label #1/X:182 > label #1/X:403 > label #1/X:344 > label #1 text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > undo > ~label (#!1 & sel) residues [Repeated 2 time(s)] > select /X 3655 atoms, 3754 bonds, 1 pseudobond, 461 residues, 2 models selected > ~label (#!1 & sel) residues > ui mousemode right label > label #1/X:182 > label #1/X:186 > label #1/X:344 > label #1/X:403 [Repeated 1 time(s)] > label #1/X:337 > save /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/lipid-binding-site-chicken1.cxs ——— End of log from Thu Oct 17 16:10:12 2024 ——— opened ChimeraX session > ui mousemode right select > select clear > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #3 models > hide #3 models > hide #!2 models > show #!2 target m > hide #!1 target m > show #!1 target m > hide #!2 target m > show #!2 target m > hide #!1 target m > show #!1 target m > hide #!2 target m > show #!2 target m > hide #!1 target m > show #!1 target m > hide #!2 target m > alias select_Ndom select #1/X:36-279 > alias select_Cdom select #1/X:280-504 > select_Ndom 1810 atoms, 1861 bonds, 232 residues, 1 model selected > ui tool show ""Color Actions"" > color sel steel blue > show sel ribbons transparency 0 Expected ',' or a keyword > show sel transparency 0 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > transparency sel 0 > transparency sel 0 r Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency sel 0 cartoons > ui mousemode right translate > select_Cdom 1777 atoms, 1823 bonds, 225 residues, 1 model selected > color sel sandy brown > transparency sel 0 cartoons > alias select_disulfide select #1/X:207,460 > select_disulfide 12 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > close #2 > close #3 > hide #1.3 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.2 models > show #1.2 models > ui tool show ""Color Actions"" > color sel orchid > color sel medium orchid > color sel orchid > color sel byhetero > ui mousemode right select > select clear > alias select_Ngly select #1/X:207,460 > select_Ngly 12 atoms, 11 bonds, 2 residues, 1 model selected > alias select_Ngly select #1/X:218,227 > select_Ngly 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > show sel target ab > select ::name=""NAG"" 28 atoms, 28 bonds, 2 residues, 1 model selected > show sel target ab > color sel dark orchid > color sel orchid > color sel medium orchid > color sel orchid > color sel byhetero > select clear > select disulfide 6 atoms, 3 bonds, 6 residues, 1 model selected > select clear > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > cartoon hide (#!1 & sel) > select ::name=""ZGS"" 35 atoms, 34 bonds, 1 residue, 1 model selected > cartoon hide (#!1 & sel) > hide (#!1 & sel) target a > graphics silhouettes true > ui mousemode right select Drag select of 73 atoms, 414 residues, 1 pseudobonds, 64 bonds > hide (#!1 & sel) target a > select clear > save /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/IFS/7mjs-twocolor-version.png format > png width 2048 transparentBackground true > select_disulfide 12 atoms, 11 bonds, 2 residues, 1 model selected > select /X 3655 atoms, 3754 bonds, 1 pseudobond, 461 residues, 2 models selected > cartoon hide (#!1 & sel) > hide (#!1 & sel) target a > select_disulfide 12 atoms, 11 bonds, 2 residues, 1 model selected > show sel target ab > cartoon sel > ui mousemode right translate > ui mousemode right rotate > ui mousemode right translate > color sel byhetero > color sel byelement > color sel byhetero > surface sel > surface hidePatches (#!1 & sel) > select disulfide 6 atoms, 3 bonds, 6 residues, 1 model selected > hide (#!1 & sel) target a > select_disulfide 12 atoms, 11 bonds, 2 residues, 1 model selected > show (#!1 & sel) target ab > color (#!1 & sel) byhetero > ui mousemode right select Drag select of 6 atoms, 2 residues, 5 bonds > show (#!1 & sel) target ab Drag select of 6 atoms, 2 residues, 5 bonds > show (#!1 & sel) target ab Drag select of 6 atoms, 2 residues, 5 bonds > show (#!1 & sel) target ab > select ~sel & ##selected 5524 atoms, 5671 bonds, 1 pseudobond, 704 residues, 2 models selected > select up 5528 atoms, 5671 bonds, 1 pseudobond, 706 residues, 4 models selected > select clear > select /X:207@CB 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 2 models selected > select up 14 atoms, 13 bonds, 2 residues, 2 models selected > select up 3620 atoms, 3720 bonds, 460 residues, 2 models selected > select up 3655 atoms, 3754 bonds, 461 residues, 2 models selected > select up 5536 atoms, 5682 bonds, 706 residues, 3 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 5 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 5 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 5 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 5 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 5 models selected > select up 5536 atoms, 5682 bonds, 1 pseudobond, 706 residues, 5 models selected > show (#!1 & sel) target ab > cartoon (#!1 & sel) > hide (#!1 & sel) target a > view orient > select /H 1018 atoms, 1045 bonds, 132 residues, 1 model selected > cartoon hide sel > select /L 863 atoms, 883 bonds, 113 residues, 1 model selected > cartoon hide sel > select_disulfide 12 atoms, 11 bonds, 2 residues, 1 model selected > show (#!1 & sel) target ab > color sel orchid > color (#!1 & sel) byhetero > select_Ngly 16 atoms, 14 bonds, 2 residues, 1 model selected > show (#!1 & sel) target ab > select ::name=""NAG"" 28 atoms, 28 bonds, 2 residues, 1 model selected > show sel target ab > save /Users/aysenur/Documents/PostDoc- > Files/Manuscripts/MFSD2A_Review/Figures/IFS/Figure3b-withextracellularparts.cxs ——— End of log from Fri Oct 18 17:00:10 2024 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-22.5.11 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. 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 Air Model Identifier: MacBookAir9,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.1 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 2 hours, 59 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a51 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.4.0 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: 2.15 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.7 ChimeraX-AtomicLibrary: 14.1.8 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.3.4 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.dev202410220943 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: 1.2.5 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: 1.4.1 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 ChimeraX-Label: 1.1.11 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: 2.7.1 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: 1.5.17 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-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 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: 3.2.1 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: 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scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 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: 6.4.1 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 Graphics nonchimerax all ChimeraX