id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7393 Pseudobond drawing: Cylinder end point, radii or rotation array not contiguous chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.2.1-arm64-arm-64bit ChimeraX Version: 1.5.dev202208030611 (2022-08-03 06:11:58 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7aue format pdb fromDatabase pdb 7aue title: Melanocortin receptor 4 (MC4R) GS protein complex [more info...] Chain information for 7aue #1 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN B | transducin β chain 1 | GBB1_HUMAN C | aminoserine | G | G γ-I | GBG2_HUMAN R | MC4-R | MC4R_HUMAN S | SCFV16 | Non-standard residues in 7aue #1 --- ACY — acetic acid CA — calcium ion DAL — D-alanine DPN — D-phenylalanine NH2 — amino group Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > select ~protein 2 atoms, 1 pseudobond, 2 residues, 2 models selected > info selection atom id /R:501@CA idatm_type Ca atom id /C:101@O idatm_type O3 > info residues sel residue id /R:501 name CA residue id /C:101 name HOH > select /R 2051 atoms, 2094 bonds, 6 pseudobonds, 264 residues, 3 models selected > hide ~sel Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > label ligand > select ~/R 6704 atoms, 6840 bonds, 4 pseudobonds, 871 residues, 2 models selected > show sel > view orient Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > preset orig Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > preset ribbons Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8753 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cylinders Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset licorice Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide sel > preset ribbons Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select clear > preset sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset chain colors Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset transparent Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset opaque Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color bychain targ s trans 0 > preset ghostly white Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset surf atom Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset surf No preset name matches 'surf' > preset transparent Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset inter Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > preset pub Multiple preset names match 'pub': publication 1 (silhouettes); publication 2 (depth-cued) > preset publication 1 Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset publication 2 Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > hide surfaces atom Expected ',' or a keyword > preset publication 1 Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ghostly white Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset publication 2 Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > color byattribute chain No known/registered numeric attribute chain > color bychain > preset cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > color bychain > color byattribute chain No known/registered numeric attribute chain > color byatom > color byelement > color bymodel > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color bychain > rainbow > rainbow chains > style stick Changed 8755 atom styles > style stick Changed 8755 atom styles > rainbow [Repeated 1 time(s)] > color byhetero > color bychain > color bypolymer > rainbow [Repeated 2 time(s)] > coulombic Traceback (most recent call last): File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1286, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 1334, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 390, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 327, in run f(s) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 61, in func_plus_tip func(cmd + "" %s"")(session) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 569, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 512, in run run_command(session, command, **kw) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/coulombic/cmd.py"", line 90, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/coulombic/coulombic.py"", line 62, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 149, in copy m = self.__class__(self.session, name = name, File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 1240, in __init__ super().__init__(*args, **kw) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 86, in __init__ self._make_drawing() File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 325, in _make_drawing pbg._update_graphics() File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 221, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py"", line 238, in _update_positions return s._halfbond_cylinder_placements(axyz0, axyz1, pbonds.radii) File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2284, in _halfbond_cylinder_placements half_cylinder_rotations(axyz0, axyz1, radii, p) ValueError: Cylinder end point, radii or rotation array not contiguous. ValueError: Cylinder end point, radii or rotation array not contiguous. File ""/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2284, in _halfbond_cylinder_placements half_cylinder_rotations(axyz0, axyz1, radii, p) See log for complete Python traceback. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 7429.81.3 OS Loader Version: 7429.81.3 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 59 days 12:57 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.5 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.7.0 certifi: 2021.10.8 cftime: 1.6.1 charset-normalizer: 2.1.0 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.5.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.7 ChimeraX-AtomicLibrary: 7.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1.1 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChangeChains: 1.0 ChimeraX-CheckWaters: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.1 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5.dev202208030611 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.6 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.2.1 ChimeraX-Help: 1.2.1 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-Label: 1.1.5 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.7 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.21.4 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.2 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 0.9.1 filelock: 3.4.2 fonttools: 4.34.4 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.33 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 4.12.0 ipykernel: 6.15.1 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.1 kiwisolver: 1.4.4 line-profiler: 3.4.0 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.3 msgpack: 1.0.4 nest-asyncio: 1.5.5 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.3 numpy: 1.23.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.12.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.30 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.1 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.1 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.2.0 qtconsole: 5.3.1 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 62.6.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.3.0 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.11 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.3.0 zipp: 3.8.1 }}} " defect closed normal Graphics duplicate all ChimeraX