id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5844 dark gray vs. gray lochuynh@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description It's not a big deal but it seems like Gray and Dark Gray colors are swapped (Dark Gray looks lighter than Gray) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/lochuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"" Log from Mon Dec 27 20:37:10 2021UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/lochuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"" format session Log from Mon Dec 27 13:49:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/lochuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v2.cxs"" Log from Wed Aug 5 22:57:52 2020UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/LocHuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"" Log from Thu May 28 14:57:35 2020UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3Q1R format mmCIF fromDatabase pdb Summary of feedback from opening 3Q1R fetched from pdb --- notes | Fetching compressed mmCIF 3q1r from http://files.rcsb.org/download/3q1r.cif | Summary of feedback from opening /Users/LocHuynh/Downloads/ChimeraX/PDB/3q1r.cif --- note | Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif 3q1r title: Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader [more info...] Chain information for 3q1r #1 --- Chain | Description A | Ribonuclease P protein component B | RNase P RNA C | TRNA (phe) D | TRNA 5' leader Non-standard residues in 3q1r #1 --- MG — magnesium ion > set bgColor black > sequence chain #1/A Alignment identifier is 1.A > sequence chain #1/B Alignment identifier is 1.B > sequence chain #1/A Destroying pre-existing alignment with identifier 1.A Alignment identifier is 1.A > show sel cartoons > sequence chain #1/C Alignment identifier is 1.C > select /C:1-86 1788 atoms, 1994 bonds, 82 pseudobonds, 2 models selected > hide sel cartoons > hide sel atoms > show sel cartoons > show sel atoms > hide sel atoms > hide sel cartoons > select /A:6-117 973 atoms, 989 bonds, 1 model selected > hide sel atoms > hide sel cartoons > select /D:-5--1 40 atoms, 39 bonds, 1 model selected > hide sel atoms > select /B:1-347 7380 atoms, 8253 bonds, 353 pseudobonds, 2 models selected > hide sel atoms > show sel atoms > style sel stick Changed 65 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 65 atom styles > show sel cartoons > show sel atoms > color sel bynucleotide > nucleotides sel atoms > style nucleic & sel stick Changed 109 atom styles > color sel bynucleotide > color sel byhetero > color sel bychain > color sel byhetero > hide sel cartoons > select :MG 5 atoms, 1 model selected > color red > color sel red > color sel green > color sel lime > color sel lime green > color-spec Unknown command: color-spec > 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 sel pink > color sel deep pink > color sel magenta > hide sel cartoons > show sel cartoons > hide sel cartoons > color sel bychain > color sel bychain > color sel green > color sel dark green > color sel sea green > color sel medium sea green > color sel sea green > color sel teal > color sel dark cyan > color sel byhetero > select up 7384 atoms, 8253 bonds, 1 model selected > select down 7380 atoms, 8253 bonds, 1 model selected > select /B:50@C4' 1 atom, 1 model selected > select /B:51@C5 1 atom, 1 model selected > select up 65 atoms, 72 bonds, 1 model selected > color sel lemonchiffon > color sel byhetero > color sel khaki > color sel wheat > color sel tan > color sel byhetero > color sel teal > color sel byhetero > color sel slate blue > color sel byhetero > color sel dark slate blue > color sel byhetero > color sel bynucleotide > color sel dark slate blue > color sel bynucleotide > color sel byhetero > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > color sel byhetero > color sel dark slate blue > color sel byhetero > set bgColor white > select :MG 5 atoms, 1 model selected > color MG lime green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color a/MG lime green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color /a MG lime green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel liime green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel lime green > save2 ""/Users/LocHuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"" > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > save2 ""/Users/LocHuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"" > hide sel atoms > show sel cartoons > hide sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > style sel stick Changed 24 atom styles > style sel sphere Changed 24 atom styles > style sel stick Changed 24 atom styles > style sel ball Changed 24 atom styles > style sel stick Changed 24 atom styles > select /D:-5--1 40 atoms, 39 bonds, 1 model selected > show sel cartoons > color sel slate blue > color sel slateblue midnight blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel midnight blue > color sel red > show sel atoms > show sel atoms > style sel stick Changed 40 atom styles > hide sel cartoons > show sel cartoons > style sel stick Changed 40 atom styles > show sel surfaces > style sel stick Changed 40 atom styles > hide sel surfaces > nucleotides sel atoms > style nucleic & sel stick Changed 40 atom styles > show sel atoms > show sel atoms > color sel byhetero > style sel stick Changed 40 atom styles > hide sel cartoons > sequence chain #1/A Destroying pre-existing alignment with identifier 1.A Alignment identifier is 1.A > mlp sel mlp: no amino acids specified > show sel cartoons > style sel stick Changed 40 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 40 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 40 atom styles > show sel atoms > hide sel cartoons > mlp sel Map values for surface ""3q1r_A SES surface"": minimum -23.53, mean -3.612, maximum 22.92 > style sel sphere Changed 973 atom styles > mlp sel Map values for surface ""3q1r_A SES surface"": minimum -23.53, mean -3.612, maximum 22.92 > color sel byhetero > color sel bychain > color sel tan > color sel brown > color sel chocolate > color sel burly wood > color sel burlywood beigh Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel burlywood beige Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel beige > color sel tan > select sequence CCCUCGG 146 atoms, 161 bonds, 1 model selected > nucleotides sel fill > style nucleic & sel stick Changed 146 atom styles > show sel atoms > hide sel atoms > nucleotides sel slab > style nucleic & sel stick Changed 7380 atom styles > nucleotides sel ladder > show sel atoms > set bgColor black > select /D:-5--1 40 atoms, 39 bonds, 1 model selected > select /C:1-86 1788 atoms, 1994 bonds, 82 pseudobonds, 2 models selected > select /B:1-347 7380 atoms, 8253 bonds, 353 pseudobonds, 2 models selected > select /A:6-117 973 atoms, 989 bonds, 1 model selected > sequence chain #1/D Alignment identifier is 1.D > sequence chain #1/C Alignment identifier is 1.C > sequence chain #1/B Destroying pre-existing alignment with identifier 1.B Alignment identifier is 1.B > select sequence AGCGUCGG 174 atoms, 194 bonds, 1 model selected > select sequence GGGGGG 138 atoms, 155 bonds, 1 model selected > select sequence GGGGGGAA 182 atoms, 205 bonds, 1 model selected > select sequence GGGGGGAA 182 atoms, 205 bonds, 1 model selected > nucleotides sel ladder > nucleotides sel fill > style nucleic & sel stick Changed 182 atom styles > select sequence GGGGGGAAACUUCC 304 atoms, 340 bonds, 15 pseudobonds, 2 models selected > nucleotides sel fill > style nucleic & sel stick Changed 304 atom styles > select clear > select sequence ggagc 333 atoms, 372 bonds, 1 model selected > select sequence ggagcg 134 atoms, 150 bonds, 1 model selected > select sequence ggagcg 134 atoms, 150 bonds, 1 model selected > nucleotides sel fill > style nucleic & sel stick Changed 237 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 237 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 237 atom styles > select clear > select /B:249 20 atoms, 21 bonds, 1 model selected > select /B:248 20 atoms, 21 bonds, 1 model selected > style sel sphere Changed 40 atom styles > style sel stick Changed 40 atom styles > mlp sel mlp: no amino acids specified > style sel sphere Changed 40 atom styles > style sel sphere Changed 40 atom styles > lighting soft > lighting simple > lighting full > lighting soft > lighting flat > lighting flat > graphics silhouettes false > lighting soft > set bgColor white > show sel cartoons > style sel stick Changed 40 atom styles > style sel sphere Changed 40 atom styles > style sel stick Changed 40 atom styles > style sel stick Changed 40 atom styles > style sel stick Changed 40 atom styles > hide sel atoms > hide sel cartoons > show sel atoms > style sel sphere Changed 40 atom styles > style sel ball Changed 40 atom styles > set bgColor black > style sel sphere Changed 40 atom styles > sequence chain #1/A Alignment identifier is 1.A > color sel bychain > color sel byhetero > mlp sel Map values for surface ""3q1r_A SES surface"": minimum -23.53, mean -3.612, maximum 22.92 > color sel bynucleotide > rainbow sel > color bfactor sel 973 atoms, 112 residues, 1 surfaces, atom bfactor range 80 to 80 > color sel byhetero > color sel bychain > color sel tan > show sel surfaces > style sel stick Changed 40 atom styles > color sel red > color sel byhetero > tan Unknown command: tan > color sel byhetero > color sel tan > color sel byhetero > color sel deeppink blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel purple > color sel byhetero > lighting simple > lighting simple > lighting soft > lighting simple > hide sel surfaces > style sel sphere Changed 40 atom styles > select /B:51 23 atoms, 25 bonds, 1 model selected > hide sel cartoons > color sel blue > color sel navy > color sel byhetero > select /B:52 20 atoms, 21 bonds, 1 model selected > hide sel cartoons > show sel cartoons > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 20 atom styles > color sel navy > color sel byhetero > lighting soft > lighting simple > select /C:1@C3' 1 atom, 1 model selected > select up 24 atoms, 26 bonds, 1 model selected > select /C:1@P 1 atom, 1 model selected > select up 24 atoms, 26 bonds, 1 model selected > select /B:52 20 atoms, 21 bonds, 1 model selected > select up 2 atoms, 1 bond, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > save2 ""/Users/LocHuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"" opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 525, in rebuild _rebuild_molecule('internal', mol) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 652, in _rebuild_molecule hide_residues = make_ladder(nd, residues, mol._ladder_params) File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 1191, in make_ladder midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1]) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' Error processing trigger ""new frame"": TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' File ""/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py"", line 1191, in make_ladder midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1]) See log for complete Python traceback. > set bgColor white Empty filename passed to function > save2 ""/Users/LocHuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v2.cxs"" > hide sel atoms > hide sel atoms > hide sel atoms > show sel cartoons > color sel bychain > color sel bychain > color bfactor sel 1788 atoms, 86 residues, atom bfactor range 80 to 80.9 > mlp sel mlp: no amino acids specified > color sel bynucleotide > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > rainbow sel > color bfactor sel 1788 atoms, 86 residues, atom bfactor range 80 to 80.9 > mlp sel mlp: no amino acids specified > color sel bynucleotide > show sel atoms > hide sel atoms > color sel bynucleotide > nucleotides sel ladder > ui favorite true Toolbar > toolshed show Toolbar > ui favorite false Toolbar > color sel silver > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1788 atom styles > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel ladder > nucleotides sel ladder > nucleotides sel atoms > style nucleic & sel stick Changed 1788 atom styles > hide sel atoms > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1788 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 1788 atom styles > hide sel atoms > nucleotides sel ladder > show sel atoms > color sel silver > show sel atoms > nucleotides sel ladder > hide sel atoms > show sel atoms > color sel red > color sel red > hide sel atoms > style sel stick Changed 40 atom styles > show sel cartoons > cartoon style sel xsection oval modeHelix default > cartoon hide sel > cartoon hide sel > hide sel atoms > cartoon sel > nucleotides sel ladder > show sel atoms > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > cartoon style sel xsection oval modeHelix default > cartoon style sel modeHelix tube sides 20 > select clear > color sel dark grey > color sel blue > color sel navy > color sel green > color sel green > color sel dark green > save2 ""/Users/LocHuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v2.cxs"" ——— End of log from Wed Aug 5 22:57:52 2020 ——— opened ChimeraX session > save ""/Users/lochuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"" > select /C:86 22 atoms, 24 bonds, 1 residue, 1 model selected > select /C:1-86 1788 atoms, 1994 bonds, 82 pseudobonds, 86 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light gray > color sel gray > select /B:302-347 913 atoms, 1012 bonds, 46 residues, 1 model selected > select /B:1-347 7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected > color sel dark blue > color sel navy > color sel medium blue > color sel blue > color sel navy > color sel indigo > color sel navy > color sel midnight blue > select /B:264-347 1726 atoms, 1921 bonds, 25 pseudobonds, 84 residues, 2 models selected > select /B:1-347 7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected > cartoon style (#!1 & sel) xsection oval modeHelix default > cartoon style (#!1 & sel) modeHelix tube sides 20 > cartoon style (#!1 & sel & coil) xsection oval > cartoon style (#!1 & sel) xsection barbell modeHelix default > cartoon hide (#!1 & sel) > cartoon style (#!1 & sel) xsection oval modeHelix default > cartoon (#!1 & sel) > cartoon style (#!1 & sel & coil) xsection oval > cartoon style (#!1 & sel) xsection barbell modeHelix default > cartoon style (#!1 & sel) modeHelix tube sides 20 > cartoon style (#!1 & sel) xsection oval modeHelix default > cartoon style (#!1 & sel & coil) xsection oval > cartoon style (#!1 & sel) xsection barbell modeHelix default > save ""/Users/lochuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"" ——— End of log from Mon Dec 27 13:49:00 2021 ——— opened ChimeraX session > alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6 > cartoon style initial defaults Expected an atoms specifier or a keyword > cartoon style nucleic xsection oval width 1.6 thickness 1.6 > cartoon style nucleic xsection oval width 2.0 thickness 2.0 > help help:user/preferences.html#startup > save ""/Users/lochuynh/OneDrive - University of Florida/LAB > RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"" [Repeated 1 time(s)] ——— End of log from Mon Dec 27 20:37:10 2021 ——— opened ChimeraX session > preset cartoons/nucleotides cylinders/stubs Changed 973 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 > cartoon style nucleic xsection oval width 1.0 thickness 1.0 > cartoon style nucleic xsection oval width 3.0 thickness 3.0 > cartoon style nucleic xsection oval width 2.0 thickness 2.0 > select clear > select /A:117 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:6-117 973 atoms, 989 bonds, 112 residues, 1 model selected > select /C:86 22 atoms, 24 bonds, 1 residue, 1 model selected > select /C:1-86 1788 atoms, 1994 bonds, 82 pseudobonds, 86 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light gray > color sel gray > color sel dark gray > color sel gray > color sel dark gray > select /B:1-347 7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected > select /B:347 23 atoms, 25 bonds, 1 residue, 1 model selected > select /B:1-347 7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected > surface (#!1 & sel) > transparency (#!1 & sel) 50 > cartoon hide (#!1 & sel) > hide (#!1 & sel) target a > color sel cornflower blue > color sel medium blue > color sel dark blue OpenGL version: 4.1 Metal - 71.7.1 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini9,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 4 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 11.6.1 (20G224) Kernel Version: Darwin 20.6.0 Time since boot: 17:37 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: LG HDR 4K: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes LG HDR 4K: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Depiction not a bug Elaine Meng all ChimeraX