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#3330 closed defect (fixed)
Sequence window unreadable in Dark Mode
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-04-03) Description It's not a technical problem; however its visualization hinder productivity here. In dark mode (MacOS Mojave) texts in sequence windows show black on grey/dark background. Log: UCSF 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 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 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 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 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 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 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 OpenGL version: 4.1 INTEL-12.10.17 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. File attachment: Screen Shot 2020-05-28 at 2.55.31 AM.png
Attachments (1)
Change History (5)
by , 5 years ago
| Attachment: | Screen Shot 2020-05-28 at 2.55.31 AM.png added |
|---|
comment:1 by , 5 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Sequence window unreadable in Dark Mode |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Hi Loc,
Thanks for reporting this problem. I have fixed it and the fix will be in tomorrow's build. Unfortunately the fix is to simply force the sequence-window background to be white. It would be nice to do something fancy to look nice in dark mode, but the sequence window uses a lot of colors that would need adjustment as well, and there are so many features it still lacks compared to Chimera's sequence viewer that it seemed prudent to go with the simple and easy change here.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:3 by , 5 years ago
Hi Eric, Thank you so much for getting it fixed so quickly! I’m sure that simple fix works just good enough. To be honest, I really the the UI in ChimeraX because it saves me a lot of time on simple tasks. Loc
follow-up: 3 comment:4 by , 5 years ago
Hi Loc
I'm happy to hear the UI is helpful! Thanks for the feedback.
--Eric
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